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Mar 17

Generative Pretrained Autoregressive Transformer Graph Neural Network applied to the Analysis and Discovery of Novel Proteins

We report a flexible language-model based deep learning strategy, applied here to solve complex forward and inverse problems in protein modeling, based on an attention neural network that integrates transformer and graph convolutional architectures in a causal multi-headed graph mechanism, to realize a generative pretrained model. The model is applied to predict secondary structure content (per-residue level and overall content), protein solubility, and sequencing tasks. Further trained on inverse tasks, the model is rendered capable of designing proteins with these properties as target features. The model is formulated as a general framework, completely prompt-based, and can be adapted for a variety of downstream tasks. We find that adding additional tasks yields emergent synergies that the model exploits in improving overall performance, beyond what would be possible by training a model on each dataset alone. Case studies are presented to validate the method, yielding protein designs specifically focused on structural proteins, but also exploring the applicability in the design of soluble, antimicrobial biomaterials. While our model is trained to ultimately perform 8 distinct tasks, with available datasets it can be extended to solve additional problems. In a broader sense, this work illustrates a form of multiscale modeling that relates a set of ultimate building blocks (here, byte-level utf8 characters) to complex output. This materiomic scheme captures complex emergent relationships between universal building block and resulting properties via a synergizing learning capacity to express a set of potentialities embedded in the knowledge used in training, via the interplay of universality and diversity.

MrT5: Dynamic Token Merging for Efficient Byte-level Language Models

Models that rely on subword tokenization have significant drawbacks, such as sensitivity to character-level noise like spelling errors and inconsistent compression rates across different languages and scripts. While character- or byte-level models like ByT5 attempt to address these concerns, they have not gained widespread adoption -- processing raw byte streams without tokenization results in significantly longer sequence lengths, making training and inference inefficient. This work introduces MrT5 (MergeT5), a more efficient variant of ByT5 that integrates a token deletion mechanism in its encoder to dynamically shorten the input sequence length. After processing through a fixed number of encoder layers, a learnt delete gate determines which tokens are to be removed and which are to be retained for subsequent layers. MrT5 effectively ``merges'' critical information from deleted tokens into a more compact sequence, leveraging contextual information from the remaining tokens. In continued pre-training experiments, we find that MrT5 can achieve significant gains in inference runtime with minimal effect on performance. When trained on English text, MrT5 demonstrates the capability to transfer its deletion feature zero-shot across several languages, with significant additional improvements following multilingual training. Furthermore, MrT5 shows comparable accuracy to ByT5 on downstream evaluations such as XNLI and character-level tasks while reducing sequence lengths by up to 80%. Our approach presents a solution to the practical limitations of existing byte-level models.

Learn Your Tokens: Word-Pooled Tokenization for Language Modeling

Language models typically tokenize text into subwords, using a deterministic, hand-engineered heuristic of combining characters into longer surface-level strings such as 'ing' or whole words. Recent literature has repeatedly shown the limitations of such a tokenization strategy, particularly for documents not written in English and for representing numbers. On the other extreme, byte/character-level language models are much less restricted but suffer from increased sequence description lengths and a subsequent quadratic expansion in self-attention computation. Recent attempts to compress and limit these context lengths with fixed size convolutions is helpful but completely ignores the word boundary. This paper considers an alternative 'learn your tokens' scheme which utilizes the word boundary to pool bytes/characters into word representations, which are fed to the primary language model, before again decoding individual characters/bytes per word in parallel. We find that our moderately expressive and moderately fast end-to-end tokenizer outperform by over 300% both subwords and byte/character models over the intrinsic language modeling metric of next-word prediction across datasets. It particularly outshines on rare words, outperforming by a factor of 30! We extensively study the language modeling setup for all three categories of tokenizers and theoretically analyze how our end-to-end models can also be a strong trade-off in efficiency and robustness.

Word-Level Representation From Bytes For Language Modeling

Modern language models mostly take sub-words as input, a design that balances the trade-off between vocabulary size, number of parameters, and performance. However, sub-word tokenization still has disadvantages like not being robust to noise and difficult to generalize to new languages. Also, the current trend of scaling up models reveals that larger models require larger embeddings but that makes parallelization hard. Previous work on image classification proves splitting raw input into a sequence of chucks is a strong, model-agnostic inductive bias. Based on this observation, we rethink the existing character-aware method that takes character-level inputs but makes word-level sequence modeling and prediction. We overhaul this method by introducing a cross-attention network that builds word-level representation directly from bytes, and a sub-word level prediction based on word-level hidden states to avoid the time and space requirement of word-level prediction. With these two improvements combined, we have a token free model with slim input embeddings for downstream tasks. We name our method Byte2Word and perform evaluations on language modeling and text classification. Experiments show that Byte2Word is on par with the strong sub-word baseline BERT but only takes up 10\% of embedding size. We further test our method on synthetic noise and cross-lingual transfer and find it competitive to baseline methods on both settings.

Romanization-based Large-scale Adaptation of Multilingual Language Models

Large multilingual pretrained language models (mPLMs) have become the de facto state of the art for cross-lingual transfer in NLP. However, their large-scale deployment to many languages, besides pretraining data scarcity, is also hindered by the increase in vocabulary size and limitations in their parameter budget. In order to boost the capacity of mPLMs to deal with low-resource and unseen languages, we explore the potential of leveraging transliteration on a massive scale. In particular, we explore the UROMAN transliteration tool, which provides mappings from UTF-8 to Latin characters for all the writing systems, enabling inexpensive romanization for virtually any language. We first focus on establishing how UROMAN compares against other language-specific and manually curated transliterators for adapting multilingual PLMs. We then study and compare a plethora of data- and parameter-efficient strategies for adapting the mPLMs to romanized and non-romanized corpora of 14 diverse low-resource languages. Our results reveal that UROMAN-based transliteration can offer strong performance for many languages, with particular gains achieved in the most challenging setups: on languages with unseen scripts and with limited training data without any vocabulary augmentation. Further analyses reveal that an improved tokenizer based on romanized data can even outperform non-transliteration-based methods in the majority of languages.

Correcting diacritics and typos with a ByT5 transformer model

Due to the fast pace of life and online communications and the prevalence of English and the QWERTY keyboard, people tend to forgo using diacritics, make typographical errors (typos) when typing in other languages. Restoring diacritics and correcting spelling is important for proper language use and the disambiguation of texts for both humans and downstream algorithms. However, both of these problems are typically addressed separately: the state-of-the-art diacritics restoration methods do not tolerate other typos, but classical spellcheckers also cannot deal adequately with all the diacritics missing. In this work, we tackle both problems at once by employing the newly-developed universal ByT5 byte-level seq2seq transformer model that requires no language-specific model structures. For a comparison, we perform diacritics restoration on benchmark datasets of 12 languages, with the addition of Lithuanian. The experimental investigation proves that our approach is able to achieve results (> 98%) comparable to the previous state-of-the-art, despite being trained less and on fewer data. Our approach is also able to restore diacritics in words not seen during training with > 76% accuracy. Our simultaneous diacritics restoration and typos correction approach reaches > 94% alpha-word accuracy on the 13 languages. It has no direct competitors and strongly outperforms classical spell-checking or dictionary-based approaches. We also demonstrate all the accuracies to further improve with more training. Taken together, this shows the great real-world application potential of our suggested methods to more data, languages, and error classes.

Hierarchical Autoregressive Transformers: Combining Byte-~and Word-Level Processing for Robust, Adaptable Language Models

Tokenization is a fundamental step in natural language processing, breaking text into units that computational models can process. While learned subword tokenizers have become the de-facto standard, they present challenges such as large vocabularies, limited adaptability to new domains or languages, and sensitivity to spelling errors and variations. To overcome these limitations, we investigate a hierarchical architecture for autoregressive language modelling that combines character-level and word-level processing. It employs a lightweight character-level encoder to convert character sequences into word embeddings, which are then processed by a word-level backbone model and decoded back into characters via a compact character-level decoder. This method retains the sequence compression benefits of word-level tokenization without relying on a rigid, predefined vocabulary. We demonstrate, at scales up to 7 billion parameters, that hierarchical transformers match the downstream task performance of subword-tokenizer-based models while exhibiting significantly greater robustness to input perturbations. Additionally, during continued pretraining on an out-of-domain language, our model trains almost twice as fast, achieves superior performance on the target language, and retains more of its previously learned knowledge. Hierarchical transformers pave the way for NLP systems that are more robust, flexible, and generalizable across languages and domains.

Chinese Text Recognition with A Pre-Trained CLIP-Like Model Through Image-IDS Aligning

Scene text recognition has been studied for decades due to its broad applications. However, despite Chinese characters possessing different characteristics from Latin characters, such as complex inner structures and large categories, few methods have been proposed for Chinese Text Recognition (CTR). Particularly, the characteristic of large categories poses challenges in dealing with zero-shot and few-shot Chinese characters. In this paper, inspired by the way humans recognize Chinese texts, we propose a two-stage framework for CTR. Firstly, we pre-train a CLIP-like model through aligning printed character images and Ideographic Description Sequences (IDS). This pre-training stage simulates humans recognizing Chinese characters and obtains the canonical representation of each character. Subsequently, the learned representations are employed to supervise the CTR model, such that traditional single-character recognition can be improved to text-line recognition through image-IDS matching. To evaluate the effectiveness of the proposed method, we conduct extensive experiments on both Chinese character recognition (CCR) and CTR. The experimental results demonstrate that the proposed method performs best in CCR and outperforms previous methods in most scenarios of the CTR benchmark. It is worth noting that the proposed method can recognize zero-shot Chinese characters in text images without fine-tuning, whereas previous methods require fine-tuning when new classes appear. The code is available at https://github.com/FudanVI/FudanOCR/tree/main/image-ids-CTR.

General Detection-based Text Line Recognition

We introduce a general detection-based approach to text line recognition, be it printed (OCR) or handwritten (HTR), with Latin, Chinese, or ciphered characters. Detection-based approaches have until now been largely discarded for HTR because reading characters separately is often challenging, and character-level annotation is difficult and expensive. We overcome these challenges thanks to three main insights: (i) synthetic pre-training with sufficiently diverse data enables learning reasonable character localization for any script; (ii) modern transformer-based detectors can jointly detect a large number of instances, and, if trained with an adequate masking strategy, leverage consistency between the different detections; (iii) once a pre-trained detection model with approximate character localization is available, it is possible to fine-tune it with line-level annotation on real data, even with a different alphabet. Our approach, dubbed DTLR, builds on a completely different paradigm than state-of-the-art HTR methods, which rely on autoregressive decoding, predicting character values one by one, while we treat a complete line in parallel. Remarkably, we demonstrate good performance on a large range of scripts, usually tackled with specialized approaches. In particular, we improve state-of-the-art performances for Chinese script recognition on the CASIA v2 dataset, and for cipher recognition on the Borg and Copiale datasets. Our code and models are available at https://github.com/raphael-baena/DTLR.

UniCoder: Scaling Code Large Language Model via Universal Code

Intermediate reasoning or acting steps have successfully improved large language models (LLMs) for handling various downstream natural language processing (NLP) tasks. When applying LLMs for code generation, recent works mainly focus on directing the models to articulate intermediate natural-language reasoning steps, as in chain-of-thought (CoT) prompting, and then output code with the natural language or other structured intermediate steps. However, such output is not suitable for code translation or generation tasks since the standard CoT has different logical structures and forms of expression with the code. In this work, we introduce the universal code (UniCode) as the intermediate representation. It is a description of algorithm steps using a mix of conventions of programming languages, such as assignment operator, conditional operator, and loop. Hence, we collect an instruction dataset UniCoder-Instruct to train our model UniCoder on multi-task learning objectives. UniCoder-Instruct comprises natural-language questions, code solutions, and the corresponding universal code. The alignment between the intermediate universal code representation and the final code solution significantly improves the quality of the generated code. The experimental results demonstrate that UniCoder with the universal code significantly outperforms the previous prompting methods by a large margin, showcasing the effectiveness of the structural clues in pseudo-code.

Machine Translation by Projecting Text into the Same Phonetic-Orthographic Space Using a Common Encoding

The use of subword embedding has proved to be a major innovation in Neural Machine Translation (NMT). It helps NMT to learn better context vectors for Low Resource Languages (LRLs) so as to predict the target words by better modelling the morphologies of the two languages and also the morphosyntax transfer. Even so, their performance for translation in Indian language to Indian language scenario is still not as good as for resource-rich languages. One reason for this is the relative morphological richness of Indian languages, while another is that most of them fall into the extremely low resource or zero-shot categories. Since most major Indian languages use Indic or Brahmi origin scripts, the text written in them is highly phonetic in nature and phonetically similar in terms of abstract letters and their arrangements. We use these characteristics of Indian languages and their scripts to propose an approach based on common multilingual Latin-based encodings (WX notation) that take advantage of language similarity while addressing the morphological complexity issue in NMT. These multilingual Latin-based encodings in NMT, together with Byte Pair Embedding (BPE) allow us to better exploit their phonetic and orthographic as well as lexical similarities to improve the translation quality by projecting different but similar languages on the same orthographic-phonetic character space. We verify the proposed approach by demonstrating experiments on similar language pairs (Gujarati-Hindi, Marathi-Hindi, Nepali-Hindi, Maithili-Hindi, Punjabi-Hindi, and Urdu-Hindi) under low resource conditions. The proposed approach shows an improvement in a majority of cases, in one case as much as ~10 BLEU points compared to baseline techniques for similar language pairs. We also get up to ~1 BLEU points improvement on distant and zero-shot language pairs.

Focus on the Whole Character: Discriminative Character Modeling for Scene Text Recognition

Recently, scene text recognition (STR) models have shown significant performance improvements. However, existing models still encounter difficulties in recognizing challenging texts that involve factors such as severely distorted and perspective characters. These challenging texts mainly cause two problems: (1) Large Intra-Class Variance. (2) Small Inter-Class Variance. An extremely distorted character may prominently differ visually from other characters within the same category, while the variance between characters from different classes is relatively small. To address the above issues, we propose a novel method that enriches the character features to enhance the discriminability of characters. Firstly, we propose the Character-Aware Constraint Encoder (CACE) with multiple blocks stacked. CACE introduces a decay matrix in each block to explicitly guide the attention region for each token. By continuously employing the decay matrix, CACE enables tokens to perceive morphological information at the character level. Secondly, an Intra-Inter Consistency Loss (I^2CL) is introduced to consider intra-class compactness and inter-class separability at feature space. I^2CL improves the discriminative capability of features by learning a long-term memory unit for each character category. Trained with synthetic data, our model achieves state-of-the-art performance on common benchmarks (94.1% accuracy) and Union14M-Benchmark (61.6% accuracy). Code is available at https://github.com/bang123-box/CFE.

DB-LLM: Accurate Dual-Binarization for Efficient LLMs

Large language models (LLMs) have significantly advanced the field of natural language processing, while the expensive memory and computation consumption impede their practical deployment. Quantization emerges as one of the most effective methods for improving the computational efficiency of LLMs. However, existing ultra-low-bit quantization always causes severe accuracy drops. In this paper, we empirically relieve the micro and macro characteristics of ultra-low bit quantization and present a novel Dual-Binarization method for LLMs, namely DB-LLM. For the micro-level, we take both the accuracy advantage of 2-bit-width and the efficiency advantage of binarization into account, introducing Flexible Dual Binarization (FDB). By splitting 2-bit quantized weights into two independent sets of binaries, FDB ensures the accuracy of representations and introduces flexibility, utilizing the efficient bitwise operations of binarization while retaining the inherent high sparsity of ultra-low bit quantization. For the macro-level, we find the distortion that exists in the prediction of LLM after quantization, which is specified as the deviations related to the ambiguity of samples. We propose the Deviation-Aware Distillation (DAD) method, enabling the model to focus differently on various samples. Comprehensive experiments show that our DB-LLM not only significantly surpasses the current State-of-The-Art (SoTA) in ultra-low bit quantization (eg, perplexity decreased from 9.64 to 7.23), but also achieves an additional 20\% reduction in computational consumption compared to the SOTA method under the same bit-width. Our code will be released soon.

Watermarking Text Generated by Black-Box Language Models

LLMs now exhibit human-like skills in various fields, leading to worries about misuse. Thus, detecting generated text is crucial. However, passive detection methods are stuck in domain specificity and limited adversarial robustness. To achieve reliable detection, a watermark-based method was proposed for white-box LLMs, allowing them to embed watermarks during text generation. The method involves randomly dividing the model vocabulary to obtain a special list and adjusting the probability distribution to promote the selection of words in the list. A detection algorithm aware of the list can identify the watermarked text. However, this method is not applicable in many real-world scenarios where only black-box language models are available. For instance, third-parties that develop API-based vertical applications cannot watermark text themselves because API providers only supply generated text and withhold probability distributions to shield their commercial interests. To allow third-parties to autonomously inject watermarks into generated text, we develop a watermarking framework for black-box language model usage scenarios. Specifically, we first define a binary encoding function to compute a random binary encoding corresponding to a word. The encodings computed for non-watermarked text conform to a Bernoulli distribution, wherein the probability of a word representing bit-1 being approximately 0.5. To inject a watermark, we alter the distribution by selectively replacing words representing bit-0 with context-based synonyms that represent bit-1. A statistical test is then used to identify the watermark. Experiments demonstrate the effectiveness of our method on both Chinese and English datasets. Furthermore, results under re-translation, polishing, word deletion, and synonym substitution attacks reveal that it is arduous to remove the watermark without compromising the original semantics.

LLM.int8(): 8-bit Matrix Multiplication for Transformers at Scale

Large language models have been widely adopted but require significant GPU memory for inference. We develop a procedure for Int8 matrix multiplication for feed-forward and attention projection layers in transformers, which cut the memory needed for inference by half while retaining full precision performance. With our method, a 175B parameter 16/32-bit checkpoint can be loaded, converted to Int8, and used immediately without performance degradation. This is made possible by understanding and working around properties of highly systematic emergent features in transformer language models that dominate attention and transformer predictive performance. To cope with these features, we develop a two-part quantization procedure, LLM.int8(). We first use vector-wise quantization with separate normalization constants for each inner product in the matrix multiplication, to quantize most of the features. However, for the emergent outliers, we also include a new mixed-precision decomposition scheme, which isolates the outlier feature dimensions into a 16-bit matrix multiplication while still more than 99.9% of values are multiplied in 8-bit. Using LLM.int8(), we show empirically it is possible to perform inference in LLMs with up to 175B parameters without any performance degradation. This result makes such models much more accessible, for example making it possible to use OPT-175B/BLOOM on a single server with consumer GPUs. We open-source our software.

Subword Dictionary Learning and Segmentation Techniques for Automatic Speech Recognition in Tamil and Kannada

We present automatic speech recognition (ASR) systems for Tamil and Kannada based on subword modeling to effectively handle unlimited vocabulary due to the highly agglutinative nature of the languages. We explore byte pair encoding (BPE), and proposed a variant of this algorithm named extended-BPE, and Morfessor tool to segment each word as subwords. We have effectively incorporated maximum likelihood (ML) and Viterbi estimation techniques with weighted finite state transducers (WFST) framework in these algorithms to learn the subword dictionary from a large text corpus. Using the learnt subword dictionary, the words in training data transcriptions are segmented to subwords and we train deep neural network ASR systems which recognize subword sequence for any given test speech utterance. The output subword sequence is then post-processed using deterministic rules to get the final word sequence such that the actual number of words that can be recognized is much larger. For Tamil ASR, We use 152 hours of data for training and 65 hours for testing, whereas for Kannada ASR, we use 275 hours for training and 72 hours for testing. Upon experimenting with different combination of segmentation and estimation techniques, we find that the word error rate (WER) reduces drastically when compared to the baseline word-level ASR, achieving a maximum absolute WER reduction of 6.24% and 6.63% for Tamil and Kannada respectively.

BitMoD: Bit-serial Mixture-of-Datatype LLM Acceleration

Large language models (LLMs) have demonstrated remarkable performance across various machine learning tasks. Yet the substantial memory footprint of LLMs significantly hinders their deployment. In this paper, we improve the accessibility of LLMs through BitMoD, an algorithm-hardware co-design solution that enables efficient LLM acceleration at low weight precision. On the algorithm side, BitMoD introduces fine-grained data type adaptation that uses a different numerical data type to quantize a group of (e.g., 128) weights. Through the careful design of these new data types, BitMoD is able to quantize LLM weights to very low precision (e.g., 4 bits and 3 bits) while maintaining high accuracy. On the hardware side, BitMoD employs a bit-serial processing element to easily support multiple numerical precisions and data types; our hardware design includes two key innovations: First, it employs a unified representation to process different weight data types, thus reducing the hardware cost. Second, it adopts a bit-serial dequantization unit to rescale the per-group partial sum with minimal hardware overhead. Our evaluation on six representative LLMs demonstrates that BitMoD significantly outperforms state-of-the-art LLM quantization and acceleration methods. For discriminative tasks, BitMoD can quantize LLM weights to 4-bit with <!0.5% accuracy loss on average. For generative tasks, BitMoD is able to quantize LLM weights to 3-bit while achieving better perplexity than prior LLM quantization scheme. Combining the superior model performance with an efficient accelerator design, BitMoD achieves an average of 1.69times and 1.48times speedups compared to prior LLM accelerators ANT and OliVe, respectively.

Out of Length Text Recognition with Sub-String Matching

Scene Text Recognition (STR) methods have demonstrated robust performance in word-level text recognition. However, in real applications the text image is sometimes long due to detected with multiple horizontal words. It triggers the requirement to build long text recognition models from readily available short (i.e., word-level) text datasets, which has been less studied previously. In this paper, we term this task Out of Length (OOL) text recognition. We establish the first Long Text Benchmark (LTB) to facilitate the assessment of different methods in long text recognition. Meanwhile, we propose a novel method called OOL Text Recognition with sub-String Matching (SMTR). SMTR comprises two cross-attention-based modules: one encodes a sub-string containing multiple characters into next and previous queries, and the other employs the queries to attend to the image features, matching the sub-string and simultaneously recognizing its next and previous character. SMTR can recognize text of arbitrary length by iterating the process above. To avoid being trapped in recognizing highly similar sub-strings, we introduce a regularization training to compel SMTR to effectively discover subtle differences between similar sub-strings for precise matching. In addition, we propose an inference augmentation strategy to alleviate confusion caused by identical sub-strings in the same text and improve the overall recognition efficiency. Extensive experimental results reveal that SMTR, even when trained exclusively on short text, outperforms existing methods in public short text benchmarks and exhibits a clear advantage on LTB. Code: https://github.com/Topdu/OpenOCR.

Detecting and recognizing characters in Greek papyri with YOLOv8, DeiT and SimCLR

Purpose: The capacity to isolate and recognize individual characters from facsimile images of papyrus manuscripts yields rich opportunities for digital analysis. For this reason the `ICDAR 2023 Competition on Detection and Recognition of Greek Letters on Papyri' was held as part of the 17th International Conference on Document Analysis and Recognition. This paper discusses our submission to the competition. Methods: We used an ensemble of YOLOv8 models to detect and classify individual characters and employed two different approaches for refining the character predictions, including a transformer based DeiT approach and a ResNet-50 model trained on a large corpus of unlabelled data using SimCLR, a self-supervised learning method. Results: Our submission won the recognition challenge with a mAP of 42.2%, and was runner-up in the detection challenge with a mean average precision (mAP) of 51.4%. At the more relaxed intersection over union threshold of 0.5, we achieved the highest mean average precision and mean average recall results for both detection and classification. Conclusion: The results demonstrate the potential for these techniques for automated character recognition on historical manuscripts. We ran the prediction pipeline on more than 4,500 images from the Oxyrhynchus Papyri to illustrate the utility of our approach, and we release the results publicly in multiple formats.