Daily Papers

Molecule discovery is a pivotal research field, impacting everything from the medicines we take to the materials we use. Recently, Large Language Models (LLMs) have been widely adopted in molecule understanding and generation, yet the alignments between molecules and their corresponding captions remain a significant challenge. Previous endeavours often treat the molecule as a general SMILES string or molecular graph, neglecting the fine-grained alignments between the molecular sub-structures and the descriptive textual phrases, which are crucial for accurate and explainable predictions. In this case, we introduce MolReFlect, a novel teacher-student framework designed to contextually perform the molecule-caption alignments in a fine-grained way. Our approach initially leverages a larger teacher LLM to label the detailed alignments by directly extracting critical phrases from molecule captions or SMILES strings and implying them to corresponding sub-structures or characteristics. To refine these alignments, we propose In-Context Selective Reflection, which retrieves previous extraction results as context examples for teacher LLM to reflect and lets a smaller student LLM select from in-context reflection and previous extraction results. Finally, we enhance the learning process of the student LLM through Chain-of-Thought In-Context Molecule Tuning, integrating the fine-grained alignments and the reasoning processes within the Chain-of-Thought format. Our experimental results demonstrate that MolReFlect enables LLMs like Mistral-7B to significantly outperform the previous baselines, achieving SOTA performance on the ChEBI-20 dataset. This advancement not only enhances the generative capabilities of LLMs in the molecule-caption translation task, but also contributes to a more explainable framework.

The adaptation of large language models (LLMs) to chemistry has shown promising performance in molecular understanding tasks, such as generating a text description from a molecule. However, proper reasoning based on molecular structural information remains a significant challenge, e.g., even advanced LLMs such as GPT-4o struggle to identify functional groups which are crucial for inferring the molecular property of interest. To address this limitation, we propose StructCoT, a structure-aware chain-of-thought (CoT) that enhances LLMs' understanding of molecular structures by explicitly injecting the key structural features of molecules. Moreover, we introduce two fine-tuning frameworks for adapting the existing LLMs to use our StructCoT. Our experiments demonstrate that incorporating StructCoT with our fine-tuning frameworks leads to consistent improvements in both molecular understanding tasks.

Large Language Models (LLMs) have demonstrated exceptional performance in biochemical tasks, especially the molecule caption translation task, which aims to bridge the gap between molecules and natural language texts. However, previous methods in adapting LLMs to the molecule-caption translation task required extra domain-specific pre-training stages, suffered weak alignment between molecular and textual spaces, or imposed stringent demands on the scale of LLMs. To resolve the challenges, we propose In-Context Molecule Adaptation (ICMA), as a new paradigm allowing LLMs to learn the molecule-text alignment from context examples via In-Context Molecule Tuning. Specifically, ICMA incorporates the following three stages: Cross-modal Retrieval, Post-retrieval Re-ranking, and In-context Molecule Tuning. Initially, Cross-modal Retrieval utilizes BM25 Caption Retrieval and Molecule Graph Retrieval to retrieve informative context examples. Additionally, we also propose Post-retrieval Re-ranking with Sequence Reversal and Random Walk to further improve the quality of retrieval results. Finally, In-Context Molecule Tuning unlocks the in-context molecule learning capability of LLMs with retrieved examples and adapts the parameters of LLMs for the molecule-caption translation task. Experimental results demonstrate that ICMT can empower LLMs to achieve state-of-the-art or comparable performance without extra training corpora and intricate structures, showing that LLMs are inherently in-context molecule learners.

Building generalist models has recently demonstrated remarkable capabilities in diverse scientific domains. Within the realm of molecular learning, several studies have explored unifying diverse tasks across diverse domains. However, negative conflicts and interference between molecules and knowledge from different domain may have a worse impact in threefold. First, conflicting molecular representations can lead to optimization difficulties for the models. Second, mixing and scaling up training data across diverse tasks is inherently challenging. Third, the computational cost of refined pretraining is prohibitively high. To address these limitations, this paper presents Omni-Mol, a scalable and unified LLM-based framework for direct instruction tuning. Omni-Mol builds on three key components to tackles conflicts: (1) a unified encoding mechanism for any task input; (2) an active-learning-driven data selection strategy that significantly reduces dataset size; (3) a novel design of the adaptive gradient stabilization module and anchor-and-reconcile MoE framework that ensures stable convergence. Experimentally, Omni-Mol achieves state-of-the-art performance across 15 molecular tasks, demonstrates the presence of scaling laws in the molecular domain, and is supported by extensive ablation studies and analyses validating the effectiveness of its design. The code and weights of the powerful AI-driven chemistry generalist are open-sourced at: https://anonymous.4open.science/r/Omni-Mol-8EDB.

Recent advances in language models have enabled framing molecule generation as sequence modeling. However, existing approaches often rely on single-objective reinforcement learning, limiting their applicability to real-world drug design, where multiple competing properties must be optimized. Traditional multi-objective reinforcement learning (MORL) methods require costly retraining for each new objective combination, making rapid exploration of trade-offs impractical. To overcome these limitations, we introduce Mol-MoE, a mixture-of-experts (MoE) architecture that enables efficient test-time steering of molecule generation without retraining. Central to our approach is a preference-based router training objective that incentivizes the router to combine experts in a way that aligns with user-specified trade-offs. This provides improved flexibility in exploring the chemical property space at test time, facilitating rapid trade-off exploration. Benchmarking against state-of-the-art methods, we show that Mol-MoE achieves superior sample quality and steerability.

Molecule generation with desired properties has grown immensely in popularity by disruptively changing the way scientists design molecular structures and providing support for chemical and materials design. However, despite the promising outcome, previous machine learning-based deep generative models suffer from a reliance on complex, task-specific fine-tuning, limited dimensional latent spaces, or the quality of expert rules. In this work, we propose MolGen, a pre-trained molecular language model that effectively learns and shares knowledge across multiple generation tasks and domains. Specifically, we pre-train MolGen with the chemical language SELFIES on more than 100 million unlabelled molecules. We further propose multi-task molecular prefix tuning across several molecular generation tasks and different molecular domains (synthetic & natural products) with a self-feedback mechanism. Extensive experiments show that MolGen can obtain superior performances on well-known molecular generation benchmark datasets. The further analysis illustrates that MolGen can accurately capture the distribution of molecules, implicitly learn their structural characteristics, and efficiently explore the chemical space with the guidance of multi-task molecular prefix tuning. Codes, datasets, and the pre-trained model will be available in https://github.com/zjunlp/MolGen.

Retrosynthetic planning aims to devise a complete multi-step synthetic route from starting materials to a target molecule. Current strategies use a decoupled approach of single-step retrosynthesis models and search algorithms, taking only the product as the input to predict the reactants for each planning step and ignoring valuable context information along the synthetic route. In this work, we propose a novel framework that utilizes context information for improved retrosynthetic planning. We view synthetic routes as reaction graphs and propose to incorporate context through three principled steps: encode molecules into embeddings, aggregate information over routes, and readout to predict reactants. Our approach is the first attempt to utilize in-context learning for retrosynthesis prediction in retrosynthetic planning. The entire framework can be efficiently optimized in an end-to-end fashion and produce more practical and accurate predictions. Comprehensive experiments demonstrate that by fusing in the context information over routes, our model significantly improves the performance of retrosynthetic planning over baselines that are not context-aware, especially for long synthetic routes. Code is available at https://github.com/SongtaoLiu0823/FusionRetro.

Generative models have demonstrated substantial promise in Natural Language Processing (NLP) and have found application in designing molecules, as seen in General Pretrained Transformer (GPT) models. In our efforts to develop such a tool for exploring the organic chemical space in search of potentially electro-active compounds, we present "LLamol", a single novel generative transformer model based on the LLama 2 architecture, which was trained on a 13M superset of organic compounds drawn from diverse public sources. To allow for a maximum flexibility in usage and robustness in view of potentially incomplete data, we introduce "Stochastic Context Learning" as a new training procedure. We demonstrate that the resulting model adeptly handles single- and multi-conditional organic molecule generation with up to four conditions, yet more are possible. The model generates valid molecular structures in SMILES notation while flexibly incorporating three numerical and/or one token sequence into the generative process, just as requested. The generated compounds are very satisfactory in all scenarios tested. In detail, we showcase the model's capability to utilize token sequences for conditioning, either individually or in combination with numerical properties, making LLamol a potent tool for de novo molecule design, easily expandable with new properties.

Understanding molecules is key to understanding organisms and driving advances in drug discovery, requiring interdisciplinary knowledge across chemistry and biology. Although large molecular language models have achieved notable success in interpreting molecular structures, their instruction datasets are limited to the specific knowledge from task-oriented datasets and do not fully cover the fundamental characteristics of molecules, hindering their abilities as general-purpose molecular assistants. To address this issue, we propose Mol-LLaMA, a large molecular language model that grasps the general knowledge centered on molecules via multi-modal instruction tuning. To this end, we design key data types that encompass the fundamental features of molecules, incorporating essential knowledge from molecular structures. In addition, to improve understanding of molecular features, we introduce a module that integrates complementary information from different molecular encoders, leveraging the distinct advantages of different molecular representations. Our experimental results demonstrate that Mol-LLaMA is capable of comprehending the general features of molecules and generating relevant responses to users' queries with detailed explanations, implying its potential as a general-purpose assistant for molecular analysis.

Despite recent advancements, most computational methods for molecule optimization are constrained to single- or double-property optimization tasks and suffer from poor scalability and generalizability to novel optimization tasks. Meanwhile, Large Language Models (LLMs) demonstrate remarkable out-of-domain generalizability to novel tasks. To demonstrate LLMs' potential for molecule optimization, we introduce MoMUInstruct, the first high-quality instruction-tuning dataset specifically focused on complex multi-property molecule optimization tasks. Leveraging MoMUInstruct, we develop GeLLM^3Os, a series of instruction-tuned LLMs for molecule optimization. Extensive evaluations across 5 in-domain and 5 out-of-domain tasks demonstrate that GeLLM^3Os consistently outperform state-of-the-art baselines. GeLLM^3Os also exhibit outstanding zero-shot generalization to unseen tasks, significantly outperforming powerful closed-source LLMs. Such strong generalizability demonstrates the tremendous potential of GeLLM^3Os as foundational models for molecule optimization, thereby tackling novel optimization tasks without resource-intensive retraining. MoMUInstruct, models, and code are accessible through https://github.com/ninglab/GeLLMO.

Machine learning, notably deep learning, has significantly propelled molecular investigations within the biochemical sphere. Traditionally, modeling for such research has centered around a handful of paradigms. For instance, the prediction paradigm is frequently deployed for tasks such as molecular property prediction. To enhance the generation and decipherability of purely data-driven models, scholars have integrated biochemical domain knowledge into these molecular study models. This integration has sparked a surge in paradigm transfer, which is solving one molecular learning task by reformulating it as another one. With the emergence of Large Language Models, these paradigms have demonstrated an escalating trend towards harmonized unification. In this work, we delineate a literature survey focused on knowledge-informed molecular learning from the perspective of paradigm transfer. We classify the paradigms, scrutinize their methodologies, and dissect the contribution of domain knowledge. Moreover, we encapsulate prevailing trends and identify intriguing avenues for future exploration in molecular learning.

Molecule discovery serves as a cornerstone in numerous scientific domains, fueling the development of new materials and innovative drug designs. Recent developments of in-silico molecule discovery have highlighted the promising results of cross-modal techniques, which bridge molecular structures with their descriptive annotations. However, these cross-modal methods frequently encounter the issue of data scarcity, hampering their performance and application. In this paper, we address the low-resource challenge by utilizing artificially-real data generated by Large Language Models (LLMs). We first introduce a retrieval-based prompting strategy to construct high-quality pseudo data, then explore the optimal method to effectively leverage this pseudo data. Experiments show that using pseudo data for domain adaptation outperforms all existing methods, while also requiring a smaller model scale, reduced data size and lower training cost, highlighting its efficiency. Furthermore, our method shows a sustained improvement as the volume of pseudo data increases, revealing the great potential of pseudo data in advancing low-resource cross-modal molecule discovery.

The efficient exploration of chemical space to design molecules with intended properties enables the accelerated discovery of drugs, materials, and catalysts, and is one of the most important outstanding challenges in chemistry. Encouraged by the recent surge in computer power and artificial intelligence development, many algorithms have been developed to tackle this problem. However, despite the emergence of many new approaches in recent years, comparatively little progress has been made in developing realistic benchmarks that reflect the complexity of molecular design for real-world applications. In this work, we develop a set of practical benchmark tasks relying on physical simulation of molecular systems mimicking real-life molecular design problems for materials, drugs, and chemical reactions. Additionally, we demonstrate the utility and ease of use of our new benchmark set by demonstrating how to compare the performance of several well-established families of algorithms. Surprisingly, we find that model performance can strongly depend on the benchmark domain. We believe that our benchmark suite will help move the field towards more realistic molecular design benchmarks, and move the development of inverse molecular design algorithms closer to designing molecules that solve existing problems in both academia and industry alike.

There is increasing adoption of artificial intelligence in drug discovery. However, existing studies use machine learning to mainly utilize the chemical structures of molecules but ignore the vast textual knowledge available in chemistry. Incorporating textual knowledge enables us to realize new drug design objectives, adapt to text-based instructions and predict complex biological activities. Here we present a multi-modal molecule structure-text model, MoleculeSTM, by jointly learning molecules' chemical structures and textual descriptions via a contrastive learning strategy. To train MoleculeSTM, we construct a large multi-modal dataset, namely, PubChemSTM, with over 280,000 chemical structure-text pairs. To demonstrate the effectiveness and utility of MoleculeSTM, we design two challenging zero-shot tasks based on text instructions, including structure-text retrieval and molecule editing. MoleculeSTM has two main properties: open vocabulary and compositionality via natural language. In experiments, MoleculeSTM obtains the state-of-the-art generalization ability to novel biochemical concepts across various benchmarks.

Molecular machine learning has been maturing rapidly over the last few years. Improved methods and the presence of larger datasets have enabled machine learning algorithms to make increasingly accurate predictions about molecular properties. However, algorithmic progress has been limited due to the lack of a standard benchmark to compare the efficacy of proposed methods; most new algorithms are benchmarked on different datasets making it challenging to gauge the quality of proposed methods. This work introduces MoleculeNet, a large scale benchmark for molecular machine learning. MoleculeNet curates multiple public datasets, establishes metrics for evaluation, and offers high quality open-source implementations of multiple previously proposed molecular featurization and learning algorithms (released as part of the DeepChem open source library). MoleculeNet benchmarks demonstrate that learnable representations are powerful tools for molecular machine learning and broadly offer the best performance. However, this result comes with caveats. Learnable representations still struggle to deal with complex tasks under data scarcity and highly imbalanced classification. For quantum mechanical and biophysical datasets, the use of physics-aware featurizations can be more important than choice of particular learning algorithm.

Chain-of-thought (CoT) has emerged as a powerful technique to elicit reasoning in large language models and improve a variety of downstream tasks. CoT mainly demonstrates excellent performance in English, but its usage in low-resource languages is constrained due to poor language generalization. To bridge the gap among different languages, we propose a cross-lingual instruction fine-tuning framework (xCOT) to transfer knowledge from high-resource languages to low-resource languages. Specifically, the multilingual instruction training data (xCOT-INSTRUCT) is created to encourage the semantic alignment of multiple languages. We introduce cross-lingual in-context few-shot learning (xICL)) to accelerate multilingual agreement in instruction tuning, where some fragments of source languages in examples are randomly substituted by their counterpart translations of target languages. During multilingual instruction tuning, we adopt the randomly online CoT strategy to enhance the multilingual reasoning ability of the large language model by first translating the query to another language and then answering in English. To further facilitate the language transfer, we leverage the high-resource CoT to supervise the training of low-resource languages with cross-lingual distillation. Experimental results on previous benchmarks demonstrate the superior performance of xCoT in reducing the gap among different languages, highlighting its potential to reduce the cross-lingual gap.

Table-based reasoning with large language models (LLMs) is a promising direction to tackle many table understanding tasks, such as table-based question answering and fact verification. Compared with generic reasoning, table-based reasoning requires the extraction of underlying semantics from both free-form questions and semi-structured tabular data. Chain-of-Thought and its similar approaches incorporate the reasoning chain in the form of textual context, but it is still an open question how to effectively leverage tabular data in the reasoning chain. We propose the Chain-of-Table framework, where tabular data is explicitly used in the reasoning chain as a proxy for intermediate thoughts. Specifically, we guide LLMs using in-context learning to iteratively generate operations and update the table to represent a tabular reasoning chain. LLMs can therefore dynamically plan the next operation based on the results of the previous ones. This continuous evolution of the table forms a chain, showing the reasoning process for a given tabular problem. The chain carries structured information of the intermediate results, enabling more accurate and reliable predictions. Chain-of-Table achieves new state-of-the-art performance on WikiTQ, FeTaQA, and TabFact benchmarks across multiple LLM choices.

Large language models (LLMs) have demonstrated remarkable performance across a wide range of tasks. Advances in prompt engineering and fine-tuning techniques have further enhanced their ability to address complex reasoning challenges. However, these advanced capabilities are often exclusive to models exceeding 100 billion parameters. Although Chain-of-Thought (CoT) fine-tuning methods have been explored for smaller models (under 10 billion parameters), they typically depend on extensive CoT training data, which can introduce inconsistencies and limit effectiveness in low-data settings. To overcome these limitations, this paper introduce a new reasoning strategy Solution Guidance (SG) and a plug-and-play training paradigm Solution-Guidance Fine-Tuning (SGFT) for enhancing the reasoning capabilities of small language models. SG focuses on problem understanding and decomposition at the semantic and logical levels, rather than specific computations, which can effectively improve the SLMs' generalization and reasoning abilities. With only a small amount of SG training data, SGFT can fine-tune a SLM to produce accurate problem-solving guidances, which can then be flexibly fed to any SLM as prompts, enabling it to generate correct answers directly. Experimental results demonstrate that our method significantly improves the performance of SLMs on various reasoning tasks, enhancing both their practicality and efficiency within resource-constrained environments.

The integration of molecule and language has garnered increasing attention in molecular science. Recent advancements in Language Models (LMs) have demonstrated potential for the comprehensive modeling of molecule and language. However, existing works exhibit notable limitations. Most existing works overlook the modeling of 3D information, which is crucial for understanding molecular structures and also functions. While some attempts have been made to leverage external structure encoding modules to inject the 3D molecular information into LMs, there exist obvious difficulties that hinder the integration of molecular structure and language text, such as modality alignment and separate tuning. To bridge this gap, we propose 3D-MolT5, a unified framework designed to model both 1D molecular sequence and 3D molecular structure. The key innovation lies in our methodology for mapping fine-grained 3D substructure representations (based on 3D molecular fingerprints) to a specialized 3D token vocabulary for 3D-MolT5. This 3D structure token vocabulary enables the seamless combination of 1D sequence and 3D structure representations in a tokenized format, allowing 3D-MolT5 to encode molecular sequence (SELFIES), molecular structure, and text sequences within a unified architecture. Alongside, we further introduce 1D and 3D joint pre-training to enhance the model's comprehension of these diverse modalities in a joint representation space and better generalize to various tasks for our foundation model. Through instruction tuning on multiple downstream datasets, our proposed 3D-MolT5 shows superior performance than existing methods in molecular property prediction, molecule captioning, and text-based molecule generation tasks. Our code will be available on GitHub soon.

Molecular representation is a foundational element in our understanding of the physical world. Its importance ranges from the fundamentals of chemical reactions to the design of new therapies and materials. Previous molecular machine learning models have employed strings, fingerprints, global features, and simple molecular graphs that are inherently information-sparse representations. However, as the complexity of prediction tasks increases, the molecular representation needs to encode higher fidelity information. This work introduces a novel approach to infusing quantum-chemical-rich information into molecular graphs via stereoelectronic effects. We show that the explicit addition of stereoelectronic interactions significantly improves the performance of molecular machine learning models. Furthermore, stereoelectronics-infused representations can be learned and deployed with a tailored double graph neural network workflow, enabling its application to any downstream molecular machine learning task. Finally, we show that the learned representations allow for facile stereoelectronic evaluation of previously intractable systems, such as entire proteins, opening new avenues of molecular design.

Efficient molecular modeling and design are crucial for the discovery and exploration of novel molecules, and the incorporation of deep learning methods has revolutionized this field. In particular, large language models (LLMs) offer a fresh approach to tackle scientific problems from a natural language processing (NLP) perspective, introducing a research paradigm called scientific language modeling (SLM). However, two key issues remain: how to quantify the match between model and data modalities and how to identify the knowledge-learning preferences of models. To address these challenges, we propose a multi-modal benchmark, named ChEBI-20-MM, and perform 1263 experiments to assess the model's compatibility with data modalities and knowledge acquisition. Through the modal transition probability matrix, we provide insights into the most suitable modalities for tasks. Furthermore, we introduce a statistically interpretable approach to discover context-specific knowledge mapping by localized feature filtering. Our pioneering analysis offers an exploration of the learning mechanism and paves the way for advancing SLM in molecular science.

Recently, pre-trained foundation models have enabled significant advancements in multiple fields. In molecular machine learning, however, where datasets are often hand-curated, and hence typically small, the lack of datasets with labeled features, and codebases to manage those datasets, has hindered the development of foundation models. In this work, we present seven novel datasets categorized by size into three distinct categories: ToyMix, LargeMix and UltraLarge. These datasets push the boundaries in both the scale and the diversity of supervised labels for molecular learning. They cover nearly 100 million molecules and over 3000 sparsely defined tasks, totaling more than 13 billion individual labels of both quantum and biological nature. In comparison, our datasets contain 300 times more data points than the widely used OGB-LSC PCQM4Mv2 dataset, and 13 times more than the quantum-only QM1B dataset. In addition, to support the development of foundational models based on our proposed datasets, we present the Graphium graph machine learning library which simplifies the process of building and training molecular machine learning models for multi-task and multi-level molecular datasets. Finally, we present a range of baseline results as a starting point of multi-task and multi-level training on these datasets. Empirically, we observe that performance on low-resource biological datasets show improvement by also training on large amounts of quantum data. This indicates that there may be potential in multi-task and multi-level training of a foundation model and fine-tuning it to resource-constrained downstream tasks.

Generating novel molecules with out-of-distribution properties is a major challenge in molecular discovery. While supervised learning methods generate high-quality molecules similar to those in a dataset, they struggle to generalize to out-of-distribution properties. Reinforcement learning can explore new chemical spaces but often conducts 'reward-hacking' and generates non-synthesizable molecules. In this work, we address this problem by integrating a state-of-the-art supervised learning method, STGG+, in an active learning loop. Our approach iteratively generates, evaluates, and fine-tunes STGG+ to continuously expand its knowledge. We denote this approach STGG+AL. We apply STGG+AL to the design of organic pi-functional materials, specifically two challenging tasks: 1) generating highly absorptive molecules characterized by high oscillator strength and 2) designing absorptive molecules with reasonable oscillator strength in the near-infrared (NIR) range. The generated molecules are validated and rationalized in-silico with time-dependent density functional theory. Our results demonstrate that our method is highly effective in generating novel molecules with high oscillator strength, contrary to existing methods such as reinforcement learning (RL) methods. We open-source our active-learning code along with our Conjugated-xTB dataset containing 2.9 million pi-conjugated molecules and the function for approximating the oscillator strength and absorption wavelength (based on sTDA-xTB).

The recent success of large foundation models in artificial intelligence has prompted the emergence of chemical pre-trained models. Despite the growing interest in large molecular pre-trained models that provide informative representations for downstream tasks, attempts for multimodal pre-training approaches on the molecule domain were limited. To address this, we present a novel multimodal molecular pre-trained model that incorporates the modalities of structure and biochemical properties, drawing inspiration from recent advances in multimodal learning techniques. Our proposed model pipeline of data handling and training objectives aligns the structure/property features in a common embedding space, which enables the model to regard bidirectional information between the molecules' structure and properties. These contributions emerge synergistic knowledge, allowing us to tackle both multimodal and unimodal downstream tasks through a single model. Through extensive experiments, we demonstrate that our model shows remarkable capabilities in solving various meaningful chemical challenges, including conditional molecule generation, property prediction, molecule classification, and reaction prediction.

Seeking answers to questions within long scientific research articles is a crucial area of study that aids readers in quickly addressing their inquiries. However, existing question-answering (QA) datasets based on scientific papers are limited in scale and focus solely on textual content. To address this limitation, we introduce SPIQA (Scientific Paper Image Question Answering), the first large-scale QA dataset specifically designed to interpret complex figures and tables within the context of scientific research articles across various domains of computer science. Leveraging the breadth of expertise and ability of multimodal large language models (MLLMs) to understand figures, we employ automatic and manual curation to create the dataset. We craft an information-seeking task involving multiple images that cover a wide variety of plots, charts, tables, schematic diagrams, and result visualizations. SPIQA comprises 270K questions divided into training, validation, and three different evaluation splits. Through extensive experiments with 12 prominent foundational models, we evaluate the ability of current multimodal systems to comprehend the nuanced aspects of research articles. Additionally, we propose a Chain-of-Thought (CoT) evaluation strategy with in-context retrieval that allows fine-grained, step-by-step assessment and improves model performance. We further explore the upper bounds of performance enhancement with additional textual information, highlighting its promising potential for future research and the dataset's impact on revolutionizing how we interact with scientific literature.

Large language models (LLMs) can refine their responses based on feedback, enabling self-improvement through iterative training or test-time refinement. However, existing methods predominantly focus on refinement within the same reasoning format, which may lead to non-correcting behaviors. We propose CaP, a novel approach that uses external tools to refine chain-of-thought (CoT) responses generated by the same or other LLMs. CaP employs a two-stage training process: supervised fine-tuning followed by preference optimization with DPO variants. Our observations highlight the critical role of preference optimization in enabling effective refinement. Additionally, we compare several sampling strategies to leverage CoT and tools at inference time. Experimental results demonstrate CaP's potential for effective cross-reasoning refinement and efficient inference.

Large-scale pre-training methodologies for chemical language models represent a breakthrough in cheminformatics. These methods excel in tasks such as property prediction and molecule generation by learning contextualized representations of input tokens through self-supervised learning on large unlabeled corpora. Typically, this involves pre-training on unlabeled data followed by fine-tuning on specific tasks, reducing dependence on annotated datasets and broadening chemical language representation understanding. This paper introduces a large encoder-decoder chemical foundation models pre-trained on a curated dataset of 91 million SMILES samples sourced from PubChem, which is equivalent to 4 billion of molecular tokens. The proposed foundation model supports different complex tasks, including quantum property prediction, and offer flexibility with two main variants (289M and 8times289M). Our experiments across multiple benchmark datasets validate the capacity of the proposed model in providing state-of-the-art results for different tasks. We also provide a preliminary assessment of the compositionality of the embedding space as a prerequisite for the reasoning tasks. We demonstrate that the produced latent space is separable compared to the state-of-the-art with few-shot learning capabilities.

While large language models (LLMs) have integrated images, adapting them to graphs remains challenging, limiting their applications in materials and drug design. This difficulty stems from the need for coherent autoregressive generation across texts and graphs. To address this, we introduce Llamole, the first multimodal LLM capable of interleaved text and graph generation, enabling molecular inverse design with retrosynthetic planning. Llamole integrates a base LLM with the Graph Diffusion Transformer and Graph Neural Networks for multi-conditional molecular generation and reaction inference within texts, while the LLM, with enhanced molecular understanding, flexibly controls activation among the different graph modules. Additionally, Llamole integrates A* search with LLM-based cost functions for efficient retrosynthetic planning. We create benchmarking datasets and conduct extensive experiments to evaluate Llamole against in-context learning and supervised fine-tuning. Llamole significantly outperforms 14 adapted LLMs across 12 metrics for controllable molecular design and retrosynthetic planning.

Generative molecular design has moved from proof-of-concept to real-world applicability, as marked by the surge in very recent papers reporting experimental validation. Key challenges in explainability and sample efficiency present opportunities to enhance generative design to directly optimize expensive high-fidelity oracles and provide actionable insights to domain experts. Here, we propose Beam Enumeration to exhaustively enumerate the most probable sub-sequences from language-based molecular generative models and show that molecular substructures can be extracted. When coupled with reinforcement learning, extracted substructures become meaningful, providing a source of explainability and improving sample efficiency through self-conditioned generation. Beam Enumeration is generally applicable to any language-based molecular generative model and notably further improves the performance of the recently reported Augmented Memory algorithm, which achieved the new state-of-the-art on the Practical Molecular Optimization benchmark for sample efficiency. The combined algorithm generates more high reward molecules and faster, given a fixed oracle budget. Beam Enumeration shows that improvements to explainability and sample efficiency for molecular design can be made synergistic.

We seek to automate the design of molecules based on specific chemical properties. In computational terms, this task involves continuous embedding and generation of molecular graphs. Our primary contribution is the direct realization of molecular graphs, a task previously approached by generating linear SMILES strings instead of graphs. Our junction tree variational autoencoder generates molecular graphs in two phases, by first generating a tree-structured scaffold over chemical substructures, and then combining them into a molecule with a graph message passing network. This approach allows us to incrementally expand molecules while maintaining chemical validity at every step. We evaluate our model on multiple tasks ranging from molecular generation to optimization. Across these tasks, our model outperforms previous state-of-the-art baselines by a significant margin.

While various models and computational tools have been proposed for structure and property analysis of molecules, generating molecules that conform to all desired structures and properties remains a challenge. Here, we introduce a multi-constraint molecular generation large language model, TSMMG, which, akin to a student, incorporates knowledge from various small models and tools, namely, the 'teachers'. To train TSMMG, we construct a large set of text-molecule pairs by extracting molecular knowledge from these 'teachers', enabling it to generate novel molecules that conform to the descriptions through various text prompts. We experimentally show that TSMMG remarkably performs in generating molecules meeting complex, natural language-described property requirements across two-, three-, and four-constraint tasks, with an average molecular validity of over 99% and success ratio of 82.58%, 68.03%, and 67.48%, respectively. The model also exhibits adaptability through zero-shot testing, creating molecules that satisfy combinations of properties that have not been encountered. It can comprehend text inputs with various language styles, extending beyond the confines of outlined prompts, as confirmed through empirical validation. Additionally, the knowledge distillation feature of TSMMG contributes to the continuous enhancement of small models, while the innovative approach to dataset construction effectively addresses the issues of data scarcity and quality, which positions TSMMG as a promising tool in the domains of drug discovery and materials science.

While chain-of-thought (CoT) prompting has revolutionized how LLMs perform reasoning tasks, its current methods and variations (e.g, Self-consistency, ReACT, Reflexion, Tree-of-Thoughts (ToT), Cumulative Reasoning (CR)) suffer from limitations like slowness, limited context grounding, hallucination and inconsistent outputs. To overcome these challenges, we introduce Evidence to Generate (E2G), a novel single-agent, two-step prompting framework. Instead of unverified reasoning claims, this innovative approach leverages the power of "evidence for decision making" by first focusing exclusively on the thought sequences (the series of intermediate steps) explicitly mentioned in the context which then serve as extracted evidence, guiding the LLM's output generation process with greater precision and efficiency. This simple yet powerful approach unlocks the true potential of chain-of-thought like prompting, paving the way for faster, more reliable, and more contextually aware reasoning in LLMs. \tool achieves remarkable results robustly across a wide range of knowledge-intensive reasoning and generation tasks, surpassing baseline approaches with state-of-the-art LLMs. For example, (i) on LogiQA benchmark using GPT-4 as backbone model, \tool achieves a new state-of-the Accuracy of 53.8% exceeding CoT by 18%, ToT by 11%, CR by 9% (ii) a variant of E2G with PaLM2 outperforms the variable-shot performance of Gemini Ultra by 0.9 F1 points, reaching an F1 score of 83.3 on a subset of DROP.

Current literature, aiming to surpass the "Chain-of-Thought" approach, often resorts to an external modus operandi involving halting, modifying, and then resuming the generation process to boost Large Language Models' (LLMs) reasoning capacities. This mode escalates the number of query requests, leading to increased costs, memory, and computational overheads. Addressing this, we propose the Algorithm of Thoughts -- a novel strategy that propels LLMs through algorithmic reasoning pathways, pioneering a new mode of in-context learning. By employing algorithmic examples, we exploit the innate recurrence dynamics of LLMs, expanding their idea exploration with merely one or a few queries. Our technique outperforms earlier single-query methods and stands on par with a recent multi-query strategy that employs an extensive tree search algorithm. Intriguingly, our results suggest that instructing an LLM using an algorithm can lead to performance surpassing that of the algorithm itself, hinting at LLM's inherent ability to weave its intuition into optimized searches. We probe into the underpinnings of our method's efficacy and its nuances in application.

Recent advancements in large language models have opened new possibilities for generative molecular drug design. We present Chemlactica and Chemma, two language models fine-tuned on a novel corpus of 110M molecules with computed properties, totaling 40B tokens. These models demonstrate strong performance in generating molecules with specified properties and predicting new molecular characteristics from limited samples. We introduce a novel optimization algorithm that leverages our language models to optimize molecules for arbitrary properties given limited access to a black box oracle. Our approach combines ideas from genetic algorithms, rejection sampling, and prompt optimization. It achieves state-of-the-art performance on multiple molecular optimization benchmarks, including an 8% improvement on Practical Molecular Optimization compared to previous methods. We publicly release the training corpus, the language models and the optimization algorithm.

Methods for designing organic materials with desired properties have high potential impact across fields such as medicine, renewable energy, petrochemical engineering, and agriculture. However, using generative modeling to design substances with desired properties is difficult because candidate compounds must satisfy multiple constraints, including synthetic accessibility and other metrics that are intuitive to domain experts but challenging to quantify. We propose C5T5, a novel self-supervised pretraining method that enables transformers to make zero-shot select-and-replace edits, altering organic substances towards desired property values. C5T5 operates on IUPAC names -- a standardized molecular representation that intuitively encodes rich structural information for organic chemists but that has been largely ignored by the ML community. Our technique requires no edited molecule pairs to train and only a rough estimate of molecular properties, and it has the potential to model long-range dependencies and symmetric molecular structures more easily than graph-based methods. C5T5 also provides a powerful interface to domain experts: it grants users fine-grained control over the generative process by selecting and replacing IUPAC name fragments, which enables experts to leverage their intuitions about structure-activity relationships. We demonstrate C5T5's effectiveness on four physical properties relevant for drug discovery, showing that it learns successful and chemically intuitive strategies for altering molecules towards desired property values.

Supervised machine learning approaches have been increasingly used in accelerating electronic structure prediction as surrogates of first-principle computational methods, such as density functional theory (DFT). While numerous quantum chemistry datasets focus on chemical properties and atomic forces, the ability to achieve accurate and efficient prediction of the Hamiltonian matrix is highly desired, as it is the most important and fundamental physical quantity that determines the quantum states of physical systems and chemical properties. In this work, we generate a new Quantum Hamiltonian dataset, named as QH9, to provide precise Hamiltonian matrices for 999 or 2998 molecular dynamics trajectories and 130,831 stable molecular geometries, based on the QM9 dataset. By designing benchmark tasks with various molecules, we show that current machine learning models have the capacity to predict Hamiltonian matrices for arbitrary molecules. Both the QH9 dataset and the baseline models are provided to the community through an open-source benchmark, which can be highly valuable for developing machine learning methods and accelerating molecular and materials design for scientific and technological applications. Our benchmark is publicly available at https://github.com/divelab/AIRS/tree/main/OpenDFT/QHBench.

The task of chemical reaction predictions (CRPs) plays a pivotal role in advancing drug discovery and material science. However, its effectiveness is constrained by the vast and uncertain chemical reaction space and challenges in capturing reaction selectivity, particularly due to existing methods' limitations in exploiting the data's inherent knowledge. To address these challenges, we introduce a data-curated self-feedback knowledge elicitation approach. This method starts from iterative optimization of molecular representations and facilitates the extraction of knowledge on chemical reaction types (RTs). Then, we employ adaptive prompt learning to infuse the prior knowledge into the large language model (LLM). As a result, we achieve significant enhancements: a 14.2% increase in retrosynthesis prediction accuracy, a 74.2% rise in reagent prediction accuracy, and an expansion in the model's capability for handling multi-task chemical reactions. This research offers a novel paradigm for knowledge elicitation in scientific research and showcases the untapped potential of LLMs in CRPs.

Reinforcement learning (RL) over text representations can be effective for finding high-value policies that can search over graphs. However, RL requires careful structuring of the search space and algorithm design to be effective in this challenge. Through extensive experiments, we explore how different design choices for text grammar and algorithmic choices for training can affect an RL policy's ability to generate molecules with desired properties. We arrive at a new RL-based molecular design algorithm (ChemRLformer) and perform a thorough analysis using 25 molecule design tasks, including computationally complex protein docking simulations. From this analysis, we discover unique insights in this problem space and show that ChemRLformer achieves state-of-the-art performance while being more straightforward than prior work by demystifying which design choices are actually helpful for text-based molecule design.

We propose a novel framework, Meta Chain-of-Thought (Meta-CoT), which extends traditional Chain-of-Thought (CoT) by explicitly modeling the underlying reasoning required to arrive at a particular CoT. We present empirical evidence from state-of-the-art models exhibiting behaviors consistent with in-context search, and explore methods for producing Meta-CoT via process supervision, synthetic data generation, and search algorithms. Finally, we outline a concrete pipeline for training a model to produce Meta-CoTs, incorporating instruction tuning with linearized search traces and reinforcement learning post-training. Finally, we discuss open research questions, including scaling laws, verifier roles, and the potential for discovering novel reasoning algorithms. This work provides a theoretical and practical roadmap to enable Meta-CoT in LLMs, paving the way for more powerful and human-like reasoning in artificial intelligence.

Large Language Models (LLMs) have demonstrated remarkable performance across multiple tasks through in-context learning. For complex reasoning tasks that require step-by-step thinking, Chain-of-Thought (CoT) prompting has given impressive results, especially when combined with self-consistency. Nonetheless, some tasks remain particularly difficult for LLMs to solve. Tree of Thoughts (ToT) and Graph of Thoughts (GoT) emerged as alternatives, dividing the complex problem into paths of subproblems. In this paper, we propose Tree of Problems (ToP), a simpler version of ToT, which we hypothesise can work better for complex tasks that can be divided into identical subtasks. Our empirical results show that our approach outperforms ToT and GoT, and in addition performs better than CoT on complex reasoning tasks. All code for this paper is publicly available here: https://github.com/ArmelRandy/tree-of-problems.

Language-Image Pre-training has demonstrated promising results on zero-shot and few-shot downstream tasks by prompting visual models with natural language prompts. However, most recent studies only use a single prompt for tuning, neglecting the inherent step-to-step cognitive reasoning process that humans conduct in complex task settings, for example, when processing images from unfamiliar domains. Chain of Thought is a simple and effective approximation to human reasoning process and has been proven useful for natural language processing (NLP) tasks. Based on this cognitive intuition, we believe that conducting effective reasoning is also an important problem in visual tasks, and a chain of thought could be a solution to this problem. In this work, we propose a novel chain of thought prompt tuning for vision-language modeling. Extensive experiments show that our method not only generalizes better in image classification tasks, has greater transferability beyond a single dataset, and has stronger domain generalization performance, but also performs much better in imagetext retrieval and visual question answering, which require more reasoning capabilities. We are the first to successfully adapt chain-of-thought prompting that combines visual and textual embeddings. We will release our codes

Molecular Representation Learning (MRL) has proven impactful in numerous biochemical applications such as drug discovery and enzyme design. While Graph Neural Networks (GNNs) are effective at learning molecular representations from a 2D molecular graph or a single 3D structure, existing works often overlook the flexible nature of molecules, which continuously interconvert across conformations via chemical bond rotations and minor vibrational perturbations. To better account for molecular flexibility, some recent works formulate MRL as an ensemble learning problem, focusing on explicitly learning from a set of conformer structures. However, most of these studies have limited datasets, tasks, and models. In this work, we introduce the first MoleculAR Conformer Ensemble Learning (MARCEL) benchmark to thoroughly evaluate the potential of learning on conformer ensembles and suggest promising research directions. MARCEL includes four datasets covering diverse molecule- and reaction-level properties of chemically diverse molecules including organocatalysts and transition-metal catalysts, extending beyond the scope of common GNN benchmarks that are confined to drug-like molecules. In addition, we conduct a comprehensive empirical study, which benchmarks representative 1D, 2D, and 3D molecular representation learning models, along with two strategies that explicitly incorporate conformer ensembles into 3D MRL models. Our findings reveal that direct learning from an accessible conformer space can improve performance on a variety of tasks and models.

Understanding the chemical structure from a graphical representation of a molecule is a challenging image caption task that would greatly benefit molecule-centric scientific discovery. Variations in molecular images and caption subtasks pose a significant challenge in both image representation learning and task modeling. Yet, existing methods only focus on a specific caption task that translates a molecular image into its graph structure, i.e., OCSR. In this paper, we propose the Optical Chemical Structure Understanding (OCSU) task, which extends OCSR to molecular image caption from motif level to molecule level and abstract level. We present two approaches for that, including an OCSR-based method and an end-to-end OCSR-free method. The proposed Double-Check achieves SOTA OCSR performance on real-world patent and journal article scenarios via attentive feature enhancement for local ambiguous atoms. Cascading with SMILES-based molecule understanding methods, it can leverage the power of existing task-specific models for OCSU. While Mol-VL is an end-to-end optimized VLM-based model. An OCSU dataset, Vis-CheBI20, is built based on the widely used CheBI20 dataset for training and evaluation. Extensive experimental results on Vis-CheBI20 demonstrate the effectiveness of the proposed approaches. Improving OCSR capability can lead to a better OCSU performance for OCSR-based approach, and the SOTA performance of Mol-VL demonstrates the great potential of end-to-end approach.

Molecular property prediction has gained significant attention due to its transformative potential in multiple scientific disciplines. Conventionally, a molecule graph can be represented either as a graph-structured data or a SMILES text. Recently, the rapid development of Large Language Models (LLMs) has revolutionized the field of NLP. Although it is natural to utilize LLMs to assist in understanding molecules represented by SMILES, the exploration of how LLMs will impact molecular property prediction is still in its early stage. In this work, we advance towards this objective through two perspectives: zero/few-shot molecular classification, and using the new explanations generated by LLMs as representations of molecules. To be specific, we first prompt LLMs to do in-context molecular classification and evaluate their performance. After that, we employ LLMs to generate semantically enriched explanations for the original SMILES and then leverage that to fine-tune a small-scale LM model for multiple downstream tasks. The experimental results highlight the superiority of text explanations as molecular representations across multiple benchmark datasets, and confirm the immense potential of LLMs in molecular property prediction tasks. Codes are available at https://github.com/ChnQ/LLM4Mol.

Molecular relational learning, whose goal is to learn the interaction behavior between molecular pairs, got a surge of interest in molecular sciences due to its wide range of applications. Recently, graph neural networks have recently shown great success in molecular relational learning by modeling a molecule as a graph structure, and considering atom-level interactions between two molecules. Despite their success, existing molecular relational learning methods tend to overlook the nature of chemistry, i.e., a chemical compound is composed of multiple substructures such as functional groups that cause distinctive chemical reactions. In this work, we propose a novel relational learning framework, called CGIB, that predicts the interaction behavior between a pair of graphs by detecting core subgraphs therein. The main idea is, given a pair of graphs, to find a subgraph from a graph that contains the minimal sufficient information regarding the task at hand conditioned on the paired graph based on the principle of conditional graph information bottleneck. We argue that our proposed method mimics the nature of chemical reactions, i.e., the core substructure of a molecule varies depending on which other molecule it interacts with. Extensive experiments on various tasks with real-world datasets demonstrate the superiority of CGIB over state-of-the-art baselines. Our code is available at https://github.com/Namkyeong/CGIB.

Prompting Large Language Models (LLMs), or providing context on the expected model of operation, is an effective way to steer the outputs of such models to satisfy human desiderata after they have been trained. But in rapidly evolving domains, there is often need to fine-tune LLMs to improve either the kind of knowledge in their memory or their abilities to perform open ended reasoning in new domains. When human's learn new concepts, we often do so by linking the new material that we are studying to concepts we have already learned before. To that end, we ask, "can prompting help us teach LLMs how to learn". In this work, we study a novel generalization of instruction tuning, called contextual fine-tuning, to fine-tune LLMs. Our method leverages instructional prompts designed to mimic human cognitive strategies in learning and problem-solving to guide the learning process during training, aiming to improve the model's interpretation and understanding of domain-specific knowledge. We empirically demonstrate that this simple yet effective modification improves the ability of LLMs to be fine-tuned rapidly on new datasets both within the medical and financial domains.

Chemical language models (CLMs) are prominent for their effectiveness in exploring chemical space and enabling molecular engineering. However, while exploring chemical-linguistic space, CLMs suffer from the gap between natural language and molecular representations. This challenge is primarily due to the inherent modeling differences between molecules and texts: molecules operate unified modeling to learn chemical space, while natural language sequentially models the semantic space. Additionally, the limited availability of high-quality text-to-molecule datasets further exacerbates this challenge. To address the problem, we first verified the information bias in molecular representations from different perspectives. We then developed the Heterogeneous Molecular Encoding (HME) framework, a unified molecular encoder compressing the molecular features from fragment sequence, topology, and conformation with Q-learning. To better model chemical-linguistic space, we further constructed the MCMoD dataset, which contains over one million molecules with various conditions, including properties, fragments, and descriptions. Experimentally, HME promotes CLMs to achieve chemical-linguistic sharing space exploration: (1) chemical space exploration with linguistic guidance, where HME achieves significant improvements (+37.8\% FCD) for molecular design in multiple constraints, even in zero-shot scenarios; (2) linguistic space exploration with molecular guidance, where HME generates textual descriptions with high qualities (+11.6\% BLEU) for molecules. These results highlight the precision of HME in handling multi-objective and cross-domain tasks, as well as its remarkable generalization capability on unseen task combinations. HME offers a new perspective on navigating chemical-linguistic sharing space, advancing the potential of CLMs in both fundamental research and practical applications in chemistry.

Language-molecule models have emerged as an exciting direction for molecular discovery and understanding. However, training these models is challenging due to the scarcity of molecule-language pair datasets. At this point, datasets have been released which are 1) small and scraped from existing databases, 2) large but noisy and constructed by performing entity linking on the scientific literature, and 3) built by converting property prediction datasets to natural language using templates. In this document, we detail the L+M-24 dataset, which has been created for the Language + Molecules Workshop shared task at ACL 2024. In particular, L+M-24 is designed to focus on three key benefits of natural language in molecule design: compositionality, functionality, and abstraction.

Large pretrained models such as GPT-3 have had tremendous impact on modern natural language processing by leveraging self-supervised learning to learn salient representations that can be used to readily finetune on a wide variety of downstream tasks. We investigate the possibility of transferring such advances to molecular machine learning by building a chemical foundation model, ChemBERTa-2, using the language of SMILES. While labeled data for molecular prediction tasks is typically scarce, libraries of SMILES strings are readily available. In this work, we build upon ChemBERTa by optimizing the pretraining process. We compare multi-task and self-supervised pretraining by varying hyperparameters and pretraining dataset size, up to 77M compounds from PubChem. To our knowledge, the 77M set constitutes one of the largest datasets used for molecular pretraining to date. We find that with these pretraining improvements, we are competitive with existing state-of-the-art architectures on the MoleculeNet benchmark suite. We analyze the degree to which improvements in pretraining translate to improvement on downstream tasks.

Transformer-based deep neural networks have revolutionized the field of molecular-related prediction tasks by treating molecules as symbolic sequences. These models have been successfully applied in various organic chemical applications by pretraining them with extensive compound libraries and subsequently fine-tuning them with smaller in-house datasets for specific tasks. However, many conventional methods primarily focus on single molecules, with limited exploration of pretraining for reactions involving multiple molecules. In this paper, we propose ReactionT5, a novel model that leverages pretraining on the Open Reaction Database (ORD), a publicly available large-scale resource. We further fine-tune this model for yield prediction and product prediction tasks, demonstrating its impressive performance even with limited fine-tuning data compared to traditional models. The pre-trained ReactionT5 model is publicly accessible on the Hugging Face platform.

Large language models have emerged as powerful tools for general intelligence, showcasing advanced natural language processing capabilities that find applications across diverse domains. Despite their impressive performance, recent studies have highlighted the potential for significant enhancements in LLMs' task-specific performance through fine-tuning strategies like Reinforcement Learning with Human Feedback (RLHF), supervised fine-tuning (SFT), and Quantized Low-Rank Adapters (Q-LoRA) method. However, previous works have shown that while fine-tuning offers significant performance gains, it also leads to challenges such as catastrophic forgetting and privacy and safety risks. To this end, there has been little to no work in understanding the impact of fine-tuning on the reasoning capabilities of LLMs. Our research investigates the effect of fine-tuning on the reasoning abilities of LLMs, addressing critical questions regarding the impact of task-specific fine-tuning on overall reasoning capabilities, the influence of fine-tuning on Chain-of-Thought (CoT) reasoning performance, and the implications for the faithfulness of CoT reasonings. By exploring these dimensions, our study shows the impact of fine-tuning on LLM reasoning capabilities, where the faithfulness of CoT reasoning, on average across four datasets, decreases, highlighting potential shifts in internal mechanisms of the LLMs resulting from fine-tuning processes.

Recent advances in Large Language Models (LLMs) have highlighted the challenge of handling long-context tasks, where models need to reason over extensive input contexts to aggregate target information. While Chain-of-Thought (CoT) prompting has shown promise for multi-step reasoning, its effectiveness for long-context scenarios remains underexplored. Through systematic investigation across diverse tasks, we demonstrate that CoT's benefits generalize across most long-context scenarios and amplify with increasing context length. Motivated by this critical observation, we propose LongRePS, a process-supervised framework that teaches models to generate high-quality reasoning paths for enhanced long-context performance. Our framework incorporates a self-sampling mechanism to bootstrap reasoning paths and a novel quality assessment protocol specifically designed for long-context scenarios. Experimental results on various long-context benchmarks demonstrate the effectiveness of our approach, achieving significant improvements over outcome supervision baselines on both in-domain tasks (+13.6/+3.8 points for LLaMA/Qwen on MuSiQue) and cross-domain generalization (+9.3/+8.1 points on average across diverse QA tasks). Our code, data and trained models are made public to facilitate future research.

Large Language Models (LLMs) with strong abilities in natural language processing tasks have emerged and have been rapidly applied in various kinds of areas such as science, finance and software engineering. However, the capability of LLMs to advance the field of chemistry remains unclear. In this paper,we establish a comprehensive benchmark containing 8 practical chemistry tasks, including 1) name prediction, 2) property prediction, 3) yield prediction, 4) reaction prediction, 5) retrosynthesis (prediction of reactants from products), 6)text-based molecule design, 7) molecule captioning, and 8) reagent selection. Our analysis draws on widely recognized datasets including BBBP, Tox21, PubChem, USPTO, and ChEBI, facilitating a broad exploration of the capacities of LLMs within the context of practical chemistry. Three GPT models (GPT-4, GPT-3.5,and Davinci-003) are evaluated for each chemistry task in zero-shot and few-shot in-context learning settings with carefully selected demonstration examples and specially crafted prompts. The key results of our investigation are 1) GPT-4 outperforms the other two models among the three evaluated; 2) GPT models exhibit less competitive performance in tasks demanding precise understanding of molecular SMILES representation, such as reaction prediction and retrosynthesis;3) GPT models demonstrate strong capabilities in text-related explanation tasks such as molecule captioning; and 4) GPT models exhibit comparable or better performance to classical machine learning models when applied to chemical problems that can be transformed into classification or ranking tasks, such as property prediction, and yield prediction.

Self-supervised learning holds promise to revolutionize molecule property prediction - a central task to drug discovery and many more industries - by enabling data efficient learning from scarce experimental data. Despite significant progress, non-pretrained methods can be still competitive in certain settings. We reason that architecture might be a key bottleneck. In particular, enriching the backbone architecture with domain-specific inductive biases has been key for the success of self-supervised learning in other domains. In this spirit, we methodologically explore the design space of the self-attention mechanism tailored to molecular data. We identify a novel variant of self-attention adapted to processing molecules, inspired by the relative self-attention layer, which involves fusing embedded graph and distance relationships between atoms. Our main contribution is Relative Molecule Attention Transformer (R-MAT): a novel Transformer-based model based on the developed self-attention layer that achieves state-of-the-art or very competitive results across a~wide range of molecule property prediction tasks.

Foundation models have been transformational in machine learning fields such as natural language processing and computer vision. Similar success in atomic property prediction has been limited due to the challenges of training effective models across multiple chemical domains. To address this, we introduce Joint Multi-domain Pre-training (JMP), a supervised pre-training strategy that simultaneously trains on multiple datasets from different chemical domains, treating each dataset as a unique pre-training task within a multi-task framework. Our combined training dataset consists of sim120M systems from OC20, OC22, ANI-1x, and Transition-1x. We evaluate performance and generalization by fine-tuning over a diverse set of downstream tasks and datasets including: QM9, rMD17, MatBench, QMOF, SPICE, and MD22. JMP demonstrates an average improvement of 59% over training from scratch, and matches or sets state-of-the-art on 34 out of 40 tasks. Our work highlights the potential of pre-training strategies that utilize diverse data to advance property prediction across chemical domains, especially for low-data tasks.

The recent development of chain-of-thought (CoT) decoding has enabled large language models (LLMs) to generate explicit logical reasoning paths for complex problem-solving. However, research indicates that these paths are not always deliberate and optimal. The tree-of-thought (ToT) method employs tree-searching to extensively explore the reasoning space and find better reasoning paths that CoT decoding might overlook. This deliberation, however, comes at the cost of significantly increased inference complexity. In this work, we demonstrate that fine-tuning LLMs leveraging the search tree constructed by ToT allows CoT to achieve similar or better performance, thereby avoiding the substantial inference burden. This is achieved through Chain of Preference Optimization (CPO), where LLMs are fine-tuned to align each step of the CoT reasoning paths with those of ToT using the inherent preference information in the tree-search process. Extensive experimental results show that CPO significantly improves LLM performance in solving a variety of complex problems, including question answering, fact verification, and arithmetic reasoning, demonstrating its effectiveness. Our code is available at https://github.com/sail-sg/CPO.

Chain-of-Thought (CoT) reasoning enables Large Language Models (LLMs) to solve complex reasoning tasks by generating intermediate reasoning steps. However, most existing approaches focus on hard token decoding, which constrains reasoning within the discrete vocabulary space and may not always be optimal. While recent efforts explore continuous-space reasoning, they often suffer from catastrophic forgetting, limiting their applicability to state-of-the-art LLMs that already perform well in zero-shot settings with a proper instruction. To address this challenge, we propose a novel approach for continuous-space reasoning that does not require modifying the underlying LLM. Specifically, we employ a lightweight assistant model to generate instance-specific soft thought tokens speculatively as the initial chain of thoughts, which are then mapped into the LLM's representation space via a projection module. Experimental results on five reasoning benchmarks demonstrate that our method enhances LLM reasoning performance through supervised, parameter-efficient fine-tuning.

The success of language models, especially transformer-based architectures, has trickled into other domains giving rise to "scientific language models" that operate on small molecules, proteins or polymers. In chemistry, language models contribute to accelerating the molecule discovery cycle as evidenced by promising recent findings in early-stage drug discovery. Here, we review the role of language models in molecular discovery, underlining their strength in de novo drug design, property prediction and reaction chemistry. We highlight valuable open-source software assets thus lowering the entry barrier to the field of scientific language modeling. Last, we sketch a vision for future molecular design that combines a chatbot interface with access to computational chemistry tools. Our contribution serves as a valuable resource for researchers, chemists, and AI enthusiasts interested in understanding how language models can and will be used to accelerate chemical discovery.

We report a series of deep learning models to solve complex forward and inverse design problems in molecular modeling and design. Using both diffusion models inspired by nonequilibrium thermodynamics and attention-based transformer architectures, we demonstrate a flexible framework to capture complex chemical structures. First trained on the QM9 dataset and a series of quantum mechanical properties (e.g. homo, lumo, free energy, heat capacity, etc.), we then generalize the model to study and design key properties of deep eutectic solvents. In addition to separate forward and inverse models, we also report an integrated fully prompt-based multi-task generative pretrained transformer model that solves multiple forward, inverse design, and prediction tasks, flexibly and within one model. We show that the multi-task generative model has the overall best performance and allows for flexible integration of multiple objectives, within one model, and for distinct chemistries, suggesting that synergies emerge during training of this large language model. Trained jointly in tasks related to the QM9 dataset and deep eutectic solvents (DESs), the model can predict various quantum mechanical properties and critical properties to achieve deep eutectic solvent behavior. Several novel combinations of DESs are proposed based on this framework.

Few-shot Chain-of-Thought (CoT) prompting has demonstrated strong performance in improving the reasoning capabilities of large language models (LLMs). While theoretical investigations have been conducted to understand CoT, the underlying transformer used in these studies isolates the CoT reasoning process into separated in-context learning steps (Stepwise ICL). In this work, we theoretically show that, compared to Stepwise ICL, the transformer gains better error correction ability and more accurate predictions if the reasoning from earlier steps (Coherent CoT) is integrated. Given that this coherent reasoning changes the behavior of the transformer, we further investigate the sensitivity of the transformer with Coherent CoT when the demonstration examples are corrupted at the inference stage. Our theoretical results indicate that the transformer is more sensitive to errors in intermediate reasoning steps than the final outcome. Building upon this observation, we propose an improvement on CoT by incorporating both correct and incorrect reasoning paths in the demonstration. Our experiments validate the effectiveness of the proposed approach.

Recent advancements in biological research leverage the integration of molecules, proteins, and natural language to enhance drug discovery. However, current models exhibit several limitations, such as the generation of invalid molecular SMILES, underutilization of contextual information, and equal treatment of structured and unstructured knowledge. To address these issues, we propose BioT5, a comprehensive pre-training framework that enriches cross-modal integration in biology with chemical knowledge and natural language associations. BioT5 utilizes SELFIES for 100% robust molecular representations and extracts knowledge from the surrounding context of bio-entities in unstructured biological literature. Furthermore, BioT5 distinguishes between structured and unstructured knowledge, leading to more effective utilization of information. After fine-tuning, BioT5 shows superior performance across a wide range of tasks, demonstrating its strong capability of capturing underlying relations and properties of bio-entities. Our code is available at https://github.com/QizhiPei/BioT5{Github}.

Language Models (LMs) have greatly influenced diverse domains. However, their inherent limitation in comprehending 3D molecular structures has considerably constrained their potential in the biomolecular domain. To bridge this gap, we focus on 3D molecule-text interpretation, and propose 3D-MoLM: 3D-Molecular Language Modeling. Specifically, 3D-MoLM enables an LM to interpret and analyze 3D molecules by equipping the LM with a 3D molecular encoder. This integration is achieved by a 3D molecule-text projector, bridging the 3D molecular encoder's representation space and the LM's input space. Moreover, to enhance 3D-MoLM's ability of cross-modal molecular understanding and instruction following, we meticulously curated a 3D molecule-centric instruction tuning dataset -- 3D-MoIT. Through 3D molecule-text alignment and 3D molecule-centric instruction tuning, 3D-MoLM establishes an integration of 3D molecular encoder and LM. It significantly surpasses existing baselines on downstream tasks, including molecule-text retrieval, molecule captioning, and more challenging open-text molecular QA tasks, especially focusing on 3D-dependent properties.

Generating novel active molecules for a given protein is an extremely challenging task for generative models that requires an understanding of the complex physical interactions between the molecule and its environment. In this paper, we present a novel generative model, BindGPT which uses a conceptually simple but powerful approach to create 3D molecules within the protein's binding site. Our model produces molecular graphs and conformations jointly, eliminating the need for an extra graph reconstruction step. We pretrain BindGPT on a large-scale dataset and fine-tune it with reinforcement learning using scores from external simulation software. We demonstrate how a single pretrained language model can serve at the same time as a 3D molecular generative model, conformer generator conditioned on the molecular graph, and a pocket-conditioned 3D molecule generator. Notably, the model does not make any representational equivariance assumptions about the domain of generation. We show how such simple conceptual approach combined with pretraining and scaling can perform on par or better than the current best specialized diffusion models, language models, and graph neural networks while being two orders of magnitude cheaper to sample.

Chain-of-Thought (CoT) has been a widely adopted prompting method, eliciting impressive reasoning abilities of Large Language Models (LLMs). Inspired by the sequential thought structure of CoT, a number of Chain-of-X (CoX) methods have been developed to address various challenges across diverse domains and tasks involving LLMs. In this paper, we provide a comprehensive survey of Chain-of-X methods for LLMs in different contexts. Specifically, we categorize them by taxonomies of nodes, i.e., the X in CoX, and application tasks. We also discuss the findings and implications of existing CoX methods, as well as potential future directions. Our survey aims to serve as a detailed and up-to-date resource for researchers seeking to apply the idea of CoT to broader scenarios.

Identifying a small molecule from its mass spectrum is the primary open problem in computational metabolomics. This is typically cast as information retrieval: an unknown spectrum is matched against spectra predicted computationally from a large database of chemical structures. However, current approaches to spectrum prediction model the output space in ways that force a tradeoff between capturing high resolution mass information and tractable learning. We resolve this tradeoff by casting spectrum prediction as a mapping from an input molecular graph to a probability distribution over molecular formulas. We discover that a large corpus of mass spectra can be closely approximated using a fixed vocabulary constituting only 2% of all observed formulas. This enables efficient spectrum prediction using an architecture similar to graph classification - GrAFF-MS - achieving significantly lower prediction error and orders-of-magnitude faster runtime than state-of-the-art methods.

Motivation: The development of novel compounds targeting proteins of interest is one of the most important tasks in the pharmaceutical industry. Deep generative models have been applied to targeted molecular design and have shown promising results. Recently, target-specific molecule generation has been viewed as a translation between the protein language and the chemical language. However, such a model is limited by the availability of interacting protein-ligand pairs. On the other hand, large amounts of unlabeled protein sequences and chemical compounds are available and have been used to train language models that learn useful representations. In this study, we propose exploiting pretrained biochemical language models to initialize (i.e. warm start) targeted molecule generation models. We investigate two warm start strategies: (i) a one-stage strategy where the initialized model is trained on targeted molecule generation (ii) a two-stage strategy containing a pre-finetuning on molecular generation followed by target specific training. We also compare two decoding strategies to generate compounds: beam search and sampling. Results: The results show that the warm-started models perform better than a baseline model trained from scratch. The two proposed warm-start strategies achieve similar results to each other with respect to widely used metrics from benchmarks. However, docking evaluation of the generated compounds for a number of novel proteins suggests that the one-stage strategy generalizes better than the two-stage strategy. Additionally, we observe that beam search outperforms sampling in both docking evaluation and benchmark metrics for assessing compound quality. Availability and implementation: The source code is available at https://github.com/boun-tabi/biochemical-lms-for-drug-design and the materials are archived in Zenodo at https://doi.org/10.5281/zenodo.6832145

Molecule-text modeling, which aims to facilitate molecule-relevant tasks with a textual interface and textual knowledge, is an emerging research direction. Beyond single molecules, studying reaction-text modeling holds promise for helping the synthesis of new materials and drugs. However, previous works mostly neglect reaction-text modeling: they primarily focus on modeling individual molecule-text pairs or learning chemical reactions without texts in context. Additionally, one key task of reaction-text modeling -- experimental procedure prediction -- is less explored due to the absence of an open-source dataset. The task is to predict step-by-step actions of conducting chemical experiments and is crucial to automating chemical synthesis. To resolve the challenges above, we propose a new pretraining method, ReactXT, for reaction-text modeling, and a new dataset, OpenExp, for experimental procedure prediction. Specifically, ReactXT features three types of input contexts to incrementally pretrain LMs. Each of the three input contexts corresponds to a pretraining task to improve the text-based understanding of either reactions or single molecules. ReactXT demonstrates consistent improvements in experimental procedure prediction and molecule captioning and offers competitive results in retrosynthesis. Our code is available at https://github.com/syr-cn/ReactXT.

Inductive Reasoning (IR), the ability to summarize rules from examples and apply on new ones, has long been viewed as a primal ability for general intelligence and widely studied by cognitive science and AI researchers. Many benchmarks have been proposed to measure such ability for Large Language Models (LLMs); however, they focus on few-shot (usually <10) setting and lack evaluation for aggregating many pieces of information from long contexts. On the other hand, the ever-growing context length of LLMs have brought forth the novel paradigm of many-shot In-Context Learning (ICL), which addresses new tasks with hundreds to thousands of examples without expensive and inefficient fine-tuning. However, many-shot evaluations are mostly focused on classification (a very limited aspect of IR), and popular long-context LLM tasks such as Needle-In-A-Haystack (NIAH) seldom require complicated intelligence for integrating many pieces of information. To fix the issues from both worlds, we propose MIR-Bench, the first many-shot in-context inductive reasoning benchmark that asks LLM to induce output via input-output examples from underlying functions with diverse data format. Based on MIR-Bench, we study many novel problems for inductive reasoning and many-shot ICL, including robustness against erroneous shots and the effect of Chain-of-Thought (CoT), and acquired insightful findings.

Planning and acting to solve `real' tasks using large language models (LLMs) in interactive environments has become a new frontier for AI methods. While recent advances allowed LLMs to interact with online tools, solve robotics tasks and many more, long range reasoning tasks remain a problem for LLMs. Existing methods to address this issue are very resource intensive and require additional data or human crafted rules, instead, we propose a simple method based on few-shot in-context learning alone to enhance `chain-of-thought' with state-tracking for planning and acting with LLMs. We show that our method establishes the new state-of-the-art on Alfworld for in-context learning methods (+14\% over the previous best few-shot in-context learning method) and performs on par with methods that use additional training data and additional tools such as code-execution. We also demonstrate that our enhanced `chain-of-states' allows the agent to both solve longer horizon problems and to be more efficient in number of steps required to solve a task. We show that our method works across a variety of LLMs for both API-based and open source ones. Finally, we also conduct ablation studies and show that `chain-of-thoughts' helps state-tracking accuracy, while a json-structure harms overall performance. We open-source our code and annotations at https://github.com/ai-nikolai/StateAct.

In Retrieval-Augmented Generation (RAG) and agent-based frameworks, the "Chain of Models" approach is widely used, where multiple specialized models work sequentially on distinct sub-tasks. This approach is effective but increases resource demands as each model must be deployed separately. Recent advancements attempt to address this by applying prompt tuning, which allows a shared base model to adapt to multiple tasks with minimal parameter changes. However, a key challenge remains: intermediate outputs, passed between models as plain text, require recomputation of hidden states (i.e., Key and Value (KV) states in Transformers) during inference. In this paper, we introduce FTHSS, a novel prompt-tuning method that enables models to share KV hidden states, eliminating redundant forward passes and reducing KV cache storage. By modifying input and attention masks during training, FTHSS allows models to effectively utilize KV hidden states from prior models in both single- and multi-round scenarios. Empirical results on four tasks show that FTHSS matches the performance of traditional model chains while improving inference efficiency.

In this work, we introduce ChemBFN, a language model that handles chemistry tasks based on Bayesian flow networks working on discrete data. A new accuracy schedule is proposed to improve the sampling quality by significantly reducing the reconstruction loss. We show evidence that our method is appropriate for generating molecules with satisfied diversity even when a smaller number of sampling steps is used. A classifier-free guidance method is adapted for conditional generation. It is also worthwhile to point out that after generative training, our model can be fine-tuned on regression and classification tasks with the state-of-the-art performance, which opens the gate of building all-in-one models in a single module style. Our model has been open sourced at https://github.com/Augus1999/bayesian-flow-network-for-chemistry.

This paper studies the problem of solving complex chemistry problems with large language models (LLMs). Despite the extensive general knowledge in LLMs (such as GPT-4), they struggle with chemistry reasoning that requires faithful grounded reasoning with diverse chemical knowledge and an integrative understanding of chemical interactions. We propose InstructChem, a new structured reasoning approach that substantially boosts the LLMs' chemical reasoning capabilities. InstructChem explicitly decomposes the reasoning into three critical phrases, including chemical formulae generation by LLMs that offers the basis for subsequent grounded reasoning, step-by-step reasoning that makes multi-step derivations with the identified formulae for a preliminary answer, and iterative review-and-refinement that steers LLMs to progressively revise the previous phases for increasing confidence, leading to the final high-confidence answer. We conduct extensive experiments on four different chemistry challenges, including quantum chemistry, quantum mechanics, physical chemistry, and chemistry kinetics. Our approach significantly enhances GPT-4 on chemistry reasoning, yielding an 8% average absolute improvement and a 30% peak improvement. We further use the generated reasoning by GPT-4 to fine-tune smaller LMs (e.g., Vicuna) and observe strong improvement of the smaller LMs. This validates our approach and enables LLMs to generate high-quality reasoning.

Commonsense reasoning is a pivotal skill for large language models, yet it presents persistent challenges in specific tasks requiring this competence. Traditional fine-tuning approaches can be resource-intensive and potentially compromise a model's generalization capacity. Furthermore, state-of-the-art language models like GPT-3.5 and Claude are primarily accessible through API calls, which makes fine-tuning models challenging. To address these challenges, we draw inspiration from the outputs of large models for tailored tasks and semi-automatically developed a set of novel prompts from several perspectives, including task-relevance, supportive evidence generation (e.g. chain-of-thought and knowledge), diverse path decoding to aid the model. Experimental results on ProtoQA dataset demonstrate that with better designed prompts we can achieve the new state-of-art(SOTA) on the ProtoQA leaderboard, improving the Max Answer@1 score by 8%, Max Incorrect@1 score by 4% (breakthrough 50% for the first time) compared to the previous SOTA model and achieved an improvement on StrategyQA and CommonsenseQA2.0 (3% and 1%, respectively). Furthermore, with the generated Chain-of-Thought and knowledge, we can improve the interpretability of the model while also surpassing the previous SOTA models. We hope that our work can provide insight for the NLP community to develop better prompts and explore the potential of large language models for more complex reasoning tasks.

Despite the strong performance of large language models (LLMs) in tasks like mathematical reasoning, their practical use is limited by high computational demands and proprietary restrictions. Chain-of-thought (CoT) and program-of-thought (PoT) fine-tuning are common methods to transfer LLM knowledge to small language models (SLMs). However, CoT often leads to calculation errors in SLMs, while PoT has shown more promise. While most PoT-based approaches focus on direct problem-to-code conversion or extracting only the key information from questions and then providing code solution for it, this work emphasizes filling the gaps in the question to clearly illustrate the solution path, which can be challenging for an SLM to understand when such information is not explicitly provided. Therefore, this paper introduces Gap-Filling Prompting (GFP), a novel two-step prompting strategy designed to enhance the problem-solving process for SLMs. The first step identifies these gaps and provides hints for filling them, while the second step adds the hints to the question to generate a final code solution. Experimental results on two benchmark datasets demonstrate that GFP significantly improves the mathematical reasoning abilities of SLMs.

Chain-of-Thought significantly enhances a model's reasoning capability, but it also comes with a considerable increase in inference costs due to long chains. With the observation that the reasoning path can be easily compressed under easy tasks but struggle on hard tasks, we explore the feasibility of elastically controlling the length of reasoning paths with only one model, thereby reducing the inference overhead of reasoning models dynamically based on task difficulty. We introduce a new tuning and inference strategy named CoT-Valve, designed to allow models to generate reasoning chains of varying lengths. To achieve this, we propose to identify a direction in the parameter space that, when manipulated, can effectively control the length of generated CoT. Moreover, we show that this property is valuable for compressing the reasoning chain. We construct datasets with chains from long to short for the same questions and explore two enhanced strategies for CoT-Valve: (1) a precise length-compressible CoT tuning method, and (2) a progressive chain length compression approach. Our experiments show that CoT-Valve successfully enables controllability and compressibility of the chain and shows better performance than the prompt-based control. We applied this method to QwQ-32B-Preview, reducing reasoning chains on GSM8K from 741 to 225 tokens with a minor performance drop (95.07% to 94.92%) and on AIME from 6827 to 4629 tokens, with only one additional incorrect answer.

Chain-of-thought (CoT) prompting with large language models has proven effective in numerous natural language processing tasks, but designing prompts that generalize well to diverse problem types can be challenging, especially in the context of math word problem (MWP) solving. Additionally, it is common to have a large amount of training data that have a better diversity coverage but CoT annotations are not available, which limits the use of supervised learning techniques. To address these issues, we investigate two approaches to leverage the training data in a few-shot prompting scenario: dynamic program prompting and program distillation. Our approach is largely inspired by Gao et al., (2022), where they proposed to replace the CoT with the programs as the intermediate reasoning step. Such a prompting strategy allows us to accurately verify the answer correctness through program execution in MWP solving. Our dynamic program prompting involves annotating the training data by sampling correct programs from a large language model, while program distillation involves adapting a smaller model to the program-annotated training data. Our experiments on three standard MWP datasets demonstrate the effectiveness of these approaches, yielding significant improvements over previous baselines for prompting and fine-tuning. Our results suggest that leveraging a large amount of training data can improve the generalization ability of prompts and boost the performance of fine-tuned small models in MWP solving.

In molecular research, simulation \& design of molecules are key areas with significant implications for drug development, material science, and other fields. Current classical computational power falls inadequate to simulate any more than small molecules, let alone protein chains on hundreds of peptide. Therefore these experiment are done physically in wet-lab, but it takes a lot of time \& not possible to examine every molecule due to the size of the search area, tens of billions of dollars are spent every year in these research experiments. Molecule simulation \& design has lately advanced significantly by machine learning models, A fresh perspective on the issue of chemical synthesis is provided by deep generative models for graph-structured data. By optimising differentiable models that produce molecular graphs directly, it is feasible to avoid costly search techniques in the discrete and huge space of chemical structures. But these models also suffer from computational limitations when dimensions become huge and consume huge amount of resources. Quantum Generative machine learning in recent years have shown some empirical results promising significant advantages over classical counterparts.

Models based on machine learning can enable accurate and fast molecular property predictions, which is of interest in drug discovery and material design. Various supervised machine learning models have demonstrated promising performance, but the vast chemical space and the limited availability of property labels make supervised learning challenging. Recently, unsupervised transformer-based language models pretrained on a large unlabelled corpus have produced state-of-the-art results in many downstream natural language processing tasks. Inspired by this development, we present molecular embeddings obtained by training an efficient transformer encoder model, MoLFormer, which uses rotary positional embeddings. This model employs a linear attention mechanism, coupled with highly distributed training, on SMILES sequences of 1.1 billion unlabelled molecules from the PubChem and ZINC datasets. We show that the learned molecular representation outperforms existing baselines, including supervised and self-supervised graph neural networks and language models, on several downstream tasks from ten benchmark datasets. They perform competitively on two others. Further analyses, specifically through the lens of attention, demonstrate that MoLFormer trained on chemical SMILES indeed learns the spatial relationships between atoms within a molecule. These results provide encouraging evidence that large-scale molecular language models can capture sufficient chemical and structural information to predict various distinct molecular properties, including quantum-chemical properties.

We identify two crucial limitations in the evaluation of recent parallel-integrated method Parallel Context Windows (PCW), which extends the maximum context lengths of language models, e.g., 2048 for LLaMA, by harnessing window-wise attention and positional embedding techniques. We first show that a simple yet strong baseline, weighted sum ensemble, is missing for the in-context few-shot classification. Moreover, on more challenging Chain-of-Thought (CoT) reasoning (e.g., HotpotQA), PCW would present unexpected deterioration regarding question miscomprehension and false inference. Based on our findings, we suggest that the existing PCW design may not guarantee sufficient improvement and practicality in handling lengthy documents in real-world applications. More community efforts on enabling language models' long context understanding ability should be paid.

Large language model (LLM) performance on reasoning problems typically does not generalize out of distribution. Previous work has claimed that this can be mitigated by modifying prompts to include examples with chains of thought--demonstrations of solution procedures--with the intuition that it is possible to in-context teach an LLM an algorithm for solving the problem. This paper presents a case study of chain of thought on problems from Blocksworld, a classical planning domain, and examine the performance of two state-of-the-art LLMs across two axes: generality of examples given in prompt, and complexity of problems queried with each prompt. While our problems are very simple, we only find meaningful performance improvements from chain of thought prompts when those prompts are exceedingly specific to their problem class, and that those improvements quickly deteriorate as the size n of the query-specified stack grows past the size of stacks shown in the examples. Our results hint that, contrary to previous claims in the literature, CoT's performance improvements do not stem from the model learning general algorithmic procedures via demonstrations and depend on carefully engineering highly problem specific prompts. This spotlights drawbacks of chain of thought, especially because of the sharp tradeoff between possible performance gains and the amount of human labor necessary to generate examples with correct reasoning traces.

In-context Learning (ICL) enables large language models (LLMs) to tackle downstream tasks through sophisticated prompting and high-quality demonstrations. However, this traditional ICL paradigm shows limitations when facing complex mathematical reasoning tasks, primarily due to its heavy dependence on example quality and the necessity for human intervention in challenging scenarios. To address these limitations, this paper presents HiAR-ICL, a High-level Automated Reasoning paradigm in ICL that shifts focus from specific examples to abstract thinking patterns, extending the conventional concept of context in ICL. HiAR-ICL introduces five atomic reasoning actions as fundamental components for constructing chain-structured patterns. Using Monte Carlo Tree Search, we explore reasoning paths and construct thought cards to guide subsequent inference. We then develop a cognitive complexity framework that dynamically matches problems with appropriate thought cards. Experimental results demonstrate HiAR-ICL's effectiveness, achieving state-of-the-art accuracy (79.6%) on the MATH benchmark with Qwen2.5-7B-Instruct, surpassing GPT-4o (76.6%) and Claude 3.5 (71.1%).

Recent literature has shown that large language models (LLMs) are generally excellent few-shot reasoners to solve text reasoning tasks. However, the capability of LLMs on table reasoning tasks is yet to be explored. In this paper, we aim at understanding how well LLMs can perform table-related tasks with few-shot in-context learning. Specifically, we evaluated LLMs on popular table QA and fact verification datasets like WikiTableQuestion, FetaQA, TabFact, and FEVEROUS and found that LLMs are competent at complex reasoning over table structures, though these models are not pre-trained on any table corpus. When combined with `chain of thoughts' prompting, LLMs can achieve very strong performance with only a 1-shot demonstration, even on par with some SoTA models. We show that LLMs are even more competent at generating comprehensive long-form answers on FetaQA than tuned T5-large. We further manually studied the reasoning chains elicited from LLMs and found that these reasoning chains are highly consistent with the underlying semantic form. We believe that LLMs can serve as a simple yet generic baseline for future research. The code and data are released in https://github.com/wenhuchen/TableCoT.

Generative models are becoming a tool of choice for exploring the molecular space. These models learn on a large training dataset and produce novel molecular structures with similar properties. Generated structures can be utilized for virtual screening or training semi-supervised predictive models in the downstream tasks. While there are plenty of generative models, it is unclear how to compare and rank them. In this work, we introduce a benchmarking platform called Molecular Sets (MOSES) to standardize training and comparison of molecular generative models. MOSES provides a training and testing datasets, and a set of metrics to evaluate the quality and diversity of generated structures. We have implemented and compared several molecular generation models and suggest to use our results as reference points for further advancements in generative chemistry research. The platform and source code are available at https://github.com/molecularsets/moses.

Recently, the impressive performance of large language models (LLMs) on a wide range of tasks has attracted an increasing number of attempts to apply LLMs in drug discovery. However, molecule optimization, a critical task in the drug discovery pipeline, is currently an area that has seen little involvement from LLMs. Most of existing approaches focus solely on capturing the underlying patterns in chemical structures provided by the data, without taking advantage of expert feedback. These non-interactive approaches overlook the fact that the drug discovery process is actually one that requires the integration of expert experience and iterative refinement. To address this gap, we propose DrugAssist, an interactive molecule optimization model which performs optimization through human-machine dialogue by leveraging LLM's strong interactivity and generalizability. DrugAssist has achieved leading results in both single and multiple property optimization, simultaneously showcasing immense potential in transferability and iterative optimization. In addition, we publicly release a large instruction-based dataset called MolOpt-Instructions for fine-tuning language models on molecule optimization tasks. We have made our code and data publicly available at https://github.com/blazerye/DrugAssist, which we hope to pave the way for future research in LLMs' application for drug discovery.

Molecular representation learning contributes to multiple downstream tasks such as molecular property prediction and drug design. To properly represent molecules, graph contrastive learning is a promising paradigm as it utilizes self-supervision signals and has no requirements for human annotations. However, prior works fail to incorporate fundamental domain knowledge into graph semantics and thus ignore the correlations between atoms that have common attributes but are not directly connected by bonds. To address these issues, we construct a Chemical Element Knowledge Graph (KG) to summarize microscopic associations between elements and propose a novel Knowledge-enhanced Contrastive Learning (KCL) framework for molecular representation learning. KCL framework consists of three modules. The first module, knowledge-guided graph augmentation, augments the original molecular graph based on the Chemical Element KG. The second module, knowledge-aware graph representation, extracts molecular representations with a common graph encoder for the original molecular graph and a Knowledge-aware Message Passing Neural Network (KMPNN) to encode complex information in the augmented molecular graph. The final module is a contrastive objective, where we maximize agreement between these two views of molecular graphs. Extensive experiments demonstrated that KCL obtained superior performances against state-of-the-art baselines on eight molecular datasets. Visualization experiments properly interpret what KCL has learned from atoms and attributes in the augmented molecular graphs. Our codes and data are available at https://github.com/ZJU-Fangyin/KCL.

Recent works have shown that chain-of-thought (CoT) prompting can elicit language models to solve complex reasoning tasks, step-by-step. However, prompt-based CoT methods are dependent on very large models such as GPT-3 175B which are prohibitive to deploy at scale. In this paper, we use these large models as reasoning teachers to enable complex reasoning in smaller models and reduce model size requirements by several orders of magnitude. We propose Fine-tune-CoT, a method that generates reasoning samples from very large teacher models to fine-tune smaller models. We evaluate our method on a wide range of public models and complex tasks. We find that Fine-tune-CoT enables substantial reasoning capability in small models, far outperforming prompt-based baselines and even the teacher model in many tasks. Additionally, we extend our method by leveraging the teacher model's ability to generate multiple distinct rationales for each original sample. Enriching the fine-tuning data with such diverse reasoning results in a substantial performance boost across datasets, even for very small models. We conduct ablations and sample studies to understand the emergence of reasoning capabilities of student models. Our code implementation and data are available at https://github.com/itsnamgyu/reasoning-teacher.

Extensive work has shown that the performance and interpretability of commonsense reasoning can be improved via knowledge-augmented reasoning methods, where the knowledge that underpins the reasoning process is explicitly verbalized and utilized. However, existing implementations, including "chain-of-thought" and its variants, fall short in capturing the introspective nature of knowledge required in commonsense reasoning, and in accounting for the mutual adaptation between the generation and utilization of knowledge. We propose a novel method to develop an introspective commonsense reasoner, Crystal. To tackle commonsense problems, it first introspects for knowledge statements related to the given question, and subsequently makes an informed prediction that is grounded in the previously introspected knowledge. The knowledge introspection and knowledge-grounded reasoning modes of the model are tuned via reinforcement learning to mutually adapt, where the reward derives from the feedback given by the model itself. Experiments show that Crystal significantly outperforms both the standard supervised finetuning and chain-of-thought distilled methods, and enhances the transparency of the commonsense reasoning process. Our work ultimately validates the feasibility and potential of reinforcing a neural model with self-feedback.

Large Language Models (LLMs), with their remarkable task-handling capabilities and innovative outputs, have catalyzed significant advancements across a spectrum of fields. However, their proficiency within specialized domains such as biomolecular studies remains limited. To address this challenge, we introduce Mol-Instructions, a meticulously curated, comprehensive instruction dataset expressly designed for the biomolecular realm. Mol-Instructions is composed of three pivotal components: molecule-oriented instructions, protein-oriented instructions, and biomolecular text instructions, each curated to enhance the understanding and prediction capabilities of LLMs concerning biomolecular features and behaviors. Through extensive instruction tuning experiments on the representative LLM, we underscore the potency of Mol-Instructions to enhance the adaptability and cognitive acuity of large models within the complex sphere of biomolecular studies, thereby promoting advancements in the biomolecular research community. Mol-Instructions is made publicly accessible for future research endeavors and will be subjected to continual updates for enhanced applicability.

There will be a paradigm shift in chemical and biological research, to be enabled by autonomous, closed-loop, real-time self-directed decision-making experimentation. Spectrum-to-structure correlation, which is to elucidate molecular structures with spectral information, is the core step in understanding the experimental results and to close the loop. However, current approaches usually divide the task into either database-dependent retrieval and database-independent generation and neglect the inherent complementarity between them. In this study, we proposed Vib2Mol, a general deep learning model designed to flexibly handle diverse spectrum-to-structure tasks according to the available prior knowledge by bridging the retrieval and generation. It achieves state-of-the-art performance, even for the most demanding Raman spectra, over previous models in predicting reaction products and sequencing peptides as well as analyzing experimental spectra and integrating multi-modal spectral data. Vib2Mol enables vibrational spectroscopy a real-time guide for autonomous scientific discovery workflows.

Large Language Models (LLMs) have shown enhanced capabilities of solving novel tasks by reasoning step-by-step known as Chain-of-Thought (CoT) reasoning; how can we instill the same capability of reasoning step-by-step on unseen tasks into LMs that possess less than <100B parameters? To address this question, we first introduce the CoT Collection, a new instruction-tuning dataset that augments 1.88 million CoT rationales across 1,060 tasks. We show that continually fine-tuning Flan-T5 (3B & 11B) with the CoT Collection enables the 3B & 11B LMs to perform CoT better on unseen tasks, leading to an improvement in the average zero-shot accuracy on 27 datasets of the BIG-Bench-Hard benchmark by +4.34% and +2.44%, respectively. Furthermore, we show that instruction tuning with CoT allows LMs to possess stronger few-shot learning capabilities, resulting in an improvement of +2.97% and +2.37% on 4 domain-specific tasks over Flan-T5 (3B & 11B), respectively. We make our CoT Collection data and our trained models publicly available at https://github.com/kaist-lklab/CoT-Collection.

With the widespread use of large language models (LLMs) in NLP tasks, researchers have discovered the potential of Chain-of-thought (CoT) to assist LLMs in accomplishing complex reasoning tasks by generating intermediate steps. However, human thought processes are often non-linear, rather than simply sequential chains of thoughts. Therefore, we propose Graph-of-Thought (GoT) reasoning, which models human thought processes not only as a chain but also as a graph. By representing thought units as nodes and connections between them as edges, our approach captures the non-sequential nature of human thinking and allows for a more realistic modeling of thought processes. Similar to Multimodal-CoT, we modeled GoT reasoning as a two-stage framework, generating rationales first and then producing the final answer. Specifically, we employ an additional graph-of-thoughts encoder for GoT representation learning and fuse the GoT representation with the original input representation through a gated fusion mechanism. We implement a GoT reasoning model on the T5 pre-trained model and evaluate its performance on a text-only reasoning task (GSM8K) and a multimodal reasoning task (ScienceQA). Our model achieves significant improvement over the strong CoT baseline with 3.41% and 5.08% on the GSM8K test set with T5-base and T5-large architectures, respectively. Additionally, our model boosts accuracy from 84.91% to 91.54% using the T5-base model and from 91.68% to 92.77% using the T5-large model over the state-of-the-art Multimodal-CoT on the ScienceQA test set. Experiments have shown that GoT achieves comparable results to Multimodal-CoT(large) with over 700M parameters, despite having fewer than 250M backbone model parameters, demonstrating the effectiveness of GoT.

Chain-of-thought reasoning, a cognitive process fundamental to human intelligence, has garnered significant attention in the realm of artificial intelligence and natural language processing. However, there still remains a lack of a comprehensive survey for this arena. To this end, we take the first step and present a thorough survey of this research field carefully and widely. We use X-of-Thought to refer to Chain-of-Thought in a broad sense. In detail, we systematically organize the current research according to the taxonomies of methods, including XoT construction, XoT structure variants, and enhanced XoT. Additionally, we describe XoT with frontier applications, covering planning, tool use, and distillation. Furthermore, we address challenges and discuss some future directions, including faithfulness, multi-modal, and theory. We hope this survey serves as a valuable resource for researchers seeking to innovate within the domain of chain-of-thought reasoning.

The recent advances in neural language models have also been successfully applied to the field of chemistry, offering generative solutions for classical problems in molecular design and synthesis planning. These new methods have the potential to optimize laboratory operations and fuel a new era of data-driven automation in scientific discovery. However, specialized models are still typically required for each task, leading to the need for problem-specific fine-tuning and neglecting task interrelations. The main obstacle in this field is the lack of a unified representation between natural language and chemical representations, complicating and limiting human-machine interaction. Here, we propose a multi-domain, multi-task language model to solve a wide range of tasks in both the chemical and natural language domains. By leveraging multi-task learning, our model can handle chemical and natural language concurrently, without requiring expensive pre-training on single domains or task-specific models. Interestingly, sharing weights across domains remarkably improves our model when benchmarked against state-of-the-art baselines on single-domain and cross-domain tasks. In particular, sharing information across domains and tasks gives rise to large improvements in cross-domain tasks, the magnitude of which increase with scale, as measured by more than a dozen of relevant metrics. Our work suggests that such models can robustly and efficiently accelerate discovery in physical sciences by superseding problem-specific fine-tuning and enhancing human-model interactions.

Chain-of-thought (CoT) reasoning has emerged as an effective approach for activating latent capabilities in large language models (LLMs). We observe that CoT shares significant similarities with self-training in terms of their learning processes. Motivated by these parallels, this paper explores the underlying relationship between CoT and self-training, demonstrating how insights from self-training can enhance CoT performance. Specifically, our study first reveals that CoT, like self-training, follows the principle of semantic entropy minimization. Leveraging this insight, we propose a novel CoT framework that incorporates two key components: (i) a task-specific prompt module designed to guide LLMs in generating high-quality initial reasoning processes, and (ii) an adaptive reasoning iteration module for progressively refining the reasoning process.

Recent studies have identified one aggravating factor of LLM hallucinations as the knowledge inconsistency between pre-training and fine-tuning, where unfamiliar fine-tuning data mislead the LLM to fabricate plausible but wrong outputs. In this paper, we propose a novel fine-tuning strategy called Prereq-Tune to address this knowledge inconsistency and reduce hallucinations. Fundamentally, Prereq-Tune disentangles the learning of skills and knowledge, so the model learns only the task skills without being impacted by the knowledge inconsistency. To achieve this, Prereq-Tune introduces an additional prerequisite learning stage to learn the necessary knowledge for SFT, allowing subsequent SFT to focus only on task skills. Prereq-Tune can also be combined with fictitious synthetic data to enhance the grounding of LLM outputs to their internal knowledge. Experiments show that Prereq-Tune outperforms existing baselines in improving LLM's factuality across short QA and long-form generation tasks. It also opens new possibilities for knowledge-controlled generation in LLMs. Our code is available at https://github.com/UCSB-NLP-Chang/Prereq_tune.git.

Research on LLM technologies is rapidly emerging, with most of them employing a 'fast thinking' approach to inference. Most LLMs generate the final result based solely on a single query and LLM's reasoning capabilities. However, with the advent of OpenAI-o1, 'slow thinking' techniques have garnered increasing attention because its process is closer to the human thought process. Inspired by the human ability to constantly associate and replenish knowledge during thinking, we developed the novel Chain-of-Associated-Thoughts (CoAT) framework, which introduces an innovative synergy between the Monte Carlo Tree Search (MCTS) algorithm and a dynamic mechanism for integrating new key information, termed 'associative memory'. By combining the structured exploration capabilities of MCTS with the adaptive learning capacity of associative memory, CoAT significantly expands the LLM search space, enabling our framework to explore diverse reasoning pathways and dynamically update its knowledge base in real-time. This allows the framework to not only revisit and refine earlier inferences but also adaptively incorporate evolving information, ensuring that the final output is both accurate and comprehensive. To validate the effectiveness of our framework, we conducted extensive experiments across a range of generative and reasoning tasks. These experiments demonstrated that our framework outperforms conventional inference processes on accuracy, coherence, and diversity. The framework's ability to iteratively expand its search space while retaining contextually relevant information results.

Modern systems for multi-hop question answering (QA) typically break questions into a sequence of reasoning steps, termed chain-of-thought (CoT), before arriving at a final answer. Often, multiple chains are sampled and aggregated through a voting mechanism over the final answers, but the intermediate steps themselves are discarded. While such approaches improve performance, they do not consider the relations between intermediate steps across chains and do not provide a unified explanation for the predicted answer. We introduce Multi-Chain Reasoning (MCR), an approach which prompts large language models to meta-reason over multiple chains of thought, rather than aggregating their answers. MCR examines different reasoning chains, mixes information between them and selects the most relevant facts in generating an explanation and predicting the answer. MCR outperforms strong baselines on 7 multi-hop QA datasets. Moreover, our analysis reveals that MCR explanations exhibit high quality, enabling humans to verify its answers.

Recent years have seen the advent of molecular simulation datasets that are orders of magnitude larger and more diverse. These new datasets differ substantially in four aspects of complexity: 1. Chemical diversity (number of different elements), 2. system size (number of atoms per sample), 3. dataset size (number of data samples), and 4. domain shift (similarity of the training and test set). Despite these large differences, benchmarks on small and narrow datasets remain the predominant method of demonstrating progress in graph neural networks (GNNs) for molecular simulation, likely due to cheaper training compute requirements. This raises the question -- does GNN progress on small and narrow datasets translate to these more complex datasets? This work investigates this question by first developing the GemNet-OC model based on the large Open Catalyst 2020 (OC20) dataset. GemNet-OC outperforms the previous state-of-the-art on OC20 by 16% while reducing training time by a factor of 10. We then compare the impact of 18 model components and hyperparameter choices on performance in multiple datasets. We find that the resulting model would be drastically different depending on the dataset used for making model choices. To isolate the source of this discrepancy we study six subsets of the OC20 dataset that individually test each of the above-mentioned four dataset aspects. We find that results on the OC-2M subset correlate well with the full OC20 dataset while being substantially cheaper to train on. Our findings challenge the common practice of developing GNNs solely on small datasets, but highlight ways of achieving fast development cycles and generalizable results via moderately-sized, representative datasets such as OC-2M and efficient models such as GemNet-OC. Our code and pretrained model weights are open-sourced.

The integration of biomolecular modeling with natural language (BL) has emerged as a promising interdisciplinary area at the intersection of artificial intelligence, chemistry and biology. This approach leverages the rich, multifaceted descriptions of biomolecules contained within textual data sources to enhance our fundamental understanding and enable downstream computational tasks such as biomolecule property prediction. The fusion of the nuanced narratives expressed through natural language with the structural and functional specifics of biomolecules described via various molecular modeling techniques opens new avenues for comprehensively representing and analyzing biomolecules. By incorporating the contextual language data that surrounds biomolecules into their modeling, BL aims to capture a holistic view encompassing both the symbolic qualities conveyed through language as well as quantitative structural characteristics. In this review, we provide an extensive analysis of recent advancements achieved through cross modeling of biomolecules and natural language. (1) We begin by outlining the technical representations of biomolecules employed, including sequences, 2D graphs, and 3D structures. (2) We then examine in depth the rationale and key objectives underlying effective multi-modal integration of language and molecular data sources. (3) We subsequently survey the practical applications enabled to date in this developing research area. (4) We also compile and summarize the available resources and datasets to facilitate future work. (5) Looking ahead, we identify several promising research directions worthy of further exploration and investment to continue advancing the field. The related resources and contents are updating in https://github.com/QizhiPei/Awesome-Biomolecule-Language-Cross-Modeling.

Machine Learning Force Fields (MLFFs) are a promising alternative to expensive ab initio quantum mechanical molecular simulations. Given the diversity of chemical spaces that are of interest and the cost of generating new data, it is important to understand how MLFFs generalize beyond their training distributions. In order to characterize and better understand distribution shifts in MLFFs, we conduct diagnostic experiments on chemical datasets, revealing common shifts that pose significant challenges, even for large foundation models trained on extensive data. Based on these observations, we hypothesize that current supervised training methods inadequately regularize MLFFs, resulting in overfitting and learning poor representations of out-of-distribution systems. We then propose two new methods as initial steps for mitigating distribution shifts for MLFFs. Our methods focus on test-time refinement strategies that incur minimal computational cost and do not use expensive ab initio reference labels. The first strategy, based on spectral graph theory, modifies the edges of test graphs to align with graph structures seen during training. Our second strategy improves representations for out-of-distribution systems at test-time by taking gradient steps using an auxiliary objective, such as a cheap physical prior. Our test-time refinement strategies significantly reduce errors on out-of-distribution systems, suggesting that MLFFs are capable of and can move towards modeling diverse chemical spaces, but are not being effectively trained to do so. Our experiments establish clear benchmarks for evaluating the generalization capabilities of the next generation of MLFFs. Our code is available at https://tkreiman.github.io/projects/mlff_distribution_shifts/.

The field of bioinformatics has seen significant progress, making the cross-modal text-molecule retrieval task increasingly vital. This task focuses on accurately retrieving molecule structures based on textual descriptions, by effectively aligning textual descriptions and molecules to assist researchers in identifying suitable molecular candidates. However, many existing approaches overlook the details inherent in molecule sub-structures. In this work, we introduce the Optimal TRansport-based Multi-grained Alignments model (ORMA), a novel approach that facilitates multi-grained alignments between textual descriptions and molecules. Our model features a text encoder and a molecule encoder. The text encoder processes textual descriptions to generate both token-level and sentence-level representations, while molecules are modeled as hierarchical heterogeneous graphs, encompassing atom, motif, and molecule nodes to extract representations at these three levels. A key innovation in ORMA is the application of Optimal Transport (OT) to align tokens with motifs, creating multi-token representations that integrate multiple token alignments with their corresponding motifs. Additionally, we employ contrastive learning to refine cross-modal alignments at three distinct scales: token-atom, multitoken-motif, and sentence-molecule, ensuring that the similarities between correctly matched text-molecule pairs are maximized while those of unmatched pairs are minimized. To our knowledge, this is the first attempt to explore alignments at both the motif and multi-token levels. Experimental results on the ChEBI-20 and PCdes datasets demonstrate that ORMA significantly outperforms existing state-of-the-art (SOTA) models.

Fine-tuning large language models (LLMs) with a collection of large and diverse instructions has improved the model's generalization to different tasks, even for unseen tasks. However, most existing instruction datasets include only single instructions, and they struggle to follow complex instructions composed of multiple subtasks (Wang et al., 2023a). In this work, we propose a novel concept of compositional instructions called chain-of-instructions (CoI), where the output of one instruction becomes an input for the next like a chain. Unlike the conventional practice of solving single instruction tasks, our proposed method encourages a model to solve each subtask step by step until the final answer is reached. CoI-tuning (i.e., fine-tuning with CoI instructions) improves the model's ability to handle instructions composed of multiple subtasks. CoI-tuned models also outperformed baseline models on multilingual summarization, demonstrating the generalizability of CoI models on unseen composite downstream tasks.

Designing a single model to address multiple tasks has been a long-standing objective in artificial intelligence. Recently, large language models have demonstrated exceptional capability in solving different tasks within the language domain. However, a unified model for various graph tasks remains underexplored, primarily due to the challenges unique to the graph learning domain. First, graph data from different areas carry distinct attributes and follow different distributions. Such discrepancy makes it hard to represent graphs in a single representation space. Second, tasks on graphs diversify into node, link, and graph tasks, requiring distinct embedding strategies. Finally, an appropriate graph prompting paradigm for in-context learning is unclear. We propose One for All (OFA), the first general framework that can use a single graph model to address the above challenges. Specifically, OFA proposes text-attributed graphs to unify different graph data by describing nodes and edges with natural language and uses language models to encode the diverse and possibly cross-domain text attributes to feature vectors in the same embedding space. Furthermore, OFA introduces the concept of nodes-of-interest to standardize different tasks with a single task representation. For in-context learning on graphs, OFA introduces a novel graph prompting paradigm that appends prompting substructures to the input graph, which enables it to address varied tasks without fine-tuning. We train the OFA model using graph data from multiple domains (including citation networks, molecular graphs, knowledge graphs, etc.) simultaneously and evaluate its ability in supervised, few-shot, and zero-shot learning scenarios. OFA performs well across different tasks, making it the first general-purpose across-domains classification model on graphs.

Multimodal reasoning stands as a pivotal capability for large vision-language models (LVLMs). The integration with Domain-Specific Languages (DSL), offering precise visual representations, equips these models with the opportunity to execute more accurate reasoning in complex and professional domains. However, the vanilla Chain-of-Thought (CoT) prompting method faces challenges in effectively leveraging the unique strengths of visual and DSL representations, primarily due to their differing reasoning mechanisms. Additionally, it often falls short in addressing critical steps in multi-step reasoning tasks. To mitigate these challenges, we introduce the Bi-Modal Behavioral Alignment (BBA) prompting method, designed to maximize the potential of DSL in augmenting complex multi-modal reasoning tasks. This method initiates by guiding LVLMs to create separate reasoning chains for visual and DSL representations. Subsequently, it aligns these chains by addressing any inconsistencies, thus achieving a cohesive integration of behaviors from different modalities. Our experiments demonstrate that BBA substantially improves the performance of GPT-4V(ision) on geometry problem solving (28.34% to 34.22%), chess positional advantage prediction (42.08% to 46.99%) and molecular property prediction (77.47% to 83.52%).

Deep learning in computational biochemistry has traditionally focused on molecular graphs neural representations; however, recent advances in language models highlight how much scientific knowledge is encoded in text. To bridge these two modalities, we investigate how molecular property information can be transferred from natural language to graph representations. We study property prediction performance gains after using contrastive learning to align neural graph representations with representations of textual descriptions of their characteristics. We implement neural relevance scoring strategies to improve text retrieval, introduce a novel chemically-valid molecular graph augmentation strategy inspired by organic reactions, and demonstrate improved performance on downstream MoleculeNet property classification tasks. We achieve a +4.26% AUROC gain versus models pre-trained on the graph modality alone, and a +1.54% gain compared to recently proposed molecular graph/text contrastively trained MoMu model (Su et al. 2022).

Large Language Models (LLMs) have shown remarkable abilities across various language tasks, but solving complex reasoning problems remains a challenge. While existing methods like Chain-of-Thought (CoT) and Tree-of-Thought (ToT) enhance reasoning by decomposing problems or structuring prompts, they typically perform a single pass of reasoning and may fail to revisit flawed paths, compromising accuracy. To address this, we propose a novel reasoning framework called Forest-of-Thought (FoT), which integrates multiple reasoning trees to leverage collective decision-making for solving complex logical problems. FoT utilizes sparse activation strategies to select the most relevant reasoning paths, improving both efficiency and accuracy. Additionally, we introduce a dynamic self-correction strategy that enables real-time error correction and learning from past mistakes, as well as consensus-guided decision making strategies to optimize correctness and computational resources. Experimental results demonstrate that the FoT framework, combined with these strategies, significantly enhances the reasoning capabilities of LLMs, enabling them to solve complex tasks with greater precision and efficiency.

The Chain-of-Thought (CoT) paradigm has emerged as a critical approach for enhancing the reasoning capabilities of large language models (LLMs). However, despite their widespread adoption and success, CoT methods often exhibit instability due to their inability to consistently ensure the quality of generated reasoning paths, leading to sub-optimal reasoning performance. To address this challenge, we propose the Strategic Chain-of-Thought (SCoT), a novel methodology designed to refine LLM performance by integrating strategic knowledge prior to generating intermediate reasoning steps. SCoT employs a two-stage approach within a single prompt: first eliciting an effective problem-solving strategy, which is then used to guide the generation of high-quality CoT paths and final answers. Our experiments across eight challenging reasoning datasets demonstrate significant improvements, including a 21.05\% increase on the GSM8K dataset and 24.13\% on the Tracking\_Objects dataset, respectively, using the Llama3-8b model. Additionally, we extend the SCoT framework to develop a few-shot method with automatically matched demonstrations, yielding even stronger results. These findings underscore the efficacy of SCoT, highlighting its potential to substantially enhance LLM performance in complex reasoning tasks.

Large Language Models (LLMs) stand at the forefront of a number of Natural Language Processing (NLP) tasks. Despite the widespread adoption of LLMs in NLP, much of their potential in broader fields remains largely unexplored, and significant limitations persist in their design and implementation. Notably, LLMs struggle with structured data, such as graphs, and often falter when tasked with answering domain-specific questions requiring deep expertise, such as those in biology and chemistry. In this paper, we explore a fundamental question: Can LLMs effectively handle molecule prediction tasks? Rather than pursuing top-tier performance, our goal is to assess how LLMs can contribute to diverse molecule tasks. We identify several classification and regression prediction tasks across six standard molecule datasets. Subsequently, we carefully design a set of prompts to query LLMs on these tasks and compare their performance with existing Machine Learning (ML) models, which include text-based models and those specifically designed for analysing the geometric structure of molecules. Our investigation reveals several key insights: Firstly, LLMs generally lag behind ML models in achieving competitive performance on molecule tasks, particularly when compared to models adept at capturing the geometric structure of molecules, highlighting the constrained ability of LLMs to comprehend graph data. Secondly, LLMs show promise in enhancing the performance of ML models when used collaboratively. Lastly, we engage in a discourse regarding the challenges and promising avenues to harness LLMs for molecule prediction tasks. The code and models are available at https://github.com/zhiqiangzhongddu/LLMaMol.

Large language models (LLMs) have attracted considerable attention in various fields for their cost-effective solutions to diverse challenges, especially with advancements in instruction tuning and quantization. E-commerce, with its complex tasks and extensive product-user interactions, presents a promising application area for LLMs. However, the domain-specific concepts and knowledge inherent in e-commerce pose significant challenges for adapting general LLMs. To address this issue, we developed EC-Guide https://github.com/fzp0424/EC-Guide-KDDUP-2024, a comprehensive e-commerce guide for instruction tuning and quantization of LLMs. We also heuristically integrated Chain-of-Thought (CoT) during inference to enhance arithmetic performance. Our approach achieved the 2nd place in Track 2 and 5th place in Track 5 at the Amazon KDD Cup'24 https://www.aicrowd.com/challenges/amazon-kdd-cup-2024-multi-task-online-shopping-challenge-for-llms. Additionally, our solution is model-agnostic, enabling effective scalability across larger systems.

We present symbol tuning - finetuning language models on in-context input-label pairs where natural language labels (e.g., "positive/negative sentiment") are replaced with arbitrary symbols (e.g., "foo/bar"). Symbol tuning leverages the intuition that when a model cannot use instructions or natural language labels to figure out a task, it must instead do so by learning the input-label mappings. We experiment with symbol tuning across Flan-PaLM models up to 540B parameters and observe benefits across various settings. First, symbol tuning boosts performance on unseen in-context learning tasks and is much more robust to underspecified prompts, such as those without instructions or without natural language labels. Second, symbol-tuned models are much stronger at algorithmic reasoning tasks, with up to 18.2% better performance on the List Functions benchmark and up to 15.3% better performance on the Simple Turing Concepts benchmark. Finally, symbol-tuned models show large improvements in following flipped-labels presented in-context, meaning that they are more capable of using in-context information to override prior semantic knowledge.

Generating a Chain of Thought (CoT) has been shown to consistently improve large language model (LLM) performance on a wide range of NLP tasks. However, prior work has mainly focused on logical reasoning tasks (e.g. arithmetic, commonsense QA); it remains unclear whether improvements hold for more diverse types of reasoning, especially in socially situated contexts. Concretely, we perform a controlled evaluation of zero-shot CoT across two socially sensitive domains: harmful questions and stereotype benchmarks. We find that zero-shot CoT reasoning in sensitive domains significantly increases a model's likelihood to produce harmful or undesirable output, with trends holding across different prompt formats and model variants. Furthermore, we show that harmful CoTs increase with model size, but decrease with improved instruction following. Our work suggests that zero-shot CoT should be used with caution on socially important tasks, especially when marginalized groups or sensitive topics are involved.

Reasoning is a cognitive process of using evidence to reach a sound conclusion. The reasoning capability is essential for large language models (LLMs) to serve as the brain of the artificial general intelligence agent. Recent studies reveal that fine-tuning LLMs on data with the chain of thought (COT) reasoning process can significantly enhance their reasoning capabilities. However, we find that the fine-tuned LLMs suffer from an Assessment Misalignment problem, i.e., they frequently assign higher scores to subpar COTs, leading to potential limitations in their reasoning abilities. To address this problem, we introduce an Alignment Fine-Tuning (AFT) paradigm, which involves three steps: 1) fine-tuning LLMs with COT training data; 2) generating multiple COT responses for each question, and categorizing them into positive and negative ones based on whether they achieve the correct answer; 3) calibrating the scores of positive and negative responses given by LLMs with a novel constraint alignment loss. Specifically, the constraint alignment loss has two objectives: a) Alignment, which guarantees that positive scores surpass negative scores to encourage answers with high-quality COTs; b) Constraint, which keeps the negative scores confined to a reasonable range to prevent the model degradation. Beyond just the binary positive and negative feedback, the constraint alignment loss can be seamlessly adapted to the ranking situations when ranking feedback is accessible. Furthermore, we also delve deeply into recent ranking-based alignment methods, such as DPO, RRHF, and PRO, and discover that the constraint, which has been overlooked by these approaches, is also crucial for their performance. Extensive experiments on four reasoning benchmarks with both binary and ranking feedback demonstrate the effectiveness of AFT.

In this paper, we propose Text-based Open Molecule Generation Benchmark (TOMG-Bench), the first benchmark to evaluate the open-domain molecule generation capability of LLMs. TOMG-Bench encompasses a dataset of three major tasks: molecule editing (MolEdit), molecule optimization (MolOpt), and customized molecule generation (MolCustom). Each task further contains three subtasks, with each subtask comprising 5,000 test samples. Given the inherent complexity of open molecule generation, we have also developed an automated evaluation system that helps measure both the quality and the accuracy of the generated molecules. Our comprehensive benchmarking of 25 LLMs reveals the current limitations and potential areas for improvement in text-guided molecule discovery. Furthermore, with the assistance of OpenMolIns, a specialized instruction tuning dataset proposed for solving challenges raised by TOMG-Bench, Llama3.1-8B could outperform all the open-source general LLMs, even surpassing GPT-3.5-turbo by 46.5\% on TOMG-Bench. Our codes and datasets are available through https://github.com/phenixace/TOMG-Bench.

Chain of Thought (CoT) was introduced in recent research as a method for improving step-by-step reasoning in Large Language Models. However, CoT has limited applications such as its need for hand-crafted few-shot exemplar prompts and no capability to adjust itself to different queries. In this work, we propose a system to automatically generate rationales using CoT. Our method improves multi-step implicit reasoning capabilities by decomposing the implicit query into several explicit questions. This provides interpretability for the model, improving reasoning in weaker LLMs. We test our approach with two Q\&A datasets: StrategyQA and HotpotQA. We show an increase in accuracy with both, especially on StrategyQA. To facilitate further research in this field, the complete source code for this study has been made publicly available on GitHub: https://github.com/miralab-ai/autoreason.

Recently, Chain-of-Thought (CoT) prompting has delivered success on complex reasoning tasks, which aims at designing a simple prompt like ``Let's think step by step'' or multiple in-context exemplars with well-designed rationales to elicit Large Language Models (LLMs) to generate intermediate reasoning steps. However, the generated rationales often come with mistakes, making unfactual and unfaithful reasoning chains. To mitigate this brittleness, we propose a novel Chain-of-Knowledge (CoK) prompting, where we aim at eliciting LLMs to generate explicit pieces of knowledge evidence in the form of structure triple. This is inspired by our human behaviors, i.e., we can draw a mind map or knowledge map as the reasoning evidence in the brain before answering a complex question. Benefiting from CoK, we additionally introduce a F^2-Verification method to estimate the reliability of the reasoning chains in terms of factuality and faithfulness. For the unreliable response, the wrong evidence can be indicated to prompt the LLM to rethink. Extensive experiments demonstrate that our method can further improve the performance of commonsense, factual, symbolic, and arithmetic reasoning tasks.

Identifying the chemical structure from a graphical representation, or image, of a molecule is a challenging pattern recognition task that would greatly benefit drug development. Yet, existing methods for chemical structure recognition do not typically generalize well, and show diminished effectiveness when confronted with domains where data is sparse, or costly to generate, such as hand-drawn molecule images. To address this limitation, we propose a new chemical structure recognition tool that delivers state-of-the-art performance and can adapt to new domains with a limited number of data samples and supervision. Unlike previous approaches, our method provides atom-level localization, and can therefore segment the image into the different atoms and bonds. Our model is the first model to perform OCSR with atom-level entity detection with only SMILES supervision. Through rigorous and extensive benchmarking, we demonstrate the preeminence of our chemical structure recognition approach in terms of data efficiency, accuracy, and atom-level entity prediction.

Chemical reasoning usually involves complex, multi-step processes that demand precise calculations, where even minor errors can lead to cascading failures. Furthermore, large language models (LLMs) encounter difficulties handling domain-specific formulas, executing reasoning steps accurately, and integrating code effectively when tackling chemical reasoning tasks. To address these challenges, we present ChemAgent, a novel framework designed to improve the performance of LLMs through a dynamic, self-updating library. This library is developed by decomposing chemical tasks into sub-tasks and compiling these sub-tasks into a structured collection that can be referenced for future queries. Then, when presented with a new problem, ChemAgent retrieves and refines pertinent information from the library, which we call memory, facilitating effective task decomposition and the generation of solutions. Our method designs three types of memory and a library-enhanced reasoning component, enabling LLMs to improve over time through experience. Experimental results on four chemical reasoning datasets from SciBench demonstrate that ChemAgent achieves performance gains of up to 46% (GPT-4), significantly outperforming existing methods. Our findings suggest substantial potential for future applications, including tasks such as drug discovery and materials science. Our code can be found at https://github.com/gersteinlab/chemagent

Chain of thought prompting successfully improves the reasoning capabilities of large language models, achieving state of the art results on a range of datasets. However, these reasoning capabilities only appear to emerge in models with a size of over 100 billion parameters. In this paper, we explore the transfer of such reasoning capabilities to models with less than 100 billion parameters via knowledge distillation. Specifically, we finetune a student model on the chain of thought outputs generated by a larger teacher model. Our experiments show that the proposed method improves task performance across arithmetic, commonsense and symbolic reasoning datasets. For example, the accuracy of T5 XXL on GSM8K improves from 8.11% to 21.99% when finetuned on PaLM-540B generated chains of thought.

The evolution from Large Language Models (LLMs) to Multimodal Large Language Models (MLLMs) has spurred research into extending In-Context Learning (ICL) to its multimodal counterpart. Existing such studies have primarily concentrated on image-to-text ICL. However, the Text-to-Image ICL (T2I-ICL), with its unique characteristics and potential applications, remains underexplored. To address this gap, we formally define the task of T2I-ICL and present CoBSAT, the first T2I-ICL benchmark dataset, encompassing ten tasks. Utilizing our dataset to benchmark six state-of-the-art MLLMs, we uncover considerable difficulties MLLMs encounter in solving T2I-ICL. We identify the primary challenges as the inherent complexity of multimodality and image generation. To overcome these challenges, we explore strategies like fine-tuning and Chain-of-Thought prompting, demonstrating notable improvements. Our code and dataset are available at https://github.com/UW-Madison-Lee-Lab/CoBSAT.

A well-known limitation of existing molecular generative models is that the generated molecules highly resemble those in the training set. To generate truly novel molecules that may have even better properties for de novo drug discovery, more powerful exploration in the chemical space is necessary. To this end, we propose Molecular Out-Of-distribution Diffusion(MOOD), a score-based diffusion scheme that incorporates out-of-distribution (OOD) control in the generative stochastic differential equation (SDE) with simple control of a hyperparameter, thus requires no additional costs. Since some novel molecules may not meet the basic requirements of real-world drugs, MOOD performs conditional generation by utilizing the gradients from a property predictor that guides the reverse-time diffusion process to high-scoring regions according to target properties such as protein-ligand interactions, drug-likeness, and synthesizability. This allows MOOD to search for novel and meaningful molecules rather than generating unseen yet trivial ones. We experimentally validate that MOOD is able to explore the chemical space beyond the training distribution, generating molecules that outscore ones found with existing methods, and even the top 0.01% of the original training pool. Our code is available at https://github.com/SeulLee05/MOOD.

Equipped with Chain-of-Thought (CoT), Large language models (LLMs) have shown impressive reasoning ability in various downstream tasks. Even so, suffering from hallucinations and the inability to access external knowledge, LLMs often come with incorrect or unfaithful intermediate reasoning steps, especially in the context of answering knowledge-intensive tasks such as KBQA. To alleviate this issue, we propose a framework called Knowledge-Driven Chain-of-Thought (KD-CoT) to verify and modify reasoning traces in CoT via interaction with external knowledge, and thus overcome the hallucinations and error propagation. Concretely, we formulate the CoT rationale process of LLMs into a structured multi-round QA format. In each round, LLMs interact with a QA system that retrieves external knowledge and produce faithful reasoning traces based on retrieved precise answers. The structured CoT reasoning of LLMs is facilitated by our developed KBQA CoT collection, which serves as in-context learning demonstrations and can also be utilized as feedback augmentation to train a robust retriever. Extensive experiments on WebQSP and ComplexWebQuestion datasets demonstrate the effectiveness of proposed KD-CoT in task-solving reasoning generation, which outperforms the vanilla CoT ICL with an absolute success rate of 8.0% and 5.1%. Furthermore, our proposed feedback-augmented retriever outperforms the state-of-the-art baselines for retrieving knowledge, achieving significant improvement in Hit performance.

In recent years, groundbreaking advancements in natural language processing have culminated in the emergence of powerful large language models (LLMs), which have showcased remarkable capabilities across a vast array of domains, including the understanding, generation, and translation of natural language, and even tasks that extend beyond language processing. In this report, we delve into the performance of LLMs within the context of scientific discovery, focusing on GPT-4, the state-of-the-art language model. Our investigation spans a diverse range of scientific areas encompassing drug discovery, biology, computational chemistry (density functional theory (DFT) and molecular dynamics (MD)), materials design, and partial differential equations (PDE). Evaluating GPT-4 on scientific tasks is crucial for uncovering its potential across various research domains, validating its domain-specific expertise, accelerating scientific progress, optimizing resource allocation, guiding future model development, and fostering interdisciplinary research. Our exploration methodology primarily consists of expert-driven case assessments, which offer qualitative insights into the model's comprehension of intricate scientific concepts and relationships, and occasionally benchmark testing, which quantitatively evaluates the model's capacity to solve well-defined domain-specific problems. Our preliminary exploration indicates that GPT-4 exhibits promising potential for a variety of scientific applications, demonstrating its aptitude for handling complex problem-solving and knowledge integration tasks. Broadly speaking, we evaluate GPT-4's knowledge base, scientific understanding, scientific numerical calculation abilities, and various scientific prediction capabilities.

Multi-modality promises to unlock further uses for large language models. Recently, the state-of-the-art language model GPT-4 was enhanced with vision capabilities. We carry out a prompting evaluation of GPT-4V and five other baselines on structured reasoning tasks, such as mathematical reasoning, visual data analysis, and code generation. We show that visual Chain-of-Thought, an extension of Chain-of-Thought to multi-modal LLMs, yields significant improvements over the vanilla model. We also present a categorized analysis of scenarios where these models perform well and where they struggle, highlighting challenges associated with coherent multimodal reasoning.

Chain-of-Thought (CoT) reasoning has emerged as a promising approach for enhancing the performance of large language models (LLMs) on complex reasoning tasks. Recently, a series of studies attempt to explain the mechanisms underlying CoT, aiming to deepen the understanding of its efficacy. Nevertheless, the existing research faces two major challenges: (1) a lack of quantitative metrics to assess CoT capabilities and (2) a dearth of guidance on optimizing CoT performance. Motivated by this, in this work, we introduce a novel reasoning boundary framework (RBF) to address these challenges. To solve the lack of quantification, we first define a reasoning boundary (RB) to quantify the upper-bound of CoT and establish a combination law for RB, enabling a practical quantitative approach applicable to various real-world CoT tasks. To address the lack of optimization, we propose three categories of RBs. We further optimize these categories with combination laws focused on RB promotion and reasoning path optimization for CoT improvement. Through extensive experiments on 27 models and 5 tasks, the study validates the existence and rationality of the proposed framework. Furthermore, it explains the effectiveness of 10 CoT strategies and guides optimization from two perspectives. We hope this work can provide a comprehensive understanding of the boundaries and optimization strategies for reasoning in LLMs. Our code and data are available at https://github.com/LightChen233/reasoning-boundary.

The discovery of novel materials and functional molecules can help to solve some of society's most urgent challenges, ranging from efficient energy harvesting and storage to uncovering novel pharmaceutical drug candidates. Traditionally matter engineering -- generally denoted as inverse design -- was based massively on human intuition and high-throughput virtual screening. The last few years have seen the emergence of significant interest in computer-inspired designs based on evolutionary or deep learning methods. The major challenge here is that the standard strings molecular representation SMILES shows substantial weaknesses in that task because large fractions of strings do not correspond to valid molecules. Here, we solve this problem at a fundamental level and introduce SELFIES (SELF-referencIng Embedded Strings), a string-based representation of molecules which is 100\% robust. Every SELFIES string corresponds to a valid molecule, and SELFIES can represent every molecule. SELFIES can be directly applied in arbitrary machine learning models without the adaptation of the models; each of the generated molecule candidates is valid. In our experiments, the model's internal memory stores two orders of magnitude more diverse molecules than a similar test with SMILES. Furthermore, as all molecules are valid, it allows for explanation and interpretation of the internal working of the generative models.

Large Language Models (LLMs) have demonstrated remarkable generalization and instruction-following capabilities with instruction tuning. The advancements in LLMs and instruction tuning have led to the development of Large Vision-Language Models (LVLMs). However, the competency of the LLMs and instruction tuning have been less explored in the molecular domain. Thus, we propose LLaMo: Large Language Model-based Molecular graph assistant, which is an end-to-end trained large molecular graph-language model. To bridge the discrepancy between the language and graph modalities, we present the multi-level graph projector that transforms graph representations into graph tokens by abstracting the output representations of each GNN layer and motif representations with the cross-attention mechanism. We also introduce machine-generated molecular graph instruction data to instruction-tune the large molecular graph-language model for general-purpose molecule and language understanding. Our extensive experiments demonstrate that LLaMo shows the best performance on diverse tasks, such as molecular description generation, property prediction, and IUPAC name prediction. The code of LLaMo is available at https://github.com/mlvlab/LLaMo.

While machine learning on graphs has demonstrated promise in drug design and molecular property prediction, significant benchmarking challenges hinder its further progress and relevance. Current benchmarking practices often lack focus on transformative, real-world applications, favoring narrow domains like two-dimensional molecular graphs over broader, impactful areas such as combinatorial optimization, relational databases, or chip design. Additionally, many benchmark datasets poorly represent the underlying data, leading to inadequate abstractions and misaligned use cases. Fragmented evaluations and an excessive focus on accuracy further exacerbate these issues, incentivizing overfitting rather than fostering generalizable insights. These limitations have prevented the development of truly useful graph foundation models. This position paper calls for a paradigm shift toward more meaningful benchmarks, rigorous evaluation protocols, and stronger collaboration with domain experts to drive impactful and reliable advances in graph learning research, unlocking the potential of graph learning.

Following the standard supervised fine-tuning (SFT) paradigm, in-context learning (ICL) has become an efficient approach propelled by the recent advancements in large language models (LLMs), yielding promising performance across various tasks in few-shot data setups. However, both paradigms are prone to suffer from the critical problem of overconfidence (i.e., miscalibration), especially in such limited data setups. In this work, we deliver an in-depth analysis of the behavior across different choices of learning methods from the perspective of both performance and calibration, as well as their interplay. Through extensive controlled experiments, we find that simultaneous gains for both task performance and calibration are difficult to achieve, and the problem of miscalibration exists across all learning methods in low-resource scenarios. To address this challenging trade-off between performance and calibration, we then investigate the potential of self-ensembling techniques applied at different modeling stages (e.g., variations of in-context examples or variations in prompts or different ensembling strategies). We justify the feasibility of self-ensembling on SFT in addition to ICL, to make the predictions more calibrated and have comparable or even better performance. Our work sheds light on which learning paradigm to choose and how to enhance both task performance and calibration of LLMs.

De novo design seeks to generate molecules with required property profiles by virtual design-make-test cycles. With the emergence of deep learning and neural generative models in many application areas, models for molecular design based on neural networks appeared recently and show promising results. However, the new models have not been profiled on consistent tasks, and comparative studies to well-established algorithms have only seldom been performed. To standardize the assessment of both classical and neural models for de novo molecular design, we propose an evaluation framework, GuacaMol, based on a suite of standardized benchmarks. The benchmark tasks encompass measuring the fidelity of the models to reproduce the property distribution of the training sets, the ability to generate novel molecules, the exploration and exploitation of chemical space, and a variety of single and multi-objective optimization tasks. The benchmarking open-source Python code, and a leaderboard can be found on https://benevolent.ai/guacamol

Generative tasks about molecules, including but not limited to molecule generation, are crucial for drug discovery and material design, and have consistently attracted significant attention. In recent years, diffusion models have emerged as an impressive class of deep generative models, sparking extensive research and leading to numerous studies on their application to molecular generative tasks. Despite the proliferation of related work, there remains a notable lack of up-to-date and systematic surveys in this area. Particularly, due to the diversity of diffusion model formulations, molecular data modalities, and generative task types, the research landscape is challenging to navigate, hindering understanding and limiting the area's growth. To address this, this paper conducts a comprehensive survey of diffusion model-based molecular generative methods. We systematically review the research from the perspectives of methodological formulations, data modalities, and task types, offering a novel taxonomy. This survey aims to facilitate understanding and further flourishing development in this area. The relevant papers are summarized at: https://github.com/AzureLeon1/awesome-molecular-diffusion-models.

Chain-of-Thought (CoT) reasoning has been extensively explored in large models to tackle complex understanding tasks. However, it still remains an open question whether such strategies can be applied to verifying and reinforcing image generation scenarios. In this paper, we provide the first comprehensive investigation of the potential of CoT reasoning to enhance autoregressive image generation. We focus on three techniques: scaling test-time computation for verification, aligning model preferences with Direct Preference Optimization (DPO), and integrating these techniques for complementary effects. Our results demonstrate that these approaches can be effectively adapted and combined to significantly improve image generation performance. Furthermore, given the pivotal role of reward models in our findings, we propose the Potential Assessment Reward Model (PARM) and PARM++, specialized for autoregressive image generation. PARM adaptively assesses each generation step through a potential assessment approach, merging the strengths of existing reward models, and PARM++ further introduces a reflection mechanism to self-correct the generated unsatisfactory image. Using our investigated reasoning strategies, we enhance a baseline model, Show-o, to achieve superior results, with a significant +24% improvement on the GenEval benchmark, surpassing Stable Diffusion 3 by +15%. We hope our study provides unique insights and paves a new path for integrating CoT reasoning with autoregressive image generation. Code and models are released at https://github.com/ZiyuGuo99/Image-Generation-CoT

In this paper, we address the challenging task of multimodal mathematical reasoning by incorporating the ability of "slow thinking" into multimodal large language models (MLLMs). Our core idea is that different levels of reasoning abilities can be combined dynamically to tackle questions with different complexity. To this end, we propose a paradigm of Self-structured Chain of Thought (SCoT), which is composed of minimal semantic atomic steps. Different from existing methods that rely on structured templates or free-form paradigms, our method can not only generate cognitive CoT structures for various complex tasks but also mitigates the phenomenon of overthinking. To introduce structured reasoning capabilities into visual understanding models, we further design a novel AtomThink framework with four key modules, including (i) a data engine to generate high-quality multimodal reasoning paths; (ii) a supervised fine-tuning process with serialized inference data; (iii) a policy-guided multi-turn inference method; and (iv) an atomic capability metric to evaluate the single step utilization rate. We conduct extensive experiments to show that the proposed AtomThink significantly improves the performance of baseline MLLMs, achieving more than 10\% average accuracy gains on MathVista and MathVerse. Compared to state-of-the-art structured CoT approaches, our method not only achieves higher accuracy but also improves data utilization by 5 times and boosts inference efficiency by 85.3\%. Our code is now public available in https://github.com/Quinn777/AtomThink.

Large Language Models (LLMs) achieve superior performance through training-time scaling, and test-time scaling further enhances their capabilities by conducting effective reasoning during inference. However, as the scale of reasoning increases, existing test-time scaling methods suffer from accumulated historical information, which not only wastes computational resources but also interferes with effective reasoning. To address this issue, we observe that complex reasoning progress is often achieved by solving a sequence of independent subquestions, each being self-contained and verifiable. These subquestions are essentially atomic questions, relying primarily on their current state rather than accumulated history, similar to the memoryless transitions in a Markov process. Based on this observation, we propose Atom of Thoughts (AoT), where each state transition in the reasoning process consists of decomposing the current question into a dependency-based directed acyclic graph and contracting its subquestions, forming a new atomic question state. This iterative decomposition-contraction process continues until reaching directly solvable atomic questions, naturally realizing Markov transitions between question states. Furthermore, these atomic questions can be seamlessly integrated into existing test-time scaling methods, enabling AoT to serve as a plug-in enhancement for improving reasoning capabilities. Experiments across six benchmarks demonstrate the effectiveness of AoT both as a standalone framework and a plug-in enhancement. Notably, on HotpotQA, when applied to gpt-4o-mini, AoT achieves an 80.6% F1 score, surpassing o3-mini by 3.4% and DeepSeek-R1 by 10.6%. The code will be available at https://github.com/qixucen/atom.

Pre-trained language models (PLMs) have shown impressive performance in various language tasks. However, they are prone to spurious correlations, and often generate illusory information. In real-world applications, PLMs should justify decisions with formalized, coherent reasoning chains, but this challenge remains under-explored. Cognitive psychology theorizes that humans are capable of utilizing fast and intuitive heuristic thinking to make decisions based on past experience, then rationalizing the decisions through slower and deliberative analytic reasoning. We incorporate these interlinked dual processes in fine-tuning and in-context learning with PLMs, applying them to two language understanding tasks that require coherent physical commonsense reasoning. We show that our proposed Heuristic-Analytic Reasoning (HAR) strategies drastically improve the coherence of rationalizations for model decisions, yielding state-of-the-art results on Tiered Reasoning for Intuitive Physics (TRIP). We also find that this improved coherence is a direct result of more faithful attention to relevant language context in each step of reasoning. Our findings suggest that human-like reasoning strategies can effectively improve the coherence and reliability of PLM reasoning.

Large language models (LLMs) solve problems more accurately and interpretably when instructed to work out the answer step by step using a ``chain-of-thought'' (CoT) prompt. One can also improve LLMs' performance on a specific task by supervised fine-tuning, i.e., by using gradient ascent on some tunable parameters to maximize the average log-likelihood of correct answers from a labeled training set. Naively combining CoT with supervised tuning requires supervision not just of the correct answers, but also of detailed rationales that lead to those answers; these rationales are expensive to produce by hand. Instead, we propose a fine-tuning strategy that tries to maximize the marginal log-likelihood of generating a correct answer using CoT prompting, approximately averaging over all possible rationales. The core challenge is sampling from the posterior over rationales conditioned on the correct answer; we address it using a simple Markov-chain Monte Carlo (MCMC) expectation-maximization (EM) algorithm inspired by the self-taught reasoner (STaR), memoized wake-sleep, Markovian score climbing, and persistent contrastive divergence. This algorithm also admits a novel control-variate technique that drives the variance of our gradient estimates to zero as the model improves. Applying our technique to GSM8K and the tasks in BIG-Bench Hard, we find that this MCMC-EM fine-tuning technique typically improves the model's accuracy on held-out examples more than STaR or prompt-tuning with or without CoT.

In recent years, Large Language Models (LLMs) have achieved significant success in natural language processing (NLP) and various interdisciplinary areas. However, applying LLMs to chemistry is a complex task that requires specialized domain knowledge. This paper provides a thorough exploration of the nuanced methodologies employed in integrating LLMs into the field of chemistry, delving into the complexities and innovations at this interdisciplinary juncture. Specifically, our analysis begins with examining how molecular information is fed into LLMs through various representation and tokenization methods. We then categorize chemical LLMs into three distinct groups based on the domain and modality of their input data, and discuss approaches for integrating these inputs for LLMs. Furthermore, this paper delves into the pretraining objectives with adaptations to chemical LLMs. After that, we explore the diverse applications of LLMs in chemistry, including novel paradigms for their application in chemistry tasks. Finally, we identify promising research directions, including further integration with chemical knowledge, advancements in continual learning, and improvements in model interpretability, paving the way for groundbreaking developments in the field.

We report a mixture of expert strategy to create fine-tuned large language models using a deep layer-wise token-level approach based on low-rank adaptation (LoRA). Starting with a set of pre-trained LoRA adapters, we propose a gating strategy that uses the hidden states to dynamically mix adapted layers, allowing the resulting X-LoRA model to draw upon different capabilities and create never-before-used deep layer-wise combinations of adaptations are established to solve specific tasks. The design is inspired by the biological principles of universality and diversity, where neural network building blocks are reused in different hierarchical manifestations. Hence, the X-LoRA model can be easily implemented for any existing large language model (LLM) without a need for modifications of the underlying structure. We develop a tailored X-LoRA model that offers scientific capabilities including forward/inverse analysis tasks and enhanced reasoning capability, focused on biomaterial analysis, protein mechanics and design. The impact of this work include access to readily expandable, adaptable and changeable models with strong domain knowledge and the capability to integrate across areas of knowledge. With the X-LoRA model featuring experts in biology, mathematics, reasoning, bio-inspired materials, mechanics and materials, chemistry, and protein mechanics we conduct a series of physics-focused case studies. We examine knowledge recall, protein mechanics forward/inverse tasks, protein design, and adversarial agentic modeling including ontological knowledge graphs. The model is capable not only of making quantitative predictions of nanomechanical properties of proteins, but also reasons over the results and correctly predicts likely mechanisms that explain distinct molecular behaviors.

Concept Bottleneck Models (CBMs) map the inputs onto a set of interpretable concepts (``the bottleneck'') and use the concepts to make predictions. A concept bottleneck enhances interpretability since it can be investigated to understand what concepts the model "sees" in an input and which of these concepts are deemed important. However, CBMs are restrictive in practice as they require dense concept annotations in the training data to learn the bottleneck. Moreover, CBMs often do not match the accuracy of an unrestricted neural network, reducing the incentive to deploy them in practice. In this work, we address these limitations of CBMs by introducing Post-hoc Concept Bottleneck models (PCBMs). We show that we can turn any neural network into a PCBM without sacrificing model performance while still retaining the interpretability benefits. When concept annotations are not available on the training data, we show that PCBM can transfer concepts from other datasets or from natural language descriptions of concepts via multimodal models. A key benefit of PCBM is that it enables users to quickly debug and update the model to reduce spurious correlations and improve generalization to new distributions. PCBM allows for global model edits, which can be more efficient than previous works on local interventions that fix a specific prediction. Through a model-editing user study, we show that editing PCBMs via concept-level feedback can provide significant performance gains without using data from the target domain or model retraining.

Instruction-tuned Large Language Models (It-LLMs) have been exhibiting outstanding abilities to reason around cognitive states, intentions, and reactions of all people involved, letting humans guide and comprehend day-to-day social interactions effectively. In fact, several multiple-choice questions (MCQ) benchmarks have been proposed to construct solid assessments of the models' abilities. However, earlier works are demonstrating the presence of inherent "order bias" in It-LLMs, posing challenges to the appropriate evaluation. In this paper, we investigate It-LLMs' resilience abilities towards a series of probing tests using four MCQ benchmarks. Introducing adversarial examples, we show a significant performance gap, mainly when varying the order of the choices, which reveals a selection bias and brings into discussion reasoning abilities. Following a correlation between first positions and model choices due to positional bias, we hypothesized the presence of structural heuristics in the decision-making process of the It-LLMs, strengthened by including significant examples in few-shot scenarios. Finally, by using the Chain-of-Thought (CoT) technique, we elicit the model to reason and mitigate the bias by obtaining more robust models.

Complex visual reasoning remains a key challenge today. Typically, the challenge is tackled using methodologies such as Chain of Thought (COT) and visual instruction tuning. However, how to organically combine these two methodologies for greater success remains unexplored. Also, issues like hallucinations and high training cost still need to be addressed. In this work, we devise an innovative multi-round training and reasoning framework suitable for lightweight Multimodal Large Language Models (MLLMs). Our self-questioning approach heuristically guides MLLMs to focus on visual clues relevant to the target problem, reducing hallucinations and enhancing the model's ability to describe fine-grained image details. This ultimately enables the model to perform well in complex visual reasoning and question-answering tasks. We have named this framework Socratic Questioning(SQ). To facilitate future research, we create a multimodal mini-dataset named CapQA, which includes 1k images of fine-grained activities, for visual instruction tuning and evaluation, our proposed SQ method leads to a 31.2% improvement in the hallucination score. Our extensive experiments on various benchmarks demonstrate SQ's remarkable capabilities in heuristic self-questioning, zero-shot visual reasoning and hallucination mitigation. Our model and code will be publicly available.

Small Language Models (SLMs) are attracting attention due to the high computational demands and privacy concerns of Large Language Models (LLMs). Some studies fine-tune SLMs using Chains of Thought (CoT) data distilled from LLMs, aiming to enhance their reasoning ability. Furthermore, Some CoT distillation methods introduce external symbolic knowledge into the generation process to improve the limited knowledge memory, reasoning ability and out-of-domain (OOD) generalization of SLMs. However, the introduction of symbolic knowledge increases computational overhead and introduces potential noise. In this paper, we introduce SKIntern, an innovative approach that empowers SLMs to internalize symbolic knowledge and few-shot examples gradually through a progressive fine-tuning process, guided by a predefined linear decay schedule under curriculum learning. By efficiently internalizing knowledge, SKIntern reduces computational overhead and speeds up the reasoning process by focusing solely on the question during inference. It outperforms state-of-the-art baselines by over 5\%, while reducing inference costs (measured in FLOPs) by up to 4times across a wide range of SLMs in both in-domain (ID) and out-of-domain (OOD) tasks. Our code will be available at https://github.com/Xnhyacinth/SKIntern.

Multimodal Large Language Models (MLLMs) have seen growing adoption across various scientific disciplines. These advancements encourage the investigation of molecule-text modeling within synthetic chemistry, a field dedicated to designing and conducting chemical reactions to synthesize new compounds with desired properties and applications. Current approaches, however, often neglect the critical role of multiple molecule graph interaction in understanding chemical reactions, leading to suboptimal performance in synthetic chemistry tasks. This study introduces PRESTO(Progressive Pretraining Enhances Synthetic Chemistry Outcomes), a new framework that bridges the molecule-text modality gap by integrating a comprehensive benchmark of pretraining strategies and dataset configurations. It progressively improves multimodal LLMs through cross-modal alignment and multi-graph understanding. Our extensive experiments demonstrate that PRESTO offers competitive results in downstream synthetic chemistry tasks. The code can be found at https://github.com/IDEA-XL/PRESTO.

Large Language Models (LLMs) possess impressive capabilities to generate meaningful code snippets given natural language intents in zero-shot, i.e., without the need for specific fine-tuning. In the perspective of unleashing their full potential, prior work has demonstrated the benefits of fine-tuning the models to task-specific data. However, fine-tuning process demands heavy computational costs and is intractable when resources are scarce, especially for models with billions of parameters. In light of these challenges, previous studies explored In-Context Learning (ICL) as an effective strategy to generate contextually appropriate code without fine-tuning. However, it operates at inference time and does not involve learning task-specific parameters, potentially limiting the model's performance on downstream tasks. In this context, we foresee that Parameter-Efficient Fine-Tuning (PEFT) techniques carry a high potential for efficiently specializing LLMs to task-specific data. In this paper, we deliver a comprehensive study of LLMs with the impact of PEFT techniques under the automated code generation scenario. Our experimental results reveal the superiority and potential of such techniques over ICL on a wide range of LLMs in reducing the computational burden and improving performance. Therefore, the study opens opportunities for broader applications of PEFT in software engineering scenarios.

Recent advances in large language models have demonstrated remarkable reasoning capabilities through Chain of Thought (CoT) prompting, but often at the cost of excessive verbosity in their intermediate outputs, which increases computational overhead. We introduce Sketch-of-Thought (SoT), a novel prompting framework that combines cognitive-inspired reasoning paradigms with linguistic constraints to minimize token usage while preserving reasoning accuracy. SoT is designed as a flexible framework that can incorporate any custom reasoning paradigms based on cognitive science, and we instantiate it with three such paradigms - Conceptual Chaining, Chunked Symbolism, and Expert Lexicons - each tailored to different reasoning tasks and selected dynamically via a lightweight routing model. Through comprehensive evaluation across 15 reasoning datasets with multiple languages and multimodal scenarios, we demonstrate that SoT achieves token reductions of 76% with negligible accuracy impact. In certain domains like mathematical and multi-hop reasoning, it even improves accuracy while using significantly fewer tokens. Our code is publicly available: https://www.github.com/SimonAytes/SoT.

Large Language Models (LLMs) have demonstrated impressive reasoning capabilities, yet their performance is highly dependent on the prompting strategy and model scale. While reinforcement learning and fine-tuning have been deployed to boost reasoning, these approaches incur substantial computational and data overhead. In this work, we introduce Adaptive Graph of Thoughts (AGoT), a dynamic, graph-based inference framework that enhances LLM reasoning solely at test time. Rather than relying on fixed-step methods like Chain of Thought (CoT) or Tree of Thoughts (ToT), AGoT recursively decomposes complex queries into structured subproblems, forming an dynamic directed acyclic graph (DAG) of interdependent reasoning steps. By selectively expanding only those subproblems that require further analysis, AGoT unifies the strengths of chain, tree, and graph paradigms into a cohesive framework that allocates computation where it is most needed. We validate our approach on diverse benchmarks spanning multi-hop retrieval, scientific reasoning, and mathematical problem-solving, achieving up to 46.2% improvement on scientific reasoning tasks (GPQA) - comparable to gains achieved through computationally intensive reinforcement learning approaches and outperforming state-of-the-art iterative approaches. These results suggest that dynamic decomposition and structured recursion offer a scalable, cost-effective alternative to post-training modifications, paving the way for more robust, general-purpose reasoning in LLMs.

The rapid advancements in large language models (LLMs) have demonstrated their potential to accelerate scientific discovery, particularly in automating the process of research ideation. LLM-based systems have shown promise in generating hypotheses and research ideas. However, current approaches predominantly rely on prompting-based pre-trained models, limiting their ability to optimize generated content effectively. Moreover, they also lack the capability to deal with the complex interdependence and inherent restrictions among novelty, feasibility, and effectiveness, which remains challenging due to the inherent trade-offs among these dimensions, such as the innovation-feasibility conflict. To address these limitations, we for the first time propose fine-tuning LLMs to be better idea proposers and introduce a novel framework that employs a two-stage approach combining Supervised Fine-Tuning (SFT) and controllable Reinforcement Learning (RL). In the SFT stage, the model learns foundational patterns from pairs of research papers and follow-up ideas. In the RL stage, multi-dimensional reward modeling, guided by fine-grained feedback, evaluates and optimizes the generated ideas across key metrics. Dimensional controllers enable dynamic adjustment of generation, while a sentence-level decoder ensures context-aware emphasis during inference. Our framework provides a balanced approach to research ideation, achieving high-quality outcomes by dynamically navigating the trade-offs among novelty, feasibility, and effectiveness.

Iterative human engagement is a common and effective means of leveraging the advanced language processing power of large language models (LLMs). Using well-structured prompts in a conversational manner, human users can effectively influence an LLM to develop more thoughtful and accurate responses. Motivated by this insight, we propose the Iteration of Thought (IoT) framework for enhancing LLM responses by generating "thought"-provoking prompts vis a vis an input query and the current iteration of an LLM's response. Unlike static or semi-static approaches, e.g. Chain of Thought (CoT) or Tree of Thoughts (ToT), IoT adapts its reasoning path dynamically, based on evolving context, and without generating alternate explorative thoughts which are ultimately discarded. The three components of the IoT framework are (1) an Inner Dialogue Agent (IDA) responsible for generating instructive, context-specific prompts; (2) an LLM Agent (LLMA) that processes these prompts to refine its responses; and (3) an iterative prompting loop that implements a conversation between the former two components. We introduce two variants of our framework: Autonomous Iteration of Thought (AIoT), where an LLM decides when to stop iterating, and Guided Iteration of Thought (GIoT), which always forces a fixed number iterations. We investigate the performance of IoT across various datasets, spanning complex reasoning tasks from the GPQA dataset, explorative problem-solving in Game of 24, puzzle solving in Mini Crosswords, and multi-hop question answering from the HotpotQA dataset. Our results show that IoT represents a viable paradigm for autonomous response refinement in LLMs, showcasing significant improvements over CoT and thereby enabling more adaptive and efficient reasoning systems that minimize human intervention.

Deep iterative chain-of-thought (CoT) reasoning enables LLMs to tackle complex tasks by progressively activating relevant pre-trained knowledge. However, it faces challenges in ensuring continual improvement and determining a stopping criterion. In this paper, we investigate whether the relevant knowledge that contributes directly to solving the given question can be activated from the initial reasoning path, thus circumventing the need for iterative refinement. Our experiments reveal that increasing the diversity of initial reasoning paths can achieve comparable or superior performance, a concept we term breadth reasoning. However, existing breadth reasoning approaches, such as self-consistency, offer limited diversity. To address this limitation, we propose a simple yet effective method that enhances reasoning breadth by integrating contextual exploration with reduced sampling randomness. Extensive experiments demonstrate that our approach significantly outperforms deep iterative reasoning. Our code is provided in https://github.com/zongqianwu/breadth.

Generative models for molecules have shown considerable promise for use in computational chemistry, but remain difficult to use for non-experts. For this reason, we introduce open-source infrastructure for easily building generative molecular models into the widely used DeepChem [Ramsundar et al., 2019] library with the aim of creating a robust and reusable molecular generation pipeline. In particular, we add high quality PyTorch [Paszke et al., 2019] implementations of the Molecular Generative Adversarial Networks (MolGAN) [Cao and Kipf, 2022] and Normalizing Flows [Papamakarios et al., 2021]. Our implementations show strong performance comparable with past work [Kuznetsov and Polykovskiy, 2021, Cao and Kipf, 2022].

In this paper, we address the challenging task of multimodal mathematical reasoning by incorporating the ability of ``slow thinking" into multimodal large language models (MLLMs). Contrary to existing methods that rely on direct or fast thinking, our key idea is to construct long chains of thought (CoT) consisting of atomic actions in a step-by-step manner, guiding MLLMs to perform complex reasoning. To this end, we design a novel AtomThink framework composed of three key modules: (i) a CoT annotation engine that automatically generates high-quality CoT annotations to address the lack of high-quality visual mathematical data; (ii) an atomic step fine-tuning strategy that jointly optimizes an MLLM and a policy reward model (PRM) for step-wise reasoning; and (iii) four different search strategies that can be applied with the PRM to complete reasoning. Additionally, we propose AtomMATH, a large-scale multimodal dataset of long CoTs, and an atomic capability evaluation metric for mathematical tasks. Extensive experimental results show that the proposed AtomThink significantly improves the performance of baseline MLLMs, achieving approximately 50\% relative accuracy gains on MathVista and 120\% on MathVerse. To support the advancement of multimodal slow-thinking models, we will make our code and dataset publicly available on https://github.com/Quinn777/AtomThink.

Large Language Models (LLMs) have revolutionized natural language processing and hold immense potential for advancing Artificial Intelligence. However, the core architecture of most mainstream LLMs -- the Transformer -- has inherent limitations in computational depth, rendering them theoretically incapable of solving many reasoning tasks that demand increasingly deep computations. Chain of Thought (CoT) prompting has emerged as a technique to address these architectural limitations, as evidenced by several theoretical studies. It offers a promising approach to solving complex reasoning tasks that were previously beyond the capabilities of these models. Despite its successes, CoT and its variants (such as Tree of Thought, Graph of Thought, etc.) rely on a "one-prompt-for-all" approach, using a single prompt structure (e.g., "think step by step") for a wide range of tasks -- from counting and sorting to solving mathematical and algorithmic problems. This approach poses significant challenges for models to generate the correct reasoning steps, as the model must navigate through a vast prompt template space to find the appropriate template for each task. In this work, we build upon previous theoretical analyses of CoT to demonstrate how the one-prompt-for-all approach can negatively affect the computability of LLMs. We partition the solution search space into two: the prompt space and the answer space. Our findings show that task-specific supervision is essential for navigating the prompt space accurately and achieving optimal performance. Through experiments with state-of-the-art LLMs, we reveal a gap in reasoning performance when supervision is applied versus when it is not.

Graph Neural Networks (GNNs) have been widely adopted for drug discovery with molecular graphs. Nevertheless, current GNNs are mainly good at leveraging short-range interactions (SRI) but struggle to capture long-range interactions (LRI), both of which are crucial for determining molecular properties. To tackle this issue, we propose a method that implicitly projects all original atoms into a few Neural Atoms, which abstracts the collective information of atomic groups within a molecule. Specifically, we explicitly exchange the information among neural atoms and project them back to the atoms' representations as an enhancement. With this mechanism, neural atoms establish the communication channels among distant nodes, effectively reducing the interaction scope of arbitrary node pairs into a single hop. To provide an inspection of our method from a physical perspective, we reveal its connection with the traditional LRI calculation method, Ewald Summation. We conduct extensive experiments on three long-range graph benchmarks, covering both graph-level and link-level tasks on molecular graphs. We empirically justify that our method can be equipped with an arbitrary GNN and help to capture LRI.

The sequential process of conceptualization and instantiation is essential to generalizable commonsense reasoning as it allows the application of existing knowledge to unfamiliar scenarios. However, existing works tend to undervalue the step of instantiation and heavily rely on pre-built concept taxonomies and human annotations to collect both types of knowledge, resulting in a lack of instantiated knowledge to complete reasoning, high cost, and limited scalability. To tackle these challenges, we introduce CANDLE, a distillation framework that iteratively performs contextualized conceptualization and instantiation over commonsense knowledge bases by instructing large language models to generate both types of knowledge with critic filtering. By applying CANDLE to ATOMIC, we construct a comprehensive knowledge base comprising six million conceptualizations and instantiated commonsense knowledge triples. Both types of knowledge are firmly rooted in the original ATOMIC dataset, and intrinsic evaluations demonstrate their exceptional quality and diversity. Empirical results indicate that distilling CANDLE on student models provides benefits across four downstream tasks. Our code, data, and models are publicly available at https://github.com/HKUST-KnowComp/CANDLE.

Large Language Models (LLMs) are known to hallucinate, whereby they generate plausible but inaccurate text. This phenomenon poses significant risks in critical applications, such as medicine or law, necessitating robust hallucination mitigation strategies. While recent works have proposed fine-tuning methods to teach LLMs to abstain from answering questions beyond their knowledge or capabilities, these methods rely on the existence of ground-truth labels or are limited to short-form responses. To address these limitations, we propose fine-tuning using semantic entropy, an uncertainty measure derived from introspection into the model which does not require external labels. We demonstrate that our approach matches or outperforms models fine-tuned using prior work and achieves strong performance for both short and long-form generations on a range of datasets.

We introduce SynFormer, a generative modeling framework designed to efficiently explore and navigate synthesizable chemical space. Unlike traditional molecular generation approaches, we generate synthetic pathways for molecules to ensure that designs are synthetically tractable. By incorporating a scalable transformer architecture and a diffusion module for building block selection, SynFormer surpasses existing models in synthesizable molecular design. We demonstrate SynFormer's effectiveness in two key applications: (1) local chemical space exploration, where the model generates synthesizable analogs of a reference molecule, and (2) global chemical space exploration, where the model aims to identify optimal molecules according to a black-box property prediction oracle. Additionally, we demonstrate the scalability of our approach via the improvement in performance as more computational resources become available. With our code and trained models openly available, we hope that SynFormer will find use across applications in drug discovery and materials science.

Chain-of-Thought (CoT) prompting empowers the reasoning abilities of Large Language Models (LLMs), eliciting them to solve complex reasoning tasks step-by-step. However, with the success of CoT methods, the ability to deliver multi-step reasoning remains limited to English due to the imbalance in the distribution of the pre-training data, making the other languages a barrier. In this work, we propose a Cross-lingual multi-step reasoning approach, aiming to align reasoning processes across different languages. In particular, our method, through a Self-consistent Cross-lingual prompting mechanism inspired by the Tree-of-Thoughts approach, delivers multi-step reasoning paths in different languages that, during the steps, lead to the final solution. Our experimental evaluations show that our method significantly outperforms existing prompting methods, reducing the number of interactions and achieving state-of-the-art performance.

Recent research trends in computational biology have increasingly focused on integrating text and bio-entity modeling, especially in the context of molecules and proteins. However, previous efforts like BioT5 faced challenges in generalizing across diverse tasks and lacked a nuanced understanding of molecular structures, particularly in their textual representations (e.g., IUPAC). This paper introduces BioT5+, an extension of the BioT5 framework, tailored to enhance biological research and drug discovery. BioT5+ incorporates several novel features: integration of IUPAC names for molecular understanding, inclusion of extensive bio-text and molecule data from sources like bioRxiv and PubChem, the multi-task instruction tuning for generality across tasks, and a novel numerical tokenization technique for improved processing of numerical data. These enhancements allow BioT5+ to bridge the gap between molecular representations and their textual descriptions, providing a more holistic understanding of biological entities, and largely improving the grounded reasoning of bio-text and bio-sequences. The model is pre-trained and fine-tuned with a large number of experiments, including 3 types of problems (classification, regression, generation), 15 kinds of tasks, and 21 total benchmark datasets, demonstrating the remarkable performance and state-of-the-art results in most cases. BioT5+ stands out for its ability to capture intricate relationships in biological data, thereby contributing significantly to bioinformatics and computational biology. Our code is available at https://github.com/QizhiPei/BioT5.

The rapid evolution of artificial intelligence in drug discovery encounters challenges with generalization and extensive training, yet Large Language Models (LLMs) offer promise in reshaping interactions with complex molecular data. Our novel contribution, InstructMol, a multi-modal LLM, effectively aligns molecular structures with natural language via an instruction-tuning approach, utilizing a two-stage training strategy that adeptly combines limited domain-specific data with molecular and textual information. InstructMol showcases substantial performance improvements in drug discovery-related molecular tasks, surpassing leading LLMs and significantly reducing the gap with specialized models, thereby establishing a robust foundation for a versatile and dependable drug discovery assistant.

Predicting drug efficacy and safety in vivo requires information on biological responses (e.g., cell morphology and gene expression) to small molecule perturbations. However, current molecular representation learning methods do not provide a comprehensive view of cell states under these perturbations and struggle to remove noise, hindering model generalization. We introduce the Information Alignment (InfoAlign) approach to learn molecular representations through the information bottleneck method in cells. We integrate molecules and cellular response data as nodes into a context graph, connecting them with weighted edges based on chemical, biological, and computational criteria. For each molecule in a training batch, InfoAlign optimizes the encoder's latent representation with a minimality objective to discard redundant structural information. A sufficiency objective decodes the representation to align with different feature spaces from the molecule's neighborhood in the context graph. We demonstrate that the proposed sufficiency objective for alignment is tighter than existing encoder-based contrastive methods. Empirically, we validate representations from InfoAlign in two downstream tasks: molecular property prediction against up to 19 baseline methods across four datasets, plus zero-shot molecule-morphology matching.

Contextual memory integration remains a high challenge in the development of language models, particularly in tasks that require maintaining coherence over extended sequences. Traditional approaches, such as self-attention mechanisms and memory-augmented architectures, often prioritize short-term dependencies, leading to fragmentation and inconsistency in long-range contextual understanding. Inspired by principles of synaptic plasticity observed in biological neural systems, a novel mechanism, Synaptic Resonance, is introduced to dynamically reinforce relevant memory pathways during training and inference. Unlike static memory representations, this mechanism continuously adjusts synaptic weight matrices based on contextual relevance, allowing for improved information retention without excessive computational overhead. Evaluations conducted on an open-source language model demonstrate reductions in perplexity, enhancements in contextual coherence, and increased robustness against input noise, highlighting the effectiveness of reinforcement-driven memory modulation. Comparative analysis against baseline models further reveals that the proposed approach achieves higher memory retention efficiency while maintaining computational feasibility. The architectural modifications integrate seamlessly into existing transformer-based frameworks, ensuring stable convergence and efficient inference without sacrificing scalability. Applications benefiting from improved long-term contextual consistency, such as dialogue systems and document summarization, stand to gain from this approach. Empirical findings suggest that dynamically reinforced memory pathways offer a promising alternative to conventional memory mechanisms, addressing longstanding limitations in extended sequence modeling.

The goal of meta-learning is to learn to adapt to a new task with only a few labeled examples. To tackle this problem in NLP, we propose in-context tuning, which recasts adaptation and prediction as a simple sequence prediction problem: to form the input sequence, we concatenate the task instruction, the labeled examples, and the target input to predict; to meta-train the model to learn from in-context examples, we fine-tune a pre-trained language model (LM) to predict the target label from the input sequences on a collection of tasks. We benchmark our method on two collections of text classification tasks: LAMA and BinaryClfs. Compared to first-order MAML which adapts the model with gradient descent, our method better leverages the inductive bias of LMs to perform pattern matching, and outperforms MAML by an absolute 6% AUC ROC score on BinaryClfs, with increasing advantage w.r.t. model size. Compared to non-fine-tuned in-context learning (i.e. prompting a raw LM), in-context tuning directly learns to learn from in-context examples. On BinaryClfs, in-context tuning improves the average AUC-ROC score by an absolute 10%, and reduces the variance with respect to example ordering by 6x and example choices by 2x.

Reducing hallucination of Large Language Models (LLMs) is imperative for use in the sciences where reproducibility is crucial. However, LLMs inherently lack long-term memory, making it a nontrivial, ad hoc, and inevitably biased task to fine-tune them on domain-specific literature and data. Here we introduce LLaMP, a multimodal retrieval-augmented generation (RAG) framework of multiple data-aware reasoning-and-acting (ReAct) agents that dynamically interact with computational and experimental data on Materials Project (MP). Without fine-tuning, LLaMP demonstrates an ability to comprehend and integrate various modalities of materials science concepts, fetch relevant data stores on the fly, process higher-order data (such as crystal structures and elastic tensors), and summarize multi-step procedures for solid-state synthesis. We show that LLaMP effectively corrects errors in GPT-3.5's intrinsic knowledge, reducing a 5.21% MAPE on frequently-documented bandgaps and a significant 1103.54% MAPE on formation energies -- errors that GPT-3.5 seems to derive from mixed data sources. Additionally, LLaMP substantially reduces the hallucinated volumetric strain in a diamond cubic silicon structure from 66.3% to 0. The proposed framework offers an intuitive and nearly hallucination-free approach to exploring materials informatics and establishes a pathway for knowledge distillation and fine-tuning other language models. We envision the framework as a valuable component for scientific hypotheses and a foundation for future autonomous laboratories where multiple LLM agents communicate and cooperate with robotics to drive material synthesis and chemical reactions without hard-coded human logic and intervention.

One way to enhance the reasoning capability of Large Language Models (LLMs) is to conduct Supervised Fine-Tuning (SFT) using Chain-of-Thought (CoT) annotations. This approach does not show sufficiently strong generalization ability, however, because the training only relies on the given CoT data. In math problem-solving, for example, there is usually only one annotated reasoning path for each question in the training data. Intuitively, it would be better for the algorithm to learn from multiple annotated reasoning paths given a question. To address this issue, we propose a simple yet effective approach called Reinforced Fine-Tuning (ReFT) to enhance the generalizability of learning LLMs for reasoning, with math problem-solving as an example. ReFT first warmups the model with SFT, and then employs on-line reinforcement learning, specifically the PPO algorithm in this paper, to further fine-tune the model, where an abundance of reasoning paths are automatically sampled given the question and the rewards are naturally derived from the ground-truth answers. Extensive experiments on GSM8K, MathQA, and SVAMP datasets show that ReFT significantly outperforms SFT, and the performance can be potentially further boosted by combining inference-time strategies such as majority voting and re-ranking. Note that ReFT obtains the improvement by learning from the same training questions as SFT, without relying on extra or augmented training questions. This indicates a superior generalization ability for ReFT.

Machine learning techniques are essential tools to compute efficient, yet accurate, force fields for atomistic simulations. This approach has recently been extended to incorporate quantum computational methods, making use of variational quantum learning models to predict potential energy surfaces and atomic forces from ab initio training data. However, the trainability and scalability of such models are still limited, due to both theoretical and practical barriers. Inspired by recent developments in geometric classical and quantum machine learning, here we design quantum neural networks that explicitly incorporate, as a data-inspired prior, an extensive set of physically relevant symmetries. We find that our invariant quantum learning models outperform their more generic counterparts on individual molecules of growing complexity. Furthermore, we study a water dimer as a minimal example of a system with multiple components, showcasing the versatility of our proposed approach and opening the way towards larger simulations. Our results suggest that molecular force fields generation can significantly profit from leveraging the framework of geometric quantum machine learning, and that chemical systems represent, in fact, an interesting and rich playground for the development and application of advanced quantum machine learning tools.

Customized generation aims to incorporate a novel concept into a pre-trained text-to-image model, enabling new generations of the concept in novel contexts guided by textual prompts. However, customized generation suffers from an inherent trade-off between concept fidelity and editability, i.e., between precisely modeling the concept and faithfully adhering to the prompts. Previous methods reluctantly seek a compromise and struggle to achieve both high concept fidelity and ideal prompt alignment simultaneously. In this paper, we propose a Divide, Conquer, then Integrate (DCI) framework, which performs a surgical adjustment in the early stage of denoising to liberate the fine-tuned model from the fidelity-editability trade-off at inference. The two conflicting components in the trade-off are decoupled and individually conquered by two collaborative branches, which are then selectively integrated to preserve high concept fidelity while achieving faithful prompt adherence. To obtain a better fine-tuned model, we introduce an Image-specific Context Optimization} (ICO) strategy for model customization. ICO replaces manual prompt templates with learnable image-specific contexts, providing an adaptive and precise fine-tuning direction to promote the overall performance. Extensive experiments demonstrate the effectiveness of our method in reconciling the fidelity-editability trade-off.

Large Language Models (LLMs) have recently demonstrated exceptional performance in various Natural Language Processing (NLP) tasks. They have also shown the ability to perform chain-of-thought (CoT) reasoning to solve complex problems. Recent studies have explored CoT reasoning in complex multimodal scenarios, such as the science question answering task, by fine-tuning multimodal models with high-quality human-annotated CoT rationales. However, collecting high-quality COT rationales is usually time-consuming and costly. Besides, the annotated rationales are hardly accurate due to the external essential information missed. To address these issues, we propose a novel method termed T-SciQ that aims at teaching science question answering with LLM signals. The T-SciQ approach generates high-quality CoT rationales as teaching signals and is advanced to train much smaller models to perform CoT reasoning in complex modalities. Additionally, we introduce a novel data mixing strategy to produce more effective teaching data samples by policy for simple and complex science question answer problems. Extensive experimental results show that our T-SciQ method achieves a new state-of-the-art performance on the ScienceQA benchmark, with an accuracy of 96.18\%. Moreover, our approach outperforms the most powerful fine-tuned baseline by 4.5\%.

This paper challenges the recent paradigm in atomic property prediction that links progress to growing dataset sizes and computational resources. We show that pretraining on a carefully selected, task-relevant dataset can match or even surpass large-scale pretraining, while using as little as 1/24th of the computational cost. We introduce the Chemical Similarity Index (CSI), a novel metric inspired by computer vision's Fr\'echet Inception Distance, for molecular graphs which quantifies the alignment between upstream pretraining datasets and downstream tasks. By selecting the most relevant dataset with minimal CSI distance, we show that models pretrained on a smaller, focused dataset consistently outperform those pretrained on massive, mixed datasets such as JMP, even when those larger datasets include the relevant dataset. Counterintuitively, we also find that indiscriminately adding more data can degrade model performance when the additional data poorly aligns with the task at hand. Our findings highlight that quality often outperforms quantity in pretraining for atomic property prediction.

Multi-modal Chain-of-Thought (MCoT) requires models to leverage knowledge from both textual and visual modalities for step-by-step reasoning, which gains increasing attention. Nevertheless, the current MCoT benchmark still faces some challenges: (1) absence of visual modal reasoning, (2) single-step visual modal reasoning, and (3) Domain missing, thereby hindering the development of MCoT. Motivated by this, we introduce a novel benchmark (M^3CoT) to address the above challenges, advancing the multi-domain, multi-step, and multi-modal CoT. Additionally, we conduct a thorough evaluation involving abundant MCoT approaches on Vision Large Language Models (VLLMs). In addition, we highlight that the current VLLMs still struggle to correctly reason in M^3CoT and there remains a large gap between existing VLLMs and human performance in M^3CoT, despite their superior results on previous MCoT benchmarks. To our knowledge, we take the first meaningful step toward the multi-domain, multi-step, and multi-modal scenario in MCoT. We hope that M^3CoT can serve as a valuable resource, providing a pioneering foundation in multi-domain, multi-step, multi-modal chain-of-thought research.

Probabilistic models of language understanding are valuable tools for investigating human language use. However, they need to be hand-designed for a particular domain. In contrast, large language models (LLMs) are trained on text that spans a wide array of domains, but they lack the structure and interpretability of probabilistic models. In this paper, we use chain-of-thought prompts to introduce structures from probabilistic models into LLMs. We explore this approach in the case of metaphor understanding. Our chain-of-thought prompts lead language models to infer latent variables and reason about their relationships in order to choose appropriate paraphrases for metaphors. The latent variables and relationships chosen are informed by theories of metaphor understanding from cognitive psychology. We apply these prompts to the two largest versions of GPT-3 and show that they can improve performance in a paraphrase selection task.

We introduce Functional Group-Aware Representations for Small Molecules (FARM), a novel foundation model designed to bridge the gap between SMILES, natural language, and molecular graphs. The key innovation of FARM lies in its functional group-aware tokenization, which incorporates functional group information directly into the representations. This strategic reduction in tokenization granularity in a way that is intentionally interfaced with key drivers of functional properties (i.e., functional groups) enhances the model's understanding of chemical language, expands the chemical lexicon, more effectively bridging SMILES and natural language, and ultimately advances the model's capacity to predict molecular properties. FARM also represents molecules from two perspectives: by using masked language modeling to capture atom-level features and by employing graph neural networks to encode the whole molecule topology. By leveraging contrastive learning, FARM aligns these two views of representations into a unified molecular embedding. We rigorously evaluate FARM on the MoleculeNet dataset, where it achieves state-of-the-art performance on 10 out of 12 tasks. These results highlight FARM's potential to improve molecular representation learning, with promising applications in drug discovery and pharmaceutical research.

Chain of Thought (CoT) of multi-step benefits from the logical structure of the reasoning steps and task-specific actions, significantly enhancing the mathematical reasoning capabilities of large language models. As the prevalence of long CoT, the number of reasoning steps exceeds manageable token limits and leads to higher computational demands. Inspired by the fundamental logic of human cognition, ``derive, then reduce'', we conceptualize the standard multi-step CoT as a novel Markov Chain of Thought (MCoT). In this study, we consider the mathematical reasoning task, defining each reasoning step as text accompanied by a Python code snippet. To facilitate a longer reasoning path, self-correction is enabled through interactions with the code interpreter. Our MCoT aims to compress previous reasoning steps into a simplified question, enabling efficient next-step inference without relying on a lengthy KV cache. In our experiments, we curate the MCoTInstruct dataset, and the empirical results indicate that MCoT not only significantly enhances efficiency but also maintains comparable accuracy. While much remains to be explored, this work paves the way for exploring the long CoT reasoning abilities of LLMs.

Identifying reliable synthesis pathways in materials chemistry is a complex task, particularly in polymer science, due to the intricate and often non-unique nomenclature of macromolecules. To address this challenge, we propose an agent system that integrates large language models (LLMs) and knowledge graphs (KGs). By leveraging LLMs' powerful capabilities for extracting and recognizing chemical substance names, and storing the extracted data in a structured knowledge graph, our system fully automates the retrieval of relevant literatures, extraction of reaction data, database querying, construction of retrosynthetic pathway trees, further expansion through the retrieval of additional literature and recommendation of optimal reaction pathways. A novel Multi-branched Reaction Pathway Search (MBRPS) algorithm enables the exploration of all pathways, with a particular focus on multi-branched ones, helping LLMs overcome weak reasoning in multi-branched paths. This work represents the first attempt to develop a fully automated retrosynthesis planning agent tailored specially for macromolecules powered by LLMs. Applied to polyimide synthesis, our new approach constructs a retrosynthetic pathway tree with hundreds of pathways and recommends optimized routes, including both known and novel pathways, demonstrating its effectiveness and potential for broader applications.

Despite the recent progress in long-context language models, it remains elusive how transformer-based models exhibit the capability to retrieve relevant information from arbitrary locations within the long context. This paper aims to address this question. Our systematic investigation across a wide spectrum of models reveals that a special type of attention heads are largely responsible for retrieving information, which we dub retrieval heads. We identify intriguing properties of retrieval heads:(1) universal: all the explored models with long-context capability have a set of retrieval heads; (2) sparse: only a small portion (less than 5\%) of the attention heads are retrieval. (3) intrinsic: retrieval heads already exist in models pretrained with short context. When extending the context length by continual pretraining, it is still the same set of heads that perform information retrieval. (4) dynamically activated: take Llama-2 7B for example, 12 retrieval heads always attend to the required information no matter how the context is changed. The rest of the retrieval heads are activated in different contexts. (5) causal: completely pruning retrieval heads leads to failure in retrieving relevant information and results in hallucination, while pruning random non-retrieval heads does not affect the model's retrieval ability. We further show that retrieval heads strongly influence chain-of-thought (CoT) reasoning, where the model needs to frequently refer back the question and previously-generated context. Conversely, tasks where the model directly generates the answer using its intrinsic knowledge are less impacted by masking out retrieval heads. These observations collectively explain which internal part of the model seeks information from the input tokens. We believe our insights will foster future research on reducing hallucination, improving reasoning, and compressing the KV cache.