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Mar 18

Enhancing Traffic Incident Management with Large Language Models: A Hybrid Machine Learning Approach for Severity Classification

This research showcases the innovative integration of Large Language Models into machine learning workflows for traffic incident management, focusing on the classification of incident severity using accident reports. By leveraging features generated by modern language models alongside conventional data extracted from incident reports, our research demonstrates improvements in the accuracy of severity classification across several machine learning algorithms. Our contributions are threefold. First, we present an extensive comparison of various machine learning models paired with multiple large language models for feature extraction, aiming to identify the optimal combinations for accurate incident severity classification. Second, we contrast traditional feature engineering pipelines with those enhanced by language models, showcasing the superiority of language-based feature engineering in processing unstructured text. Third, our study illustrates how merging baseline features from accident reports with language-based features can improve the severity classification accuracy. This comprehensive approach not only advances the field of incident management but also highlights the cross-domain application potential of our methodology, particularly in contexts requiring the prediction of event outcomes from unstructured textual data or features translated into textual representation. Specifically, our novel methodology was applied to three distinct datasets originating from the United States, the United Kingdom, and Queensland, Australia. This cross-continental application underlines the robustness of our approach, suggesting its potential for widespread adoption in improving incident management processes globally.

PerSEval: Assessing Personalization in Text Summarizers

Personalized summarization models cater to individuals' subjective understanding of saliency, as represented by their reading history and current topics of attention. Existing personalized text summarizers are primarily evaluated based on accuracy measures such as BLEU, ROUGE, and METEOR. However, a recent study argued that accuracy measures are inadequate for evaluating the degree of personalization of these models and proposed EGISES, the first metric to evaluate personalized text summaries. It was suggested that accuracy is a separate aspect and should be evaluated standalone. In this paper, we challenge the necessity of an accuracy leaderboard, suggesting that relying on accuracy-based aggregated results might lead to misleading conclusions. To support this, we delve deeper into EGISES, demonstrating both theoretically and empirically that it measures the degree of responsiveness, a necessary but not sufficient condition for degree-of-personalization. We subsequently propose PerSEval, a novel measure that satisfies the required sufficiency condition. Based on the benchmarking of ten SOTA summarization models on the PENS dataset, we empirically establish that -- (i) PerSEval is reliable w.r.t human-judgment correlation (Pearson's r = 0.73; Spearman's rho = 0.62; Kendall's tau = 0.42), (ii) PerSEval has high rank-stability, (iii) PerSEval as a rank-measure is not entailed by EGISES-based ranking, and (iv) PerSEval can be a standalone rank-measure without the need of any aggregated ranking.

Summarizing Patients Problems from Hospital Progress Notes Using Pre-trained Sequence-to-Sequence Models

Automatically summarizing patients' main problems from daily progress notes using natural language processing methods helps to battle against information and cognitive overload in hospital settings and potentially assists providers with computerized diagnostic decision support. Problem list summarization requires a model to understand, abstract, and generate clinical documentation. In this work, we propose a new NLP task that aims to generate a list of problems in a patient's daily care plan using input from the provider's progress notes during hospitalization. We investigate the performance of T5 and BART, two state-of-the-art seq2seq transformer architectures, in solving this problem. We provide a corpus built on top of progress notes from publicly available electronic health record progress notes in the Medical Information Mart for Intensive Care (MIMIC)-III. T5 and BART are trained on general domain text, and we experiment with a data augmentation method and a domain adaptation pre-training method to increase exposure to medical vocabulary and knowledge. Evaluation methods include ROUGE, BERTScore, cosine similarity on sentence embedding, and F-score on medical concepts. Results show that T5 with domain adaptive pre-training achieves significant performance gains compared to a rule-based system and general domain pre-trained language models, indicating a promising direction for tackling the problem summarization task.

Neural Rankers for Effective Screening Prioritisation in Medical Systematic Review Literature Search

Medical systematic reviews typically require assessing all the documents retrieved by a search. The reason is two-fold: the task aims for ``total recall''; and documents retrieved using Boolean search are an unordered set, and thus it is unclear how an assessor could examine only a subset. Screening prioritisation is the process of ranking the (unordered) set of retrieved documents, allowing assessors to begin the downstream processes of the systematic review creation earlier, leading to earlier completion of the review, or even avoiding screening documents ranked least relevant. Screening prioritisation requires highly effective ranking methods. Pre-trained language models are state-of-the-art on many IR tasks but have yet to be applied to systematic review screening prioritisation. In this paper, we apply several pre-trained language models to the systematic review document ranking task, both directly and fine-tuned. An empirical analysis compares how effective neural methods compare to traditional methods for this task. We also investigate different types of document representations for neural methods and their impact on ranking performance. Our results show that BERT-based rankers outperform the current state-of-the-art screening prioritisation methods. However, BERT rankers and existing methods can actually be complementary, and thus, further improvements may be achieved if used in conjunction.

Training Models to Extract Treatment Plans from Clinical Notes Using Contents of Sections with Headings

Objective: Using natural language processing (NLP) to find sentences that state treatment plans in a clinical note, would automate plan extraction and would further enable their use in tools that help providers and care managers. However, as in the most NLP tasks on clinical text, creating gold standard to train and test NLP models is tedious and expensive. Fortuitously, sometimes but not always clinical notes contain sections with a heading that identifies the section as a plan. Leveraging contents of such labeled sections as a noisy training data, we assessed accuracy of NLP models trained with the data. Methods: We used common variations of plan headings and rule-based heuristics to find plan sections with headings in clinical notes, and we extracted sentences from them and formed a noisy training data of plan sentences. We trained Support Vector Machine (SVM) and Convolutional Neural Network (CNN) models with the data. We measured accuracy of the trained models on the noisy dataset using ten-fold cross validation and separately on a set-aside manually annotated dataset. Results: About 13% of 117,730 clinical notes contained treatment plans sections with recognizable headings in the 1001 longitudinal patient records that were obtained from Cleveland Clinic under an IRB approval. We were able to extract and create a noisy training data of 13,492 plan sentences from the clinical notes. CNN achieved best F measures, 0.91 and 0.97 in the cross-validation and set-aside evaluation experiments respectively. SVM slightly underperformed with F measures of 0.89 and 0.96 in the same experiments. Conclusion: Our study showed that the training supervised learning models using noisy plan sentences was effective in identifying them in all clinical notes. More broadly, sections with informal headings in clinical notes can be a good source for generating effective training data.

MedAlign: A Clinician-Generated Dataset for Instruction Following with Electronic Medical Records

The ability of large language models (LLMs) to follow natural language instructions with human-level fluency suggests many opportunities in healthcare to reduce administrative burden and improve quality of care. However, evaluating LLMs on realistic text generation tasks for healthcare remains challenging. Existing question answering datasets for electronic health record (EHR) data fail to capture the complexity of information needs and documentation burdens experienced by clinicians. To address these challenges, we introduce MedAlign, a benchmark dataset of 983 natural language instructions for EHR data. MedAlign is curated by 15 clinicians (7 specialities), includes clinician-written reference responses for 303 instructions, and provides 276 longitudinal EHRs for grounding instruction-response pairs. We used MedAlign to evaluate 6 general domain LLMs, having clinicians rank the accuracy and quality of each LLM response. We found high error rates, ranging from 35% (GPT-4) to 68% (MPT-7B-Instruct), and an 8.3% drop in accuracy moving from 32k to 2k context lengths for GPT-4. Finally, we report correlations between clinician rankings and automated natural language generation metrics as a way to rank LLMs without human review. We make MedAlign available under a research data use agreement to enable LLM evaluations on tasks aligned with clinician needs and preferences.

A Systematic Literature Review of Automated ICD Coding and Classification Systems using Discharge Summaries

Codification of free-text clinical narratives have long been recognised to be beneficial for secondary uses such as funding, insurance claim processing and research. The current scenario of assigning codes is a manual process which is very expensive, time-consuming and error prone. In recent years, many researchers have studied the use of Natural Language Processing (NLP), related Machine Learning (ML) and Deep Learning (DL) methods and techniques to resolve the problem of manual coding of clinical narratives and to assist human coders to assign clinical codes more accurately and efficiently. This systematic literature review provides a comprehensive overview of automated clinical coding systems that utilises appropriate NLP, ML and DL methods and techniques to assign ICD codes to discharge summaries. We have followed the Preferred Reporting Items for Systematic Reviews and Meta-Analyses(PRISMA) guidelines and conducted a comprehensive search of publications from January, 2010 to December 2020 in four academic databases- PubMed, ScienceDirect, Association for Computing Machinery(ACM) Digital Library, and the Association for Computational Linguistics(ACL) Anthology. We reviewed 7,556 publications; 38 met the inclusion criteria. This review identified: datasets having discharge summaries; NLP techniques along with some other data extraction processes, different feature extraction and embedding techniques. To measure the performance of classification methods, different evaluation metrics are used. Lastly, future research directions are provided to scholars who are interested in automated ICD code assignment. Efforts are still required to improve ICD code prediction accuracy, availability of large-scale de-identified clinical corpora with the latest version of the classification system. This can be a platform to guide and share knowledge with the less experienced coders and researchers.

More efficient manual review of automatically transcribed tabular data

Machine learning methods have proven useful in transcribing historical data. However, results from even highly accurate methods require manual verification and correction. Such manual review can be time-consuming and expensive, therefore the objective of this paper was to make it more efficient. Previously, we used machine learning to transcribe 2.3 million handwritten occupation codes from the Norwegian 1950 census with high accuracy (97%). We manually reviewed the 90,000 (3%) codes with the lowest model confidence. We allocated those 90,000 codes to human reviewers, who used our annotation tool to review the codes. To assess reviewer agreement, some codes were assigned to multiple reviewers. We then analyzed the review results to understand the relationship between accuracy improvements and effort. Additionally, we interviewed the reviewers to improve the workflow. The reviewers corrected 62.8% of the labels and agreed with the model label in 31.9% of cases. About 0.2% of the images could not be assigned a label, while for 5.1% the reviewers were uncertain, or they assigned an invalid label. 9,000 images were independently reviewed by multiple reviewers, resulting in an agreement of 86.43% and disagreement of 8.96%. We learned that our automatic transcription is biased towards the most frequent codes, with a higher degree of misclassification for the lowest frequency codes. Our interview findings show that the reviewers did internal quality control and found our custom tool well-suited. So, only one reviewer is needed, but they should report uncertainty.

VacancySBERT: the approach for representation of titles and skills for semantic similarity search in the recruitment domain

The paper focuses on deep learning semantic search algorithms applied in the HR domain. The aim of the article is developing a novel approach to training a Siamese network to link the skills mentioned in the job ad with the title. It has been shown that the title normalization process can be based either on classification or similarity comparison approaches. While classification algorithms strive to classify a sample into predefined set of categories, similarity search algorithms take a more flexible approach, since they are designed to find samples that are similar to a given query sample, without requiring pre-defined classes and labels. In this article semantic similarity search to find candidates for title normalization has been used. A pre-trained language model has been adapted while teaching it to match titles and skills based on co-occurrence information. For the purpose of this research fifty billion title-descriptions pairs had been collected for training the model and thirty three thousand title-description-normalized title triplets, where normalized job title was picked up manually by job ad creator for testing purposes. As baselines FastText, BERT, SentenceBert and JobBert have been used. As a metric of the accuracy of the designed algorithm is Recall in top one, five and ten model's suggestions. It has been shown that the novel training objective lets it achieve significant improvement in comparison to other generic and specific text encoders. Two settings with treating titles as standalone strings, and with included skills as additional features during inference have been used and the results have been compared in this article. Improvements by 10% and 21.5% have been achieved using VacancySBERT and VacancySBERT (with skills) respectively. The benchmark has been developed as open-source to foster further research in the area.

A Corpus for Detecting High-Context Medical Conditions in Intensive Care Patient Notes Focusing on Frequently Readmitted Patients

A crucial step within secondary analysis of electronic health records (EHRs) is to identify the patient cohort under investigation. While EHRs contain medical billing codes that aim to represent the conditions and treatments patients may have, much of the information is only present in the patient notes. Therefore, it is critical to develop robust algorithms to infer patients' conditions and treatments from their written notes. In this paper, we introduce a dataset for patient phenotyping, a task that is defined as the identification of whether a patient has a given medical condition (also referred to as clinical indication or phenotype) based on their patient note. Nursing Progress Notes and Discharge Summaries from the Intensive Care Unit of a large tertiary care hospital were manually annotated for the presence of several high-context phenotypes relevant to treatment and risk of re-hospitalization. This dataset contains 1102 Discharge Summaries and 1000 Nursing Progress Notes. Each Discharge Summary and Progress Note has been annotated by at least two expert human annotators (one clinical researcher and one resident physician). Annotated phenotypes include treatment non-adherence, chronic pain, advanced/metastatic cancer, as well as 10 other phenotypes. This dataset can be utilized for academic and industrial research in medicine and computer science, particularly within the field of medical natural language processing.

Evaluating Unsupervised Text Classification: Zero-shot and Similarity-based Approaches

Text classification of unseen classes is a challenging Natural Language Processing task and is mainly attempted using two different types of approaches. Similarity-based approaches attempt to classify instances based on similarities between text document representations and class description representations. Zero-shot text classification approaches aim to generalize knowledge gained from a training task by assigning appropriate labels of unknown classes to text documents. Although existing studies have already investigated individual approaches to these categories, the experiments in literature do not provide a consistent comparison. This paper addresses this gap by conducting a systematic evaluation of different similarity-based and zero-shot approaches for text classification of unseen classes. Different state-of-the-art approaches are benchmarked on four text classification datasets, including a new dataset from the medical domain. Additionally, novel SimCSE and SBERT-based baselines are proposed, as other baselines used in existing work yield weak classification results and are easily outperformed. Finally, the novel similarity-based Lbl2TransformerVec approach is presented, which outperforms previous state-of-the-art approaches in unsupervised text classification. Our experiments show that similarity-based approaches significantly outperform zero-shot approaches in most cases. Additionally, using SimCSE or SBERT embeddings instead of simpler text representations increases similarity-based classification results even further.

Generalization in Healthcare AI: Evaluation of a Clinical Large Language Model

Advances in large language models (LLMs) provide new opportunities in healthcare for improved patient care, clinical decision-making, and enhancement of physician and administrator workflows. However, the potential of these models importantly depends on their ability to generalize effectively across clinical environments and populations, a challenge often underestimated in early development. To better understand reasons for these challenges and inform mitigation approaches, we evaluated ClinicLLM, an LLM trained on [HOSPITAL]'s clinical notes, analyzing its performance on 30-day all-cause readmission prediction focusing on variability across hospitals and patient characteristics. We found poorer generalization particularly in hospitals with fewer samples, among patients with government and unspecified insurance, the elderly, and those with high comorbidities. To understand reasons for lack of generalization, we investigated sample sizes for fine-tuning, note content (number of words per note), patient characteristics (comorbidity level, age, insurance type, borough), and health system aspects (hospital, all-cause 30-day readmission, and mortality rates). We used descriptive statistics and supervised classification to identify features. We found that, along with sample size, patient age, number of comorbidities, and the number of words in notes are all important factors related to generalization. Finally, we compared local fine-tuning (hospital specific), instance-based augmented fine-tuning and cluster-based fine-tuning for improving generalization. Among these, local fine-tuning proved most effective, increasing AUC by 0.25% to 11.74% (most helpful in settings with limited data). Overall, this study provides new insights for enhancing the deployment of large language models in the societally important domain of healthcare, and improving their performance for broader populations.

Using clarification questions to improve software developers' Web search

Context: Recent research indicates that Web queries written by software developers are not very successful in retrieving relevant results, performing measurably worse compared to general purpose Web queries. Most approaches up to this point have addressed this problem with software engineering-specific automated query reformulation techniques, which work without developer involvement but are limited by the content of the original query. In other words, these techniques automatically improve the existing query but can not contribute new, previously unmentioned, concepts. Objective: In this paper, we propose a technique to guide software developers in manually improving their own Web search queries. We examine a conversational approach that follows unsuccessful queries with a clarification question aimed at eliciting additional query terms, thus providing to the developer a clear dimension along which the query could be improved. Methods: We describe a set of clarification questions derived from a corpus of software developer queries and a neural approach to recommending them for a newly issued query. Results: Our evaluation indicates that the recommendation technique is accurate, predicting a valid clarification question 80% of the time and outperforms simple baselines, as well as, state-of-the-art Learning To Rank (LTR) baselines. Conclusion: As shown in the experimental results, the described approach is capable at recommending appropriate clarification questions to software developers and considered useful by a sample of developers ranging from novices to experienced professionals.

Accuracy of a Vision-Language Model on Challenging Medical Cases

Background: General-purpose large language models that utilize both text and images have not been evaluated on a diverse array of challenging medical cases. Methods: Using 934 cases from the NEJM Image Challenge published between 2005 and 2023, we evaluated the accuracy of the recently released Generative Pre-trained Transformer 4 with Vision model (GPT-4V) compared to human respondents overall and stratified by question difficulty, image type, and skin tone. We further conducted a physician evaluation of GPT-4V on 69 NEJM clinicopathological conferences (CPCs). Analyses were conducted for models utilizing text alone, images alone, and both text and images. Results: GPT-4V achieved an overall accuracy of 61% (95% CI, 58 to 64%) compared to 49% (95% CI, 49 to 50%) for humans. GPT-4V outperformed humans at all levels of difficulty and disagreement, skin tones, and image types; the exception was radiographic images, where performance was equivalent between GPT-4V and human respondents. Longer, more informative captions were associated with improved performance for GPT-4V but similar performance for human respondents. GPT-4V included the correct diagnosis in its differential for 80% (95% CI, 68 to 88%) of CPCs when using text alone, compared to 58% (95% CI, 45 to 70%) of CPCs when using both images and text. Conclusions: GPT-4V outperformed human respondents on challenging medical cases and was able to synthesize information from both images and text, but performance deteriorated when images were added to highly informative text. Overall, our results suggest that multimodal AI models may be useful in medical diagnostic reasoning but that their accuracy may depend heavily on context.

Effective Transfer Learning for Identifying Similar Questions: Matching User Questions to COVID-19 FAQs

People increasingly search online for answers to their medical questions but the rate at which medical questions are asked online significantly exceeds the capacity of qualified people to answer them. This leaves many questions unanswered or inadequately answered. Many of these questions are not unique, and reliable identification of similar questions would enable more efficient and effective question answering schema. COVID-19 has only exacerbated this problem. Almost every government agency and healthcare organization has tried to meet the informational need of users by building online FAQs, but there is no way for people to ask their question and know if it is answered on one of these pages. While many research efforts have focused on the problem of general question similarity, these approaches do not generalize well to domains that require expert knowledge to determine semantic similarity, such as the medical domain. In this paper, we show how a double fine-tuning approach of pretraining a neural network on medical question-answer pairs followed by fine-tuning on medical question-question pairs is a particularly useful intermediate task for the ultimate goal of determining medical question similarity. While other pretraining tasks yield an accuracy below 78.7% on this task, our model achieves an accuracy of 82.6% with the same number of training examples, an accuracy of 80.0% with a much smaller training set, and an accuracy of 84.5% when the full corpus of medical question-answer data is used. We also describe a currently live system that uses the trained model to match user questions to COVID-related FAQs.

MEDEC: A Benchmark for Medical Error Detection and Correction in Clinical Notes

Several studies showed that Large Language Models (LLMs) can answer medical questions correctly, even outperforming the average human score in some medical exams. However, to our knowledge, no study has been conducted to assess the ability of language models to validate existing or generated medical text for correctness and consistency. In this paper, we introduce MEDEC (https://github.com/abachaa/MEDEC), the first publicly available benchmark for medical error detection and correction in clinical notes, covering five types of errors (Diagnosis, Management, Treatment, Pharmacotherapy, and Causal Organism). MEDEC consists of 3,848 clinical texts, including 488 clinical notes from three US hospital systems that were not previously seen by any LLM. The dataset has been used for the MEDIQA-CORR shared task to evaluate seventeen participating systems [Ben Abacha et al., 2024]. In this paper, we describe the data creation methods and we evaluate recent LLMs (e.g., o1-preview, GPT-4, Claude 3.5 Sonnet, and Gemini 2.0 Flash) for the tasks of detecting and correcting medical errors requiring both medical knowledge and reasoning capabilities. We also conducted a comparative study where two medical doctors performed the same task on the MEDEC test set. The results showed that MEDEC is a sufficiently challenging benchmark to assess the ability of models to validate existing or generated notes and to correct medical errors. We also found that although recent LLMs have a good performance in error detection and correction, they are still outperformed by medical doctors in these tasks. We discuss the potential factors behind this gap, the insights from our experiments, the limitations of current evaluation metrics, and share potential pointers for future research.

Large Language Models to Identify Social Determinants of Health in Electronic Health Records

Social determinants of health (SDoH) have an important impact on patient outcomes but are incompletely collected from the electronic health records (EHR). This study researched the ability of large language models to extract SDoH from free text in EHRs, where they are most commonly documented, and explored the role of synthetic clinical text for improving the extraction of these scarcely documented, yet extremely valuable, clinical data. 800 patient notes were annotated for SDoH categories, and several transformer-based models were evaluated. The study also experimented with synthetic data generation and assessed for algorithmic bias. Our best-performing models were fine-tuned Flan-T5 XL (macro-F1 0.71) for any SDoH, and Flan-T5 XXL (macro-F1 0.70). The benefit of augmenting fine-tuning with synthetic data varied across model architecture and size, with smaller Flan-T5 models (base and large) showing the greatest improvements in performance (delta F1 +0.12 to +0.23). Model performance was similar on the in-hospital system dataset but worse on the MIMIC-III dataset. Our best-performing fine-tuned models outperformed zero- and few-shot performance of ChatGPT-family models for both tasks. These fine-tuned models were less likely than ChatGPT to change their prediction when race/ethnicity and gender descriptors were added to the text, suggesting less algorithmic bias (p<0.05). At the patient-level, our models identified 93.8% of patients with adverse SDoH, while ICD-10 codes captured 2.0%. Our method can effectively extracted SDoH information from clinic notes, performing better compare to GPT zero- and few-shot settings. These models could enhance real-world evidence on SDoH and aid in identifying patients needing social support.

Question-Answering Model for Schizophrenia Symptoms and Their Impact on Daily Life using Mental Health Forums Data

In recent years, there is strong emphasis on mining medical data using machine learning techniques. A common problem is to obtain a noiseless set of textual documents, with a relevant content for the research question, and developing a Question Answering (QA) model for a specific medical field. The purpose of this paper is to present a new methodology for building a medical dataset and obtain a QA model for analysis of symptoms and impact on daily life for a specific disease domain. The ``Mental Health'' forum was used, a forum dedicated to people suffering from schizophrenia and different mental disorders. Relevant posts of active users, who regularly participate, were extrapolated providing a new method of obtaining low-bias content and without privacy issues. Furthermore, it is shown how to pre-process the dataset to convert it into a QA dataset. The Bidirectional Encoder Representations from Transformers (BERT), DistilBERT, RoBERTa, and BioBERT models were fine-tuned and evaluated via F1-Score, Exact Match, Precision and Recall. Accurate empirical experiments demonstrated the effectiveness of the proposed method for obtaining an accurate dataset for QA model implementation. By fine-tuning the BioBERT QA model, we achieved an F1 score of 0.885, showing a considerable improvement and outperforming the state-of-the-art model for mental disorders domain.

Exploring Multimodal Large Language Models for Radiology Report Error-checking

This paper proposes one of the first clinical applications of multimodal large language models (LLMs) as an assistant for radiologists to check errors in their reports. We created an evaluation dataset from two real-world radiology datasets (MIMIC-CXR and IU-Xray), with 1,000 subsampled reports each. A subset of original reports was modified to contain synthetic errors by introducing various type of mistakes. The evaluation contained two difficulty levels: SIMPLE for binary error-checking and COMPLEX for identifying error types. LLaVA (Large Language and Visual Assistant) variant models, including our instruction-tuned model, were used for the evaluation. Additionally, a domain expert evaluation was conducted on a small test set. At the SIMPLE level, the LLaVA v1.5 model outperformed other publicly available models. Instruction tuning significantly enhanced performance by 47.4% and 25.4% on MIMIC-CXR and IU-Xray data, respectively. The model also surpassed the domain experts accuracy in the MIMIC-CXR dataset by 1.67%. Notably, among the subsets (N=21) of the test set where a clinician did not achieve the correct conclusion, the LLaVA ensemble mode correctly identified 71.4% of these cases. This study marks a promising step toward utilizing multi-modal LLMs to enhance diagnostic accuracy in radiology. The ensemble model demonstrated comparable performance to clinicians, even capturing errors overlooked by humans. Nevertheless, future work is needed to improve the model ability to identify the types of inconsistency.

Modeling of learning curves with applications to pos tagging

An algorithm to estimate the evolution of learning curves on the whole of a training data base, based on the results obtained from a portion and using a functional strategy, is introduced. We approximate iteratively the sought value at the desired time, independently of the learning technique used and once a point in the process, called prediction level, has been passed. The proposal proves to be formally correct with respect to our working hypotheses and includes a reliable proximity condition. This allows the user to fix a convergence threshold with respect to the accuracy finally achievable, which extends the concept of stopping criterion and seems to be effective even in the presence of distorting observations. Our aim is to evaluate the training effort, supporting decision making in order to reduce the need for both human and computational resources during the learning process. The proposal is of interest in at least three operational procedures. The first is the anticipation of accuracy gain, with the purpose of measuring how much work is needed to achieve a certain degree of performance. The second relates the comparison of efficiency between systems at training time, with the objective of completing this task only for the one that best suits our requirements. The prediction of accuracy is also a valuable item of information for customizing systems, since we can estimate in advance the impact of settings on both the performance and the development costs. Using the generation of part-of-speech taggers as an example application, the experimental results are consistent with our expectations.

Natural Language Processing in Electronic Health Records in Relation to Healthcare Decision-making: A Systematic Review

Background: Natural Language Processing (NLP) is widely used to extract clinical insights from Electronic Health Records (EHRs). However, the lack of annotated data, automated tools, and other challenges hinder the full utilisation of NLP for EHRs. Various Machine Learning (ML), Deep Learning (DL) and NLP techniques are studied and compared to understand the limitations and opportunities in this space comprehensively. Methodology: After screening 261 articles from 11 databases, we included 127 papers for full-text review covering seven categories of articles: 1) medical note classification, 2) clinical entity recognition, 3) text summarisation, 4) deep learning (DL) and transfer learning architecture, 5) information extraction, 6) Medical language translation and 7) other NLP applications. This study follows the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Result and Discussion: EHR was the most commonly used data type among the selected articles, and the datasets were primarily unstructured. Various ML and DL methods were used, with prediction or classification being the most common application of ML or DL. The most common use cases were: the International Classification of Diseases, Ninth Revision (ICD-9) classification, clinical note analysis, and named entity recognition (NER) for clinical descriptions and research on psychiatric disorders. Conclusion: We find that the adopted ML models were not adequately assessed. In addition, the data imbalance problem is quite important, yet we must find techniques to address this underlining problem. Future studies should address key limitations in studies, primarily identifying Lupus Nephritis, Suicide Attempts, perinatal self-harmed and ICD-9 classification.

A Supervised Machine Learning Approach for Assessing Grant Peer Review Reports

Peer review in grant evaluation informs funding decisions, but the contents of peer review reports are rarely analyzed. In this work, we develop a thoroughly tested pipeline to analyze the texts of grant peer review reports using methods from applied Natural Language Processing (NLP) and machine learning. We start by developing twelve categories reflecting content of grant peer review reports that are of interest to research funders. This is followed by multiple human annotators' iterative annotation of these categories in a novel text corpus of grant peer review reports submitted to the Swiss National Science Foundation. After validating the human annotation, we use the annotated texts to fine-tune pre-trained transformer models to classify these categories at scale, while conducting several robustness and validation checks. Our results show that many categories can be reliably identified by human annotators and machine learning approaches. However, the choice of text classification approach considerably influences the classification performance. We also find a high correspondence between out-of-sample classification performance and human annotators' perceived difficulty in identifying categories. Our results and publicly available fine-tuned transformer models will allow researchers and research funders and anybody interested in peer review to examine and report on the contents of these reports in a structured manner. Ultimately, we hope our approach can contribute to ensuring the quality and trustworthiness of grant peer review.

T2Ranking: A large-scale Chinese Benchmark for Passage Ranking

Passage ranking involves two stages: passage retrieval and passage re-ranking, which are important and challenging topics for both academics and industries in the area of Information Retrieval (IR). However, the commonly-used datasets for passage ranking usually focus on the English language. For non-English scenarios, such as Chinese, the existing datasets are limited in terms of data scale, fine-grained relevance annotation and false negative issues. To address this problem, we introduce T2Ranking, a large-scale Chinese benchmark for passage ranking. T2Ranking comprises more than 300K queries and over 2M unique passages from real-world search engines. Expert annotators are recruited to provide 4-level graded relevance scores (fine-grained) for query-passage pairs instead of binary relevance judgments (coarse-grained). To ease the false negative issues, more passages with higher diversities are considered when performing relevance annotations, especially in the test set, to ensure a more accurate evaluation. Apart from the textual query and passage data, other auxiliary resources are also provided, such as query types and XML files of documents which passages are generated from, to facilitate further studies. To evaluate the dataset, commonly used ranking models are implemented and tested on T2Ranking as baselines. The experimental results show that T2Ranking is challenging and there is still scope for improvement. The full data and all codes are available at https://github.com/THUIR/T2Ranking/

Review GIDE -- Restaurant Review Gastrointestinal Illness Detection and Extraction with Large Language Models

Foodborne gastrointestinal (GI) illness is a common cause of ill health in the UK. However, many cases do not interact with the healthcare system, posing significant challenges for traditional surveillance methods. The growth of publicly available online restaurant reviews and advancements in large language models (LLMs) present potential opportunities to extend disease surveillance by identifying public reports of GI illness. In this study, we introduce a novel annotation schema, developed with experts in GI illness, applied to the Yelp Open Dataset of reviews. Our annotations extend beyond binary disease detection, to include detailed extraction of information on symptoms and foods. We evaluate the performance of open-weight LLMs across these three tasks: GI illness detection, symptom extraction, and food extraction. We compare this performance to RoBERTa-based classification models fine-tuned specifically for these tasks. Our results show that using prompt-based approaches, LLMs achieve micro-F1 scores of over 90% for all three of our tasks. Using prompting alone, we achieve micro-F1 scores that exceed those of smaller fine-tuned models. We further demonstrate the robustness of LLMs in GI illness detection across three bias-focused experiments. Our results suggest that publicly available review text and LLMs offer substantial potential for public health surveillance of GI illness by enabling highly effective extraction of key information. While LLMs appear to exhibit minimal bias in processing, the inherent limitations of restaurant review data highlight the need for cautious interpretation of results.

Are Neural Ranking Models Robust?

Recently, we have witnessed the bloom of neural ranking models in the information retrieval (IR) field. So far, much effort has been devoted to developing effective neural ranking models that can generalize well on new data. There has been less attention paid to the robustness perspective. Unlike the effectiveness which is about the average performance of a system under normal purpose, robustness cares more about the system performance in the worst case or under malicious operations instead. When a new technique enters into the real-world application, it is critical to know not only how it works in average, but also how would it behave in abnormal situations. So we raise the question in this work: Are neural ranking models robust? To answer this question, firstly, we need to clarify what we refer to when we talk about the robustness of ranking models in IR. We show that robustness is actually a multi-dimensional concept and there are three ways to define it in IR: 1) The performance variance under the independent and identically distributed (I.I.D.) setting; 2) The out-of-distribution (OOD) generalizability; and 3) The defensive ability against adversarial operations. The latter two definitions can be further specified into two different perspectives respectively, leading to 5 robustness tasks in total. Based on this taxonomy, we build corresponding benchmark datasets, design empirical experiments, and systematically analyze the robustness of several representative neural ranking models against traditional probabilistic ranking models and learning-to-rank (LTR) models. The empirical results show that there is no simple answer to our question. While neural ranking models are less robust against other IR models in most cases, some of them can still win 1 out of 5 tasks. This is the first comprehensive study on the robustness of neural ranking models.

Comparing Rule-Based and Deep Learning Models for Patient Phenotyping

Objective: We investigate whether deep learning techniques for natural language processing (NLP) can be used efficiently for patient phenotyping. Patient phenotyping is a classification task for determining whether a patient has a medical condition, and is a crucial part of secondary analysis of healthcare data. We assess the performance of deep learning algorithms and compare them with classical NLP approaches. Materials and Methods: We compare convolutional neural networks (CNNs), n-gram models, and approaches based on cTAKES that extract pre-defined medical concepts from clinical notes and use them to predict patient phenotypes. The performance is tested on 10 different phenotyping tasks using 1,610 discharge summaries extracted from the MIMIC-III database. Results: CNNs outperform other phenotyping algorithms in all 10 tasks. The average F1-score of our model is 76 (PPV of 83, and sensitivity of 71) with our model having an F1-score up to 37 points higher than alternative approaches. We additionally assess the interpretability of our model by presenting a method that extracts the most salient phrases for a particular prediction. Conclusion: We show that NLP methods based on deep learning improve the performance of patient phenotyping. Our CNN-based algorithm automatically learns the phrases associated with each patient phenotype. As such, it reduces the annotation complexity for clinical domain experts, who are normally required to develop task-specific annotation rules and identify relevant phrases. Our method performs well in terms of both performance and interpretability, which indicates that deep learning is an effective approach to patient phenotyping based on clinicians' notes.

Using the Tsetlin Machine to Learn Human-Interpretable Rules for High-Accuracy Text Categorization with Medical Applications

Medical applications challenge today's text categorization techniques by demanding both high accuracy and ease-of-interpretation. Although deep learning has provided a leap ahead in accuracy, this leap comes at the sacrifice of interpretability. To address this accuracy-interpretability challenge, we here introduce, for the first time, a text categorization approach that leverages the recently introduced Tsetlin Machine. In all brevity, we represent the terms of a text as propositional variables. From these, we capture categories using simple propositional formulae, such as: if "rash" and "reaction" and "penicillin" then Allergy. The Tsetlin Machine learns these formulae from a labelled text, utilizing conjunctive clauses to represent the particular facets of each category. Indeed, even the absence of terms (negated features) can be used for categorization purposes. Our empirical comparison with Na\"ive Bayes, decision trees, linear support vector machines (SVMs), random forest, long short-term memory (LSTM) neural networks, and other techniques, is quite conclusive. The Tsetlin Machine either performs on par with or outperforms all of the evaluated methods on both the 20 Newsgroups and IMDb datasets, as well as on a non-public clinical dataset. On average, the Tsetlin Machine delivers the best recall and precision scores across the datasets. Finally, our GPU implementation of the Tsetlin Machine executes 5 to 15 times faster than the CPU implementation, depending on the dataset. We thus believe that our novel approach can have a significant impact on a wide range of text analysis applications, forming a promising starting point for deeper natural language understanding with the Tsetlin Machine.

The Critique of Critique

Critique, as a natural language description for assessing the quality of model-generated content, has been proven to play an essential role in the training, evaluation, and refinement of Large Language Models (LLMs). However, there is a lack of principled understanding in evaluating the quality of the critique itself. In this paper, we pioneer the critique of critique, termed MetaCritique, which is a framework to evaluate the critique from two aspects, i.e., factuality as precision score and comprehensiveness as recall score. We calculate the harmonic mean of precision and recall as the overall rating called F1 score. To obtain a reliable evaluation outcome, we propose Atomic Information Units (AIUs), which describe the critique in a more fine-grained manner. MetaCritique takes each AIU into account and aggregates each AIU's judgment for the overall score. Moreover, given the evaluation process involves intricate reasoning, our MetaCritique provides a natural language rationale to support each judgment. We construct a meta-evaluation dataset containing 300 critiques (2653 AIUs) across four tasks (question answering, reasoning, entailment, and summarization), and we conduct a comparative study to demonstrate the feasibility and effectiveness. Experiments also show superior critique judged by MetaCritique leads to better refinement, indicating generative artificial intelligence indeed has the potential to be significantly advanced with our MetaCritique. We will release relevant code and meta-evaluation datasets at https://github.com/GAIR-NLP/MetaCritique.

Language Models And A Second Opinion Use Case: The Pocket Professional

This research tests the role of Large Language Models (LLMs) as formal second opinion tools in professional decision-making, particularly focusing on complex medical cases where even experienced physicians seek peer consultation. The work analyzed 183 challenging medical cases from Medscape over a 20-month period, testing multiple LLMs' performance against crowd-sourced physician responses. A key finding was the high overall score possible in the latest foundational models (>80% accuracy compared to consensus opinion), which exceeds most human metrics reported on the same clinical cases (450 pages of patient profiles, test results). The study rates the LLMs' performance disparity between straightforward cases (>81% accuracy) and complex scenarios (43% accuracy), particularly in these cases generating substantial debate among human physicians. The research demonstrates that LLMs may be valuable as generators of comprehensive differential diagnoses rather than as primary diagnostic tools, potentially helping to counter cognitive biases in clinical decision-making, reduce cognitive loads, and thus remove some sources of medical error. The inclusion of a second comparative legal dataset (Supreme Court cases, N=21) provides added empirical context to the AI use to foster second opinions, though these legal challenges proved considerably easier for LLMs to analyze. In addition to the original contributions of empirical evidence for LLM accuracy, the research aggregated a novel benchmark for others to score highly contested question and answer reliability between both LLMs and disagreeing human practitioners. These results suggest that the optimal deployment of LLMs in professional settings may differ substantially from current approaches that emphasize automation of routine tasks.

Enhancing Large Language Models with Domain-specific Retrieval Augment Generation: A Case Study on Long-form Consumer Health Question Answering in Ophthalmology

Despite the potential of Large Language Models (LLMs) in medicine, they may generate responses lacking supporting evidence or based on hallucinated evidence. While Retrieval Augment Generation (RAG) is popular to address this issue, few studies implemented and evaluated RAG in downstream domain-specific applications. We developed a RAG pipeline with 70,000 ophthalmology-specific documents that retrieve relevant documents to augment LLMs during inference time. In a case study on long-form consumer health questions, we systematically evaluated the responses including over 500 references of LLMs with and without RAG on 100 questions with 10 healthcare professionals. The evaluation focuses on factuality of evidence, selection and ranking of evidence, attribution of evidence, and answer accuracy and completeness. LLMs without RAG provided 252 references in total. Of which, 45.3% hallucinated, 34.1% consisted of minor errors, and 20.6% were correct. In contrast, LLMs with RAG significantly improved accuracy (54.5% being correct) and reduced error rates (18.8% with minor hallucinations and 26.7% with errors). 62.5% of the top 10 documents retrieved by RAG were selected as the top references in the LLM response, with an average ranking of 4.9. The use of RAG also improved evidence attribution (increasing from 1.85 to 2.49 on a 5-point scale, P<0.001), albeit with slight decreases in accuracy (from 3.52 to 3.23, P=0.03) and completeness (from 3.47 to 3.27, P=0.17). The results demonstrate that LLMs frequently exhibited hallucinated and erroneous evidence in the responses, raising concerns for downstream applications in the medical domain. RAG substantially reduced the proportion of such evidence but encountered challenges.

On the State of German (Abstractive) Text Summarization

With recent advancements in the area of Natural Language Processing, the focus is slowly shifting from a purely English-centric view towards more language-specific solutions, including German. Especially practical for businesses to analyze their growing amount of textual data are text summarization systems, which transform long input documents into compressed and more digestible summary texts. In this work, we assess the particular landscape of German abstractive text summarization and investigate the reasons why practically useful solutions for abstractive text summarization are still absent in industry. Our focus is two-fold, analyzing a) training resources, and b) publicly available summarization systems. We are able to show that popular existing datasets exhibit crucial flaws in their assumptions about the original sources, which frequently leads to detrimental effects on system generalization and evaluation biases. We confirm that for the most popular training dataset, MLSUM, over 50% of the training set is unsuitable for abstractive summarization purposes. Furthermore, available systems frequently fail to compare to simple baselines, and ignore more effective and efficient extractive summarization approaches. We attribute poor evaluation quality to a variety of different factors, which are investigated in more detail in this work: A lack of qualitative (and diverse) gold data considered for training, understudied (and untreated) positional biases in some of the existing datasets, and the lack of easily accessible and streamlined pre-processing strategies or analysis tools. We provide a comprehensive assessment of available models on the cleaned datasets, and find that this can lead to a reduction of more than 20 ROUGE-1 points during evaluation. The code for dataset filtering and reproducing results can be found online at https://github.com/dennlinger/summaries

Lawma: The Power of Specialization for Legal Tasks

Annotation and classification of legal text are central components of empirical legal research. Traditionally, these tasks are often delegated to trained research assistants. Motivated by the advances in language modeling, empirical legal scholars are increasingly turning to prompting commercial models, hoping that it will alleviate the significant cost of human annotation. Despite growing use, our understanding of how to best utilize large language models for legal tasks remains limited. We conduct a comprehensive study of 260 legal text classification tasks, nearly all new to the machine learning community. Starting from GPT-4 as a baseline, we show that it has non-trivial but highly varied zero-shot accuracy, often exhibiting performance that may be insufficient for legal work. We then demonstrate that a lightly fine-tuned Llama 3 model vastly outperforms GPT-4 on almost all tasks, typically by double-digit percentage points. We find that larger models respond better to fine-tuning than smaller models. A few tens to hundreds of examples suffice to achieve high classification accuracy. Notably, we can fine-tune a single model on all 260 tasks simultaneously at a small loss in accuracy relative to having a separate model for each task. Our work points to a viable alternative to the predominant practice of prompting commercial models. For concrete legal tasks with some available labeled data, researchers are better off using a fine-tuned open-source model.

Revisiting the Gold Standard: Grounding Summarization Evaluation with Robust Human Evaluation

Human evaluation is the foundation upon which the evaluation of both summarization systems and automatic metrics rests. However, existing human evaluation studies for summarization either exhibit a low inter-annotator agreement or have insufficient scale, and an in-depth analysis of human evaluation is lacking. Therefore, we address the shortcomings of existing summarization evaluation along the following axes: (1) We propose a modified summarization salience protocol, Atomic Content Units (ACUs), which is based on fine-grained semantic units and allows for a high inter-annotator agreement. (2) We curate the Robust Summarization Evaluation (RoSE) benchmark, a large human evaluation dataset consisting of 22,000 summary-level annotations over 28 top-performing systems on three datasets. (3) We conduct a comparative study of four human evaluation protocols, underscoring potential confounding factors in evaluation setups. (4) We evaluate 50 automatic metrics and their variants using the collected human annotations across evaluation protocols and demonstrate how our benchmark leads to more statistically stable and significant results. The metrics we benchmarked include recent methods based on large language models (LLMs), GPTScore and G-Eval. Furthermore, our findings have important implications for evaluating LLMs, as we show that LLMs adjusted by human feedback (e.g., GPT-3.5) may overfit unconstrained human evaluation, which is affected by the annotators' prior, input-agnostic preferences, calling for more robust, targeted evaluation methods.

Automated Coding of Under-Studied Medical Concept Domains: Linking Physical Activity Reports to the International Classification of Functioning, Disability, and Health

Linking clinical narratives to standardized vocabularies and coding systems is a key component of unlocking the information in medical text for analysis. However, many domains of medical concepts lack well-developed terminologies that can support effective coding of medical text. We present a framework for developing natural language processing (NLP) technologies for automated coding of under-studied types of medical information, and demonstrate its applicability via a case study on physical mobility function. Mobility is a component of many health measures, from post-acute care and surgical outcomes to chronic frailty and disability, and is coded in the International Classification of Functioning, Disability, and Health (ICF). However, mobility and other types of functional activity remain under-studied in medical informatics, and neither the ICF nor commonly-used medical terminologies capture functional status terminology in practice. We investigated two data-driven paradigms, classification and candidate selection, to link narrative observations of mobility to standardized ICF codes, using a dataset of clinical narratives from physical therapy encounters. Recent advances in language modeling and word embedding were used as features for established machine learning models and a novel deep learning approach, achieving a macro F-1 score of 84% on linking mobility activity reports to ICF codes. Both classification and candidate selection approaches present distinct strengths for automated coding in under-studied domains, and we highlight that the combination of (i) a small annotated data set; (ii) expert definitions of codes of interest; and (iii) a representative text corpus is sufficient to produce high-performing automated coding systems. This study has implications for the ongoing growth of NLP tools for a variety of specialized applications in clinical care and research.

SORRY-Bench: Systematically Evaluating Large Language Model Safety Refusal Behaviors

Evaluating aligned large language models' (LLMs) ability to recognize and reject unsafe user requests is crucial for safe, policy-compliant deployments. Existing evaluation efforts, however, face three limitations that we address with SORRY-Bench, our proposed benchmark. First, existing methods often use coarse-grained taxonomies of unsafe topics, and are over-representing some fine-grained topics. For example, among the ten existing datasets that we evaluated, tests for refusals of self-harm instructions are over 3x less represented than tests for fraudulent activities. SORRY-Bench improves on this by using a fine-grained taxonomy of 45 potentially unsafe topics, and 450 class-balanced unsafe instructions, compiled through human-in-the-loop methods. Second, linguistic characteristics and formatting of prompts are often overlooked, like different languages, dialects, and more -- which are only implicitly considered in many evaluations. We supplement SORRY-Bench with 20 diverse linguistic augmentations to systematically examine these effects. Third, existing evaluations rely on large LLMs (e.g., GPT-4) for evaluation, which can be computationally expensive. We investigate design choices for creating a fast, accurate automated safety evaluator. By collecting 7K+ human annotations and conducting a meta-evaluation of diverse LLM-as-a-judge designs, we show that fine-tuned 7B LLMs can achieve accuracy comparable to GPT-4 scale LLMs, with lower computational cost. Putting these together, we evaluate over 40 proprietary and open-source LLMs on SORRY-Bench, analyzing their distinctive refusal behaviors. We hope our effort provides a building block for systematic evaluations of LLMs' safety refusal capabilities, in a balanced, granular, and efficient manner.

A Text Classification Framework for Simple and Effective Early Depression Detection Over Social Media Streams

With the rise of the Internet, there is a growing need to build intelligent systems that are capable of efficiently dealing with early risk detection (ERD) problems on social media, such as early depression detection, early rumor detection or identification of sexual predators. These systems, nowadays mostly based on machine learning techniques, must be able to deal with data streams since users provide their data over time. In addition, these systems must be able to decide when the processed data is sufficient to actually classify users. Moreover, since ERD tasks involve risky decisions by which people's lives could be affected, such systems must also be able to justify their decisions. However, most standard and state-of-the-art supervised machine learning models are not well suited to deal with this scenario. This is due to the fact that they either act as black boxes or do not support incremental classification/learning. In this paper we introduce SS3, a novel supervised learning model for text classification that naturally supports these aspects. SS3 was designed to be used as a general framework to deal with ERD problems. We evaluated our model on the CLEF's eRisk2017 pilot task on early depression detection. Most of the 30 contributions submitted to this competition used state-of-the-art methods. Experimental results show that our classifier was able to outperform these models and standard classifiers, despite being less computationally expensive and having the ability to explain its rationale.

How Discriminative Are Your Qrels? How To Study the Statistical Significance of Document Adjudication Methods

Creating test collections for offline retrieval evaluation requires human effort to judge documents' relevance. This expensive activity motivated much work in developing methods for constructing benchmarks with fewer assessment costs. In this respect, adjudication methods actively decide both which documents and the order in which experts review them, in order to better exploit the assessment budget or to lower it. Researchers evaluate the quality of those methods by measuring the correlation between the known gold ranking of systems under the full collection and the observed ranking of systems under the lower-cost one. This traditional analysis ignores whether and how the low-cost judgements impact on the statistically significant differences among systems with respect to the full collection. We fill this void by proposing a novel methodology to evaluate how the low-cost adjudication methods preserve the pairwise significant differences between systems as the full collection. In other terms, while traditional approaches look for stability in answering the question "is system A better than system B?", our proposed approach looks for stability in answering the question "is system A significantly better than system B?", which is the ultimate questions researchers need to answer to guarantee the generalisability of their results. Among other results, we found that the best methods in terms of ranking of systems correlation do not always match those preserving statistical significance.

Yet Another ICU Benchmark: A Flexible Multi-Center Framework for Clinical ML

Medical applications of machine learning (ML) have experienced a surge in popularity in recent years. The intensive care unit (ICU) is a natural habitat for ML given the abundance of available data from electronic health records. Models have been proposed to address numerous ICU prediction tasks like the early detection of complications. While authors frequently report state-of-the-art performance, it is challenging to verify claims of superiority. Datasets and code are not always published, and cohort definitions, preprocessing pipelines, and training setups are difficult to reproduce. This work introduces Yet Another ICU Benchmark (YAIB), a modular framework that allows researchers to define reproducible and comparable clinical ML experiments; we offer an end-to-end solution from cohort definition to model evaluation. The framework natively supports most open-access ICU datasets (MIMIC III/IV, eICU, HiRID, AUMCdb) and is easily adaptable to future ICU datasets. Combined with a transparent preprocessing pipeline and extensible training code for multiple ML and deep learning models, YAIB enables unified model development. Our benchmark comes with five predefined established prediction tasks (mortality, acute kidney injury, sepsis, kidney function, and length of stay) developed in collaboration with clinicians. Adding further tasks is straightforward by design. Using YAIB, we demonstrate that the choice of dataset, cohort definition, and preprocessing have a major impact on the prediction performance - often more so than model class - indicating an urgent need for YAIB as a holistic benchmarking tool. We provide our work to the clinical ML community to accelerate method development and enable real-world clinical implementations. Software Repository: https://github.com/rvandewater/YAIB.

Predicting the duration of traffic incidents for Sydney greater metropolitan area using machine learning methods

This research presents a comprehensive approach to predicting the duration of traffic incidents and classifying them as short-term or long-term across the Sydney Metropolitan Area. Leveraging a dataset that encompasses detailed records of traffic incidents, road network characteristics, and socio-economic indicators, we train and evaluate a variety of advanced machine learning models including Gradient Boosted Decision Trees (GBDT), Random Forest, LightGBM, and XGBoost. The models are assessed using Root Mean Square Error (RMSE) for regression tasks and F1 score for classification tasks. Our experimental results demonstrate that XGBoost and LightGBM outperform conventional models with XGBoost achieving the lowest RMSE of 33.7 for predicting incident duration and highest classification F1 score of 0.62 for a 30-minute duration threshold. For classification, the 30-minute threshold balances performance with 70.84% short-term duration classification accuracy and 62.72% long-term duration classification accuracy. Feature importance analysis, employing both tree split counts and SHAP values, identifies the number of affected lanes, traffic volume, and types of primary and secondary vehicles as the most influential features. The proposed methodology not only achieves high predictive accuracy but also provides stakeholders with vital insights into factors contributing to incident durations. These insights enable more informed decision-making for traffic management and response strategies. The code is available by the link: https://github.com/Future-Mobility-Lab/SydneyIncidents

LongHealth: A Question Answering Benchmark with Long Clinical Documents

Background: Recent advancements in large language models (LLMs) offer potential benefits in healthcare, particularly in processing extensive patient records. However, existing benchmarks do not fully assess LLMs' capability in handling real-world, lengthy clinical data. Methods: We present the LongHealth benchmark, comprising 20 detailed fictional patient cases across various diseases, with each case containing 5,090 to 6,754 words. The benchmark challenges LLMs with 400 multiple-choice questions in three categories: information extraction, negation, and sorting, challenging LLMs to extract and interpret information from large clinical documents. Results: We evaluated nine open-source LLMs with a minimum of 16,000 tokens and also included OpenAI's proprietary and cost-efficient GPT-3.5 Turbo for comparison. The highest accuracy was observed for Mixtral-8x7B-Instruct-v0.1, particularly in tasks focused on information retrieval from single and multiple patient documents. However, all models struggled significantly in tasks requiring the identification of missing information, highlighting a critical area for improvement in clinical data interpretation. Conclusion: While LLMs show considerable potential for processing long clinical documents, their current accuracy levels are insufficient for reliable clinical use, especially in scenarios requiring the identification of missing information. The LongHealth benchmark provides a more realistic assessment of LLMs in a healthcare setting and highlights the need for further model refinement for safe and effective clinical application. We make the benchmark and evaluation code publicly available.

Clinical Text Summarization: Adapting Large Language Models Can Outperform Human Experts

Sifting through vast textual data and summarizing key information imposes a substantial burden on how clinicians allocate their time. Although large language models (LLMs) have shown immense promise in natural language processing (NLP) tasks, their efficacy across diverse clinical summarization tasks has not yet been rigorously examined. In this work, we employ domain adaptation methods on eight LLMs, spanning six datasets and four distinct summarization tasks: radiology reports, patient questions, progress notes, and doctor-patient dialogue. Our thorough quantitative assessment reveals trade-offs between models and adaptation methods in addition to instances where recent advances in LLMs may not lead to improved results. Further, in a clinical reader study with six physicians, we depict that summaries from the best adapted LLM are preferable to human summaries in terms of completeness and correctness. Our ensuing qualitative analysis delineates mutual challenges faced by both LLMs and human experts. Lastly, we correlate traditional quantitative NLP metrics with reader study scores to enhance our understanding of how these metrics align with physician preferences. Our research marks the first evidence of LLMs outperforming human experts in clinical text summarization across multiple tasks. This implies that integrating LLMs into clinical workflows could alleviate documentation burden, empowering clinicians to focus more on personalized patient care and other irreplaceable human aspects of medicine.

Enhancing Health Information Retrieval with RAG by Prioritizing Topical Relevance and Factual Accuracy

The exponential surge in online health information, coupled with its increasing use by non-experts, highlights the pressing need for advanced Health Information Retrieval models that consider not only topical relevance but also the factual accuracy of the retrieved information, given the potential risks associated with health misinformation. To this aim, this paper introduces a solution driven by Retrieval-Augmented Generation (RAG), which leverages the capabilities of generative Large Language Models (LLMs) to enhance the retrieval of health-related documents grounded in scientific evidence. In particular, we propose a three-stage model: in the first stage, the user's query is employed to retrieve topically relevant passages with associated references from a knowledge base constituted by scientific literature. In the second stage, these passages, alongside the initial query, are processed by LLMs to generate a contextually relevant rich text (GenText). In the last stage, the documents to be retrieved are evaluated and ranked both from the point of view of topical relevance and factual accuracy by means of their comparison with GenText, either through stance detection or semantic similarity. In addition to calculating factual accuracy, GenText can offer a layer of explainability for it, aiding users in understanding the reasoning behind the retrieval. Experimental evaluation of our model on benchmark datasets and against baseline models demonstrates its effectiveness in enhancing the retrieval of both topically relevant and factually accurate health information, thus presenting a significant step forward in the health misinformation mitigation problem.

Detecting automatically the layout of clinical documents to enhance the performances of downstream natural language processing

Objective:Develop and validate an algorithm for analyzing the layout of PDF clinical documents to improve the performance of downstream natural language processing tasks. Materials and Methods: We designed an algorithm to process clinical PDF documents and extract only clinically relevant text. The algorithm consists of several steps: initial text extraction using a PDF parser, followed by classification into categories such as body text, left notes, and footers using a Transformer deep neural network architecture, and finally an aggregation step to compile the lines of a given label in the text. We evaluated the technical performance of the body text extraction algorithm by applying it to a random sample of documents that were annotated. Medical performance was evaluated by examining the extraction of medical concepts of interest from the text in their respective sections. Finally, we tested an end-to-end system on a medical use case of automatic detection of acute infection described in the hospital report. Results:Our algorithm achieved per-line precision, recall, and F1 score of 98.4, 97.0, and 97.7, respectively, for body line extraction. The precision, recall, and F1 score per document for the acute infection detection algorithm were 82.54 (95CI 72.86-91.60), 85.24 (95CI 76.61-93.70), 83.87 (95CI 76, 92-90.08) with exploitation of the results of the advanced body extraction algorithm, respectively. Conclusion:We have developed and validated a system for extracting body text from clinical documents in PDF format by identifying their layout. We were able to demonstrate that this preprocessing allowed us to obtain better performances for a common downstream task, i.e., the extraction of medical concepts in their respective sections, thus proving the interest of this method on a clinical use case.

Evaluating Correctness and Faithfulness of Instruction-Following Models for Question Answering

Retriever-augmented instruction-following models are attractive alternatives to fine-tuned approaches for information-seeking tasks such as question answering (QA). By simply prepending retrieved documents in its input along with an instruction, these models can be adapted to various information domains and tasks without additional fine-tuning. While the model responses tend to be natural and fluent, the additional verbosity makes traditional QA evaluation metrics such as exact match (EM) and F1 unreliable for accurately quantifying model performance. In this work, we investigate the performance of instruction-following models across three information-seeking QA tasks. We use both automatic and human evaluation to evaluate these models along two dimensions: 1) how well they satisfy the user's information need (correctness), and 2) whether they produce a response based on the provided knowledge (faithfulness). Guided by human evaluation and analysis, we highlight the shortcomings of traditional metrics for both correctness and faithfulness. We then propose simple token-overlap based and model-based metrics that reflect the true performance of these models. Our analysis reveals that instruction-following models are competitive, and sometimes even outperform fine-tuned models for correctness. However, these models struggle to stick to the provided knowledge and often hallucinate in their responses. We hope our work encourages a more holistic evaluation of instruction-following models for QA. Our code and data is available at https://github.com/McGill-NLP/instruct-qa

A Closer Look at AUROC and AUPRC under Class Imbalance

In machine learning (ML), a widespread adage is that the area under the precision-recall curve (AUPRC) is a superior metric for model comparison to the area under the receiver operating characteristic (AUROC) for binary classification tasks with class imbalance. This paper challenges this notion through novel mathematical analysis, illustrating that AUROC and AUPRC can be concisely related in probabilistic terms. We demonstrate that AUPRC, contrary to popular belief, is not superior in cases of class imbalance and might even be a harmful metric, given its inclination to unduly favor model improvements in subpopulations with more frequent positive labels. This bias can inadvertently heighten algorithmic disparities. Prompted by these insights, a thorough review of existing ML literature was conducted, utilizing large language models to analyze over 1.5 million papers from arXiv. Our investigation focused on the prevalence and substantiation of the purported AUPRC superiority. The results expose a significant deficit in empirical backing and a trend of misattributions that have fuelled the widespread acceptance of AUPRC's supposed advantages. Our findings represent a dual contribution: a significant technical advancement in understanding metric behaviors and a stark warning about unchecked assumptions in the ML community. All experiments are accessible at https://github.com/mmcdermott/AUC_is_all_you_need.

The Validity of Evaluation Results: Assessing Concurrence Across Compositionality Benchmarks

NLP models have progressed drastically in recent years, according to numerous datasets proposed to evaluate performance. Questions remain, however, about how particular dataset design choices may impact the conclusions we draw about model capabilities. In this work, we investigate this question in the domain of compositional generalization. We examine the performance of six modeling approaches across 4 datasets, split according to 8 compositional splitting strategies, ranking models by 18 compositional generalization splits in total. Our results show that: i) the datasets, although all designed to evaluate compositional generalization, rank modeling approaches differently; ii) datasets generated by humans align better with each other than they with synthetic datasets, or than synthetic datasets among themselves; iii) generally, whether datasets are sampled from the same source is more predictive of the resulting model ranking than whether they maintain the same interpretation of compositionality; and iv) which lexical items are used in the data can strongly impact conclusions. Overall, our results demonstrate that much work remains to be done when it comes to assessing whether popular evaluation datasets measure what they intend to measure, and suggest that elucidating more rigorous standards for establishing the validity of evaluation sets could benefit the field.

Zebra-Llama: A Context-Aware Large Language Model for Democratizing Rare Disease Knowledge

Rare diseases present unique challenges in healthcare, often suffering from delayed diagnosis and fragmented information landscapes. The scarcity of reliable knowledge in these conditions poses a distinct challenge for Large Language Models (LLMs) in supporting clinical management and delivering precise patient information underscoring the need for focused training on these 'zebra' cases. We present Zebra-Llama, a specialized context-aware language model with high precision Retrieval Augmented Generation (RAG) capability, focusing on Ehlers-Danlos Syndrome (EDS) as our case study. EDS, affecting 1 in 5,000 individuals, exemplifies the complexities of rare diseases with its diverse symptoms, multiple subtypes, and evolving diagnostic criteria. By implementing a novel context-aware fine-tuning methodology trained on questions derived from medical literature, patient experiences, and clinical resources, along with expertly curated responses, Zebra-Llama demonstrates unprecedented capabilities in handling EDS-related queries. On a test set of real-world questions collected from EDS patients and clinicians, medical experts evaluated the responses generated by both models, revealing Zebra-Llama's substantial improvements over base model (Llama 3.1-8B-Instruct) in thoroughness (77.5% vs. 70.1%), accuracy (83.0% vs. 78.8%), clarity (74.7% vs. 72.0%) and citation reliability (70.6% vs. 52.3%). Released as an open-source resource, Zebra-Llama not only provides more accessible and reliable EDS information but also establishes a framework for developing specialized AI solutions for other rare conditions. This work represents a crucial step towards democratizing expert-level knowledge in rare disease management, potentially transforming how healthcare providers and patients navigate the complex landscape of rare diseases.

Pervasive Label Errors in Test Sets Destabilize Machine Learning Benchmarks

We identify label errors in the test sets of 10 of the most commonly-used computer vision, natural language, and audio datasets, and subsequently study the potential for these label errors to affect benchmark results. Errors in test sets are numerous and widespread: we estimate an average of at least 3.3% errors across the 10 datasets, where for example label errors comprise at least 6% of the ImageNet validation set. Putative label errors are identified using confident learning algorithms and then human-validated via crowdsourcing (51% of the algorithmically-flagged candidates are indeed erroneously labeled, on average across the datasets). Traditionally, machine learning practitioners choose which model to deploy based on test accuracy - our findings advise caution here, proposing that judging models over correctly labeled test sets may be more useful, especially for noisy real-world datasets. Surprisingly, we find that lower capacity models may be practically more useful than higher capacity models in real-world datasets with high proportions of erroneously labeled data. For example, on ImageNet with corrected labels: ResNet-18 outperforms ResNet-50 if the prevalence of originally mislabeled test examples increases by just 6%. On CIFAR-10 with corrected labels: VGG-11 outperforms VGG-19 if the prevalence of originally mislabeled test examples increases by just 5%. Test set errors across the 10 datasets can be viewed at https://labelerrors.com and all label errors can be reproduced by https://github.com/cleanlab/label-errors.

Constructing interval variables via faceted Rasch measurement and multitask deep learning: a hate speech application

We propose a general method for measuring complex variables on a continuous, interval spectrum by combining supervised deep learning with the Constructing Measures approach to faceted Rasch item response theory (IRT). We decompose the target construct, hate speech in our case, into multiple constituent components that are labeled as ordinal survey items. Those survey responses are transformed via IRT into a debiased, continuous outcome measure. Our method estimates the survey interpretation bias of the human labelers and eliminates that influence on the generated continuous measure. We further estimate the response quality of each labeler using faceted IRT, allowing responses from low-quality labelers to be removed. Our faceted Rasch scaling procedure integrates naturally with a multitask deep learning architecture for automated prediction on new data. The ratings on the theorized components of the target outcome are used as supervised, ordinal variables for the neural networks' internal concept learning. We test the use of an activation function (ordinal softmax) and loss function (ordinal cross-entropy) designed to exploit the structure of ordinal outcome variables. Our multitask architecture leads to a new form of model interpretation because each continuous prediction can be directly explained by the constituent components in the penultimate layer. We demonstrate this new method on a dataset of 50,000 social media comments sourced from YouTube, Twitter, and Reddit and labeled by 11,000 U.S.-based Amazon Mechanical Turk workers to measure a continuous spectrum from hate speech to counterspeech. We evaluate Universal Sentence Encoders, BERT, and RoBERTa as language representation models for the comment text, and compare our predictive accuracy to Google Jigsaw's Perspective API models, showing significant improvement over this standard benchmark.

Do We Still Need Clinical Language Models?

Although recent advances in scaling large language models (LLMs) have resulted in improvements on many NLP tasks, it remains unclear whether these models trained primarily with general web text are the right tool in highly specialized, safety critical domains such as clinical text. Recent results have suggested that LLMs encode a surprising amount of medical knowledge. This raises an important question regarding the utility of smaller domain-specific language models. With the success of general-domain LLMs, is there still a need for specialized clinical models? To investigate this question, we conduct an extensive empirical analysis of 12 language models, ranging from 220M to 175B parameters, measuring their performance on 3 different clinical tasks that test their ability to parse and reason over electronic health records. As part of our experiments, we train T5-Base and T5-Large models from scratch on clinical notes from MIMIC III and IV to directly investigate the efficiency of clinical tokens. We show that relatively small specialized clinical models substantially outperform all in-context learning approaches, even when finetuned on limited annotated data. Further, we find that pretraining on clinical tokens allows for smaller, more parameter-efficient models that either match or outperform much larger language models trained on general text. We release the code and the models used under the PhysioNet Credentialed Health Data license and data use agreement.

MOTIF: A Large Malware Reference Dataset with Ground Truth Family Labels

Malware family classification is a significant issue with public safety and research implications that has been hindered by the high cost of expert labels. The vast majority of corpora use noisy labeling approaches that obstruct definitive quantification of results and study of deeper interactions. In order to provide the data needed to advance further, we have created the Malware Open-source Threat Intelligence Family (MOTIF) dataset. MOTIF contains 3,095 malware samples from 454 families, making it the largest and most diverse public malware dataset with ground truth family labels to date, nearly 3x larger than any prior expert-labeled corpus and 36x larger than the prior Windows malware corpus. MOTIF also comes with a mapping from malware samples to threat reports published by reputable industry sources, which both validates the labels and opens new research opportunities in connecting opaque malware samples to human-readable descriptions. This enables important evaluations that are normally infeasible due to non-standardized reporting in industry. For example, we provide aliases of the different names used to describe the same malware family, allowing us to benchmark for the first time accuracy of existing tools when names are obtained from differing sources. Evaluation results obtained using the MOTIF dataset indicate that existing tasks have significant room for improvement, with accuracy of antivirus majority voting measured at only 62.10% and the well-known AVClass tool having just 46.78% accuracy. Our findings indicate that malware family classification suffers a type of labeling noise unlike that studied in most ML literature, due to the large open set of classes that may not be known from the sample under consideration

Predicting sepsis in multi-site, multi-national intensive care cohorts using deep learning

Despite decades of clinical research, sepsis remains a global public health crisis with high mortality, and morbidity. Currently, when sepsis is detected and the underlying pathogen is identified, organ damage may have already progressed to irreversible stages. Effective sepsis management is therefore highly time-sensitive. By systematically analysing trends in the plethora of clinical data available in the intensive care unit (ICU), an early prediction of sepsis could lead to earlier pathogen identification, resistance testing, and effective antibiotic and supportive treatment, and thereby become a life-saving measure. Here, we developed and validated a machine learning (ML) system for the prediction of sepsis in the ICU. Our analysis represents the largest multi-national, multi-centre in-ICU study for sepsis prediction using ML to date. Our dataset contains 156,309 unique ICU admissions, which represent a refined and harmonised subset of five large ICU databases originating from three countries. Using the international consensus definition Sepsis-3, we derived hourly-resolved sepsis label annotations, amounting to 26,734 (17.1%) septic stays. We compared our approach, a deep self-attention model, to several clinical baselines as well as ML baselines and performed an extensive internal and external validation within and across databases. On average, our model was able to predict sepsis with an AUROC of 0.847 pm 0.050 (internal out-of sample validation) and 0.761 pm 0.052 (external validation). For a harmonised prevalence of 17%, at 80% recall our model detects septic patients with 39% precision 3.7 hours in advance.

SMOTE: Synthetic Minority Over-sampling Technique

An approach to the construction of classifiers from imbalanced datasets is described. A dataset is imbalanced if the classification categories are not approximately equally represented. Often real-world data sets are predominately composed of "normal" examples with only a small percentage of "abnormal" or "interesting" examples. It is also the case that the cost of misclassifying an abnormal (interesting) example as a normal example is often much higher than the cost of the reverse error. Under-sampling of the majority (normal) class has been proposed as a good means of increasing the sensitivity of a classifier to the minority class. This paper shows that a combination of our method of over-sampling the minority (abnormal) class and under-sampling the majority (normal) class can achieve better classifier performance (in ROC space) than only under-sampling the majority class. This paper also shows that a combination of our method of over-sampling the minority class and under-sampling the majority class can achieve better classifier performance (in ROC space) than varying the loss ratios in Ripper or class priors in Naive Bayes. Our method of over-sampling the minority class involves creating synthetic minority class examples. Experiments are performed using C4.5, Ripper and a Naive Bayes classifier. The method is evaluated using the area under the Receiver Operating Characteristic curve (AUC) and the ROC convex hull strategy.

Eureka: Evaluating and Understanding Large Foundation Models

Rigorous and reproducible evaluation is critical for assessing the state of the art and for guiding scientific advances in Artificial Intelligence. Evaluation is challenging in practice due to several reasons, including benchmark saturation, lack of transparency in methods used for measurement, development challenges in extracting measurements for generative tasks, and, more generally, the extensive number of capabilities required for a well-rounded comparison across models. We make three contributions to alleviate the above challenges. First, we present Eureka, an open-source framework for standardizing evaluations of large foundation models beyond single-score reporting and rankings. Second, we introduce Eureka-Bench as an extensible collection of benchmarks testing capabilities that (i) are still challenging for state-of-the-art models and (ii) represent fundamental but overlooked language and multimodal capabilities. The inherent space for improvement in non-saturated benchmarks enables us to discover meaningful differences between models at a capability level. Third, using Eureka, we conduct an analysis of 12 state-of-the-art models, providing in-depth insights into failure understanding and model comparison, which can be leveraged to plan targeted improvements. In contrast to recent trends in reports and leaderboards showing absolute rankings and claims for one model or another to be the best, our analysis shows that there is no such best model. Different models have different strengths, but there are models that appear more often than others as best performers for some capabilities. Despite the recent improvements, current models still struggle with several fundamental capabilities including detailed image understanding, benefiting from multimodal input when available rather than fully relying on language, factuality and grounding for information retrieval, and over refusals.

PMC-Patients: A Large-scale Dataset of Patient Notes and Relations Extracted from Case Reports in PubMed Central

Objective: Data unavailability has been one of the biggest barriers in clinical natural language processing. This paper is aimed at providing a large-scale and publicly available patient note dataset, named PMC-Patients, with relevant articles and similar patients annotations. The ultimate goal of PMC-Patients is to facilitate the development of retrieval-based clinical decision support systems. Materials and Methods: To collect PMC-Patients, we extract patient notes from case reports in PubMed Central by recognizing certain section patterns. Patient-article relevance and patient-patient similarity are annotated by citation relationships in PubMed. In addition, we perform three tasks with PMC-Patients to demonstrate its utility in providing clinical decision support for a given patient, including (1) classifying whether another patient is similar, (2) retrieving similar patients in PMC-Patients, and (3) retrieving relevant articles in PubMed. Results: We collect and release PMC-Patients under the CC BY-NC-SA license, which becomes the largest publicly available patient note dataset so far. PMC-Patients contains 167k patient notes that are annotated with 3.1M relevant articles and 293k similar patients. Qualitative and quantitative analyses reveal the high quality and richness of our dataset. Experiments show that classifying the similarity of patient pairs is relatively easy, but it is hard to retrieve similar patients or relevant articles for a given patient from a large set of candidates. Conclusion: We present PMC-Patients, a large-scale dataset of patient notes with high quality, easy access, diverse conditions, and rich annotations. The proposed dataset can also serve as a hard benchmark for evaluating retrieval-based clinical decision support systems.

LitSearch: A Retrieval Benchmark for Scientific Literature Search

Literature search questions, such as "where can I find research on the evaluation of consistency in generated summaries?" pose significant challenges for modern search engines and retrieval systems. These questions often require a deep understanding of research concepts and the ability to reason over entire articles. In this work, we introduce LitSearch, a retrieval benchmark comprising 597 realistic literature search queries about recent ML and NLP papers. LitSearch is constructed using a combination of (1) questions generated by GPT-4 based on paragraphs containing inline citations from research papers and (2) questions about recently published papers, manually written by their authors. All LitSearch questions were manually examined or edited by experts to ensure high quality. We extensively benchmark state-of-the-art retrieval models and also evaluate two LLM-based reranking pipelines. We find a significant performance gap between BM25 and state-of-the-art dense retrievers, with a 24.8% difference in absolute recall@5. The LLM-based reranking strategies further improve the best-performing dense retriever by 4.4%. Additionally, commercial search engines and research tools like Google Search perform poorly on LitSearch, lagging behind the best dense retriever by 32 points. Taken together, these results show that LitSearch is an informative new testbed for retrieval systems while catering to a real-world use case.

Application of NotebookLM, a Large Language Model with Retrieval-Augmented Generation, for Lung Cancer Staging

Purpose: In radiology, large language models (LLMs), including ChatGPT, have recently gained attention, and their utility is being rapidly evaluated. However, concerns have emerged regarding their reliability in clinical applications due to limitations such as hallucinations and insufficient referencing. To address these issues, we focus on the latest technology, retrieval-augmented generation (RAG), which enables LLMs to reference reliable external knowledge (REK). Specifically, this study examines the utility and reliability of a recently released RAG-equipped LLM (RAG-LLM), NotebookLM, for staging lung cancer. Materials and methods: We summarized the current lung cancer staging guideline in Japan and provided this as REK to NotebookLM. We then tasked NotebookLM with staging 100 fictional lung cancer cases based on CT findings and evaluated its accuracy. For comparison, we performed the same task using a gold-standard LLM, GPT-4 Omni (GPT-4o), both with and without the REK. Results: NotebookLM achieved 86% diagnostic accuracy in the lung cancer staging experiment, outperforming GPT-4o, which recorded 39% accuracy with the REK and 25% without it. Moreover, NotebookLM demonstrated 95% accuracy in searching reference locations within the REK. Conclusion: NotebookLM successfully performed lung cancer staging by utilizing the REK, demonstrating superior performance compared to GPT-4o. Additionally, it provided highly accurate reference locations within the REK, allowing radiologists to efficiently evaluate the reliability of NotebookLM's responses and detect possible hallucinations. Overall, this study highlights the potential of NotebookLM, a RAG-LLM, in image diagnosis.

Training Curricula for Open Domain Answer Re-Ranking

In precision-oriented tasks like answer ranking, it is more important to rank many relevant answers highly than to retrieve all relevant answers. It follows that a good ranking strategy would be to learn how to identify the easiest correct answers first (i.e., assign a high ranking score to answers that have characteristics that usually indicate relevance, and a low ranking score to those with characteristics that do not), before incorporating more complex logic to handle difficult cases (e.g., semantic matching or reasoning). In this work, we apply this idea to the training of neural answer rankers using curriculum learning. We propose several heuristics to estimate the difficulty of a given training sample. We show that the proposed heuristics can be used to build a training curriculum that down-weights difficult samples early in the training process. As the training process progresses, our approach gradually shifts to weighting all samples equally, regardless of difficulty. We present a comprehensive evaluation of our proposed idea on three answer ranking datasets. Results show that our approach leads to superior performance of two leading neural ranking architectures, namely BERT and ConvKNRM, using both pointwise and pairwise losses. When applied to a BERT-based ranker, our method yields up to a 4% improvement in MRR and a 9% improvement in P@1 (compared to the model trained without a curriculum). This results in models that can achieve comparable performance to more expensive state-of-the-art techniques.

An Integrated Optimization and Machine Learning Models to Predict the Admission Status of Emergency Patients

This work proposes a framework for optimizing machine learning algorithms. The practicality of the framework is illustrated using an important case study from the healthcare domain, which is predicting the admission status of emergency department (ED) patients (e.g., admitted vs. discharged) using patient data at the time of triage. The proposed framework can mitigate the crowding problem by proactively planning the patient boarding process. A large retrospective dataset of patient records is obtained from the electronic health record database of all ED visits over three years from three major locations of a healthcare provider in the Midwest of the US. Three machine learning algorithms are proposed: T-XGB, T-ADAB, and T-MLP. T-XGB integrates extreme gradient boosting (XGB) and Tabu Search (TS), T-ADAB integrates Adaboost and TS, and T-MLP integrates multi-layer perceptron (MLP) and TS. The proposed algorithms are compared with the traditional algorithms: XGB, ADAB, and MLP, in which their parameters are tunned using grid search. The three proposed algorithms and the original ones are trained and tested using nine data groups that are obtained from different feature selection methods. In other words, 54 models are developed. Performance was evaluated using five measures: Area under the curve (AUC), sensitivity, specificity, F1, and accuracy. The results show that the newly proposed algorithms resulted in high AUC and outperformed the traditional algorithms. The T-ADAB performs the best among the newly developed algorithms. The AUC, sensitivity, specificity, F1, and accuracy of the best model are 95.4%, 99.3%, 91.4%, 95.2%, 97.2%, respectively.

A Deep Look into Neural Ranking Models for Information Retrieval

Ranking models lie at the heart of research on information retrieval (IR). During the past decades, different techniques have been proposed for constructing ranking models, from traditional heuristic methods, probabilistic methods, to modern machine learning methods. Recently, with the advance of deep learning technology, we have witnessed a growing body of work in applying shallow or deep neural networks to the ranking problem in IR, referred to as neural ranking models in this paper. The power of neural ranking models lies in the ability to learn from the raw text inputs for the ranking problem to avoid many limitations of hand-crafted features. Neural networks have sufficient capacity to model complicated tasks, which is needed to handle the complexity of relevance estimation in ranking. Since there have been a large variety of neural ranking models proposed, we believe it is the right time to summarize the current status, learn from existing methodologies, and gain some insights for future development. In contrast to existing reviews, in this survey, we will take a deep look into the neural ranking models from different dimensions to analyze their underlying assumptions, major design principles, and learning strategies. We compare these models through benchmark tasks to obtain a comprehensive empirical understanding of the existing techniques. We will also discuss what is missing in the current literature and what are the promising and desired future directions.

ModernBERT is More Efficient than Conventional BERT for Chest CT Findings Classification in Japanese Radiology Reports

Objective: This study aims to evaluate and compare the performance of two Japanese language models-conventional Bidirectional Encoder Representations from Transformers (BERT) and the newer ModernBERT-in classifying findings from chest CT reports, with a focus on tokenization efficiency, processing time, and classification performance. Methods: We conducted a retrospective study using the CT-RATE-JPN dataset containing 22,778 training reports and 150 test reports. Both models were fine-tuned for multi-label classification of 18 common chest CT conditions. The training data was split in 18,222:4,556 for training and validation. Performance was evaluated using F1 scores for each condition and exact match accuracy across all 18 labels. Results: ModernBERT demonstrated superior tokenization efficiency, requiring 24.0% fewer tokens per document (258.1 vs. 339.6) compared to BERT Base. This translated to significant performance improvements, with ModernBERT completing training in 1877.67 seconds versus BERT's 3090.54 seconds (39% reduction). ModernBERT processed 38.82 samples per second during training (1.65x faster) and 139.90 samples per second during inference (1.66x faster). Despite these efficiency gains, classification performance remained comparable, with ModernBERT achieving superior F1 scores in 8 conditions, while BERT performed better in 4 conditions. Overall exact match accuracy was slightly higher for ModernBERT (74.67% vs. 72.67%), though this difference was not statistically significant (p=0.6291). Conclusion: ModernBERT offers substantial improvements in tokenization efficiency and training speed without sacrificing classification performance. These results suggest that ModernBERT is a promising candidate for clinical applications in Japanese radiology reports analysis.

What are the Desired Characteristics of Calibration Sets? Identifying Correlates on Long Form Scientific Summarization

Summarization models often generate text that is poorly calibrated to quality metrics because they are trained to maximize the likelihood of a single reference (MLE). To address this, recent work has added a calibration step, which exposes a model to its own ranked outputs to improve relevance or, in a separate line of work, contrasts positive and negative sets to improve faithfulness. While effective, much of this work has focused on how to generate and optimize these sets. Less is known about why one setup is more effective than another. In this work, we uncover the underlying characteristics of effective sets. For each training instance, we form a large, diverse pool of candidates and systematically vary the subsets used for calibration fine-tuning. Each selection strategy targets distinct aspects of the sets, such as lexical diversity or the size of the gap between positive and negatives. On three diverse scientific long-form summarization datasets (spanning biomedical, clinical, and chemical domains), we find, among others, that faithfulness calibration is optimal when the negative sets are extractive and more likely to be generated, whereas for relevance calibration, the metric margin between candidates should be maximized and surprise--the disagreement between model and metric defined candidate rankings--minimized. Code to create, select, and optimize calibration sets is available at https://github.com/griff4692/calibrating-summaries

RULE: Reliable Multimodal RAG for Factuality in Medical Vision Language Models

The recent emergence of Medical Large Vision Language Models (Med-LVLMs) has enhanced medical diagnosis. However, current Med-LVLMs frequently encounter factual issues, often generating responses that do not align with established medical facts. Retrieval-Augmented Generation (RAG), which utilizes external knowledge, can improve the factual accuracy of these models but introduces two major challenges. First, limited retrieved contexts might not cover all necessary information, while excessive retrieval can introduce irrelevant and inaccurate references, interfering with the model's generation. Second, in cases where the model originally responds correctly, applying RAG can lead to an over-reliance on retrieved contexts, resulting in incorrect answers. To address these issues, we propose RULE, which consists of two components. First, we introduce a provably effective strategy for controlling factuality risk through the calibrated selection of the number of retrieved contexts. Second, based on samples where over-reliance on retrieved contexts led to errors, we curate a preference dataset to fine-tune the model, balancing its dependence on inherent knowledge and retrieved contexts for generation. We demonstrate the effectiveness of RULE on three medical VQA datasets, achieving an average improvement of 20.8% in factual accuracy. We publicly release our benchmark and code in https://github.com/richard-peng-xia/RULE.

Reshaping Free-Text Radiology Notes Into Structured Reports With Generative Transformers

BACKGROUND: Radiology reports are typically written in a free-text format, making clinical information difficult to extract and use. Recently the adoption of structured reporting (SR) has been recommended by various medical societies thanks to the advantages it offers, e.g. standardization, completeness and information retrieval. We propose a pipeline to extract information from free-text radiology reports, that fits with the items of the reference SR registry proposed by a national society of interventional and medical radiology, focusing on CT staging of patients with lymphoma. METHODS: Our work aims to leverage the potential of Natural Language Processing (NLP) and Transformer-based models to deal with automatic SR registry filling. With the availability of 174 radiology reports, we investigate a rule-free generative Question Answering approach based on a domain-specific version of T5 (IT5). Two strategies (batch-truncation and ex-post combination) are implemented to comply with the model's context length limitations. Performance is evaluated in terms of strict accuracy, F1, and format accuracy, and compared with the widely used GPT-3.5 Large Language Model. A 5-point Likert scale questionnaire is used to collect human-expert feedback on the similarity between medical annotations and generated answers. RESULTS: The combination of fine-tuning and batch splitting allows IT5 to achieve notable results; it performs on par with GPT-3.5 albeit its size being a thousand times smaller in terms of parameters. Human-based assessment scores show a high correlation (Spearman's correlation coefficients>0.88, p-values<0.001) with AI performance metrics (F1) and confirm the superior ability of LLMs (i.e., GPT-3.5, 175B of parameters) in generating plausible human-like statements.

DataMan: Data Manager for Pre-training Large Language Models

The performance emergence of large language models (LLMs) driven by data scaling laws makes the selection of pre-training data increasingly important. However, existing methods rely on limited heuristics and human intuition, lacking comprehensive and clear guidelines. To address this, we are inspired by ``reverse thinking'' -- prompting LLMs to self-identify which criteria benefit its performance. As its pre-training capabilities are related to perplexity (PPL), we derive 14 quality criteria from the causes of text perplexity anomalies and introduce 15 common application domains to support domain mixing. In this paper, we train a Data Manager (DataMan) to learn quality ratings and domain recognition from pointwise rating, and use it to annotate a 447B token pre-training corpus with 14 quality ratings and domain type. Our experiments validate our approach, using DataMan to select 30B tokens to train a 1.3B-parameter language model, demonstrating significant improvements in in-context learning (ICL), perplexity, and instruction-following ability over the state-of-the-art baseline. The best-performing model, based on the Overall Score l=5 surpasses a model trained with 50% more data using uniform sampling. We continue pre-training with high-rated, domain-specific data annotated by DataMan to enhance domain-specific ICL performance and thus verify DataMan's domain mixing ability. Our findings emphasize the importance of quality ranking, the complementary nature of quality criteria, and their low correlation with perplexity, analyzing misalignment between PPL and ICL performance. We also thoroughly analyzed our pre-training dataset, examining its composition, the distribution of quality ratings, and the original document sources.

Rapid Biomedical Research Classification: The Pandemic PACT Advanced Categorisation Engine

This paper introduces the Pandemic PACT Advanced Categorisation Engine (PPACE) along with its associated dataset. PPACE is a fine-tuned model developed to automatically classify research abstracts from funded biomedical projects according to WHO-aligned research priorities. This task is crucial for monitoring research trends and identifying gaps in global health preparedness and response. Our approach builds on human-annotated projects, which are allocated one or more categories from a predefined list. A large language model is then used to generate `rationales' explaining the reasoning behind these annotations. This augmented data, comprising expert annotations and rationales, is subsequently used to fine-tune a smaller, more efficient model. Developed as part of the Pandemic PACT project, which aims to track and analyse research funding and clinical evidence for a wide range of diseases with outbreak potential, PPACE supports informed decision-making by research funders, policymakers, and independent researchers. We introduce and release both the trained model and the instruction-based dataset used for its training. Our evaluation shows that PPACE significantly outperforms its baselines. The release of PPACE and its associated dataset offers valuable resources for researchers in multilabel biomedical document classification and supports advancements in aligning biomedical research with key global health priorities.

Improving Prototypical Parts Abstraction for Case-Based Reasoning Explanations Designed for the Kidney Stone Type Recognition

The in-vivo identification of the kidney stone types during an ureteroscopy would be a major medical advance in urology, as it could reduce the time of the tedious renal calculi extraction process, while diminishing infection risks. Furthermore, such an automated procedure would make possible to prescribe anti-recurrence treatments immediately. Nowadays, only few experienced urologists are able to recognize the kidney stone types in the images of the videos displayed on a screen during the endoscopy. Thus, several deep learning (DL) models have recently been proposed to automatically recognize the kidney stone types using ureteroscopic images. However, these DL models are of black box nature whicl limits their applicability in clinical settings. This contribution proposes a case-based reasoning DL model which uses prototypical parts (PPs) and generates local and global descriptors. The PPs encode for each class (i.e., kidney stone type) visual feature information (hue, saturation, intensity and textures) similar to that used by biologists. The PPs are optimally generated due a new loss function used during the model training. Moreover, the local and global descriptors of PPs allow to explain the decisions ("what" information, "where in the images") in an understandable way for biologists and urologists. The proposed DL model has been tested on a database including images of the six most widespread kidney stone types. The overall average classification accuracy was 90.37. When comparing this results with that of the eight other DL models of the kidney stone state-of-the-art, it can be seen that the valuable gain in explanability was not reached at the expense of accuracy which was even slightly increased with respect to that (88.2) of the best method of the literature. These promising and interpretable results also encourage urologists to put their trust in AI-based solutions.

DICES Dataset: Diversity in Conversational AI Evaluation for Safety

Machine learning approaches often require training and evaluation datasets with a clear separation between positive and negative examples. This risks simplifying and even obscuring the inherent subjectivity present in many tasks. Preserving such variance in content and diversity in datasets is often expensive and laborious. This is especially troubling when building safety datasets for conversational AI systems, as safety is both socially and culturally situated. To demonstrate this crucial aspect of conversational AI safety, and to facilitate in-depth model performance analyses, we introduce the DICES (Diversity In Conversational AI Evaluation for Safety) dataset that contains fine-grained demographic information about raters, high replication of ratings per item to ensure statistical power for analyses, and encodes rater votes as distributions across different demographics to allow for in-depth explorations of different aggregation strategies. In short, the DICES dataset enables the observation and measurement of variance, ambiguity, and diversity in the context of conversational AI safety. We also illustrate how the dataset offers a basis for establishing metrics to show how raters' ratings can intersects with demographic categories such as racial/ethnic groups, age groups, and genders. The goal of DICES is to be used as a shared resource and benchmark that respects diverse perspectives during safety evaluation of conversational AI systems.

The Limited Impact of Medical Adaptation of Large Language and Vision-Language Models

Several recent works seek to develop foundation models specifically for medical applications, adapting general-purpose large language models (LLMs) and vision-language models (VLMs) via continued pretraining on publicly available biomedical corpora. These works typically claim that such domain-adaptive pretraining (DAPT) improves performance on downstream medical tasks, such as answering medical licensing exam questions. In this paper, we compare ten public "medical" LLMs and two VLMs against their corresponding base models, arriving at a different conclusion: all medical VLMs and nearly all medical LLMs fail to consistently improve over their base models in the zero-/few-shot prompting and supervised fine-tuning regimes for medical question-answering (QA). For instance, across all tasks and model pairs we consider in the 3-shot setting, medical LLMs only outperform their base models in 22.7% of cases, reach a (statistical) tie in 36.8% of cases, and are significantly worse than their base models in the remaining 40.5% of cases. Our conclusions are based on (i) comparing each medical model head-to-head, directly against the corresponding base model; (ii) optimizing the prompts for each model separately in zero-/few-shot prompting; and (iii) accounting for statistical uncertainty in comparisons. While these basic practices are not consistently adopted in the literature, our ablations show that they substantially impact conclusions. Meanwhile, we find that after fine-tuning on specific QA tasks, medical LLMs can show performance improvements, but the benefits do not carry over to tasks based on clinical notes. Our findings suggest that state-of-the-art general-domain models may already exhibit strong medical knowledge and reasoning capabilities, and offer recommendations to strengthen the conclusions of future studies.

VHELM: A Holistic Evaluation of Vision Language Models

Current benchmarks for assessing vision-language models (VLMs) often focus on their perception or problem-solving capabilities and neglect other critical aspects such as fairness, multilinguality, or toxicity. Furthermore, they differ in their evaluation procedures and the scope of the evaluation, making it difficult to compare models. To address these issues, we extend the HELM framework to VLMs to present the Holistic Evaluation of Vision Language Models (VHELM). VHELM aggregates various datasets to cover one or more of the 9 aspects: visual perception, knowledge, reasoning, bias, fairness, multilinguality, robustness, toxicity, and safety. In doing so, we produce a comprehensive, multi-dimensional view of the capabilities of the VLMs across these important factors. In addition, we standardize the standard inference parameters, methods of prompting, and evaluation metrics to enable fair comparisons across models. Our framework is designed to be lightweight and automatic so that evaluation runs are cheap and fast. Our initial run evaluates 22 VLMs on 21 existing datasets to provide a holistic snapshot of the models. We uncover new key findings, such as the fact that efficiency-focused models (e.g., Claude 3 Haiku or Gemini 1.5 Flash) perform significantly worse than their full models (e.g., Claude 3 Opus or Gemini 1.5 Pro) on the bias benchmark but not when evaluated on the other aspects. For transparency, we release the raw model generations and complete results on our website (https://crfm.stanford.edu/helm/vhelm/v2.0.1). VHELM is intended to be a living benchmark, and we hope to continue adding new datasets and models over time.

Where Does the Performance Improvement Come From? -- A Reproducibility Concern about Image-Text Retrieval

This article aims to provide the information retrieval community with some reflections on recent advances in retrieval learning by analyzing the reproducibility of image-text retrieval models. Due to the increase of multimodal data over the last decade, image-text retrieval has steadily become a major research direction in the field of information retrieval. Numerous researchers train and evaluate image-text retrieval algorithms using benchmark datasets such as MS-COCO and Flickr30k. Research in the past has mostly focused on performance, with multiple state-of-the-art methodologies being suggested in a variety of ways. According to their assertions, these techniques provide improved modality interactions and hence more precise multimodal representations. In contrast to previous works, we focus on the reproducibility of the approaches and the examination of the elements that lead to improved performance by pretrained and nonpretrained models in retrieving images and text. To be more specific, we first examine the related reproducibility concerns and explain why our focus is on image-text retrieval tasks. Second, we systematically summarize the current paradigm of image-text retrieval models and the stated contributions of those approaches. Third, we analyze various aspects of the reproduction of pretrained and nonpretrained retrieval models. To complete this, we conducted ablation experiments and obtained some influencing factors that affect retrieval recall more than the improvement claimed in the original paper. Finally, we present some reflections and challenges that the retrieval community should consider in the future. Our source code is publicly available at https://github.com/WangFei-2019/Image-text-Retrieval.

The order in speech disorder: a scoping review of state of the art machine learning methods for clinical speech classification

Background:Speech patterns have emerged as potential diagnostic markers for conditions with varying etiologies. Machine learning (ML) presents an opportunity to harness these patterns for accurate disease diagnosis. Objective: This review synthesized findings from studies exploring ML's capability in leveraging speech for the diagnosis of neurological, laryngeal and mental disorders. Methods: A systematic examination of 564 articles was conducted with 91 articles included in the study, which encompassed a wide spectrum of conditions, ranging from voice pathologies to mental and neurological disorders. Methods for speech classifications were assessed based on the relevant studies and scored between 0-10 based on the reported diagnostic accuracy of their ML models. Results: High diagnostic accuracies were consistently observed for laryngeal disorders, dysarthria, and changes related to speech in Parkinsons disease. These findings indicate the robust potential of speech as a diagnostic tool. Disorders like depression, schizophrenia, mild cognitive impairment and Alzheimers dementia also demonstrated high accuracies, albeit with some variability across studies. Meanwhile, disorders like OCD and autism highlighted the need for more extensive research to ascertain the relationship between speech patterns and the respective conditions. Conclusion: ML models utilizing speech patterns demonstrate promising potential in diagnosing a range of mental, laryngeal, and neurological disorders. However, the efficacy varies across conditions, and further research is needed. The integration of these models into clinical practice could potentially revolutionize the evaluation and diagnosis of a number of different medical conditions.

QuRating: Selecting High-Quality Data for Training Language Models

Selecting high-quality pre-training data is important for creating capable language models, but existing methods rely on simple heuristics. We introduce QuRating, a method for selecting pre-training data that captures the abstract qualities of texts which humans intuitively perceive. In this paper, we investigate four qualities - writing style, required expertise, facts & trivia, and educational value. We find that LLMs are able to discern these qualities and observe that they are better at making pairwise judgments of texts than at rating the quality of a text directly. We train a QuRater model to learn scalar ratings from pairwise judgments, and use it to annotate a 260B training corpus with quality ratings for each of the four criteria. In our experiments, we select 30B tokens according to the different quality ratings and train 1.3B-parameter language models on the selected data. We find that it is important to balance quality and diversity, as selecting only the highest-rated documents leads to poor results. When we sample using quality ratings as logits over documents, our models achieve lower perplexity and stronger in-context learning performance than baselines. Beyond data selection, we use the quality ratings to construct a training curriculum which improves performance without changing the training dataset. We extensively analyze the quality ratings and discuss their characteristics, biases, and wider implications.

Style Over Substance: Evaluation Biases for Large Language Models

As large language models (LLMs) continue to advance, accurately and comprehensively evaluating their performance becomes increasingly challenging. Human evaluations are conventionally considered the gold standard in natural language generation, but recent advancements incorporate state-of-the-art LLMs as proxies for human judges in evaluation processes. However, the extent to which humans and LLMs are capable evaluators remains uncertain. This study investigates the behavior of crowd-sourced and expert annotators, as well as LLMs, when comparing outputs from different models. To achieve this, we curate a dataset of intentionally flawed machine-generated answers. Our findings reveal a concerning bias in the evaluation process, as answers with factual errors are rated more favorably than answers that are too short or contained grammatical errors. To address this issue, we propose independently evaluating machine-generated text across multiple dimensions, rather than merging all the evaluation aspects into a single score. We instantiate this idea with the Elo rating system, resulting in the Multi-Elo Rating System. Empirical results from our study reveal that this proposed approach significantly enhances the quality of LLM-based evaluations, particularly in terms of factual accuracy. However, there is no significant improvement in crowd-sourced-based evaluations, indicating the need for further investigation and refinement.

Semixup: In- and Out-of-Manifold Regularization for Deep Semi-Supervised Knee Osteoarthritis Severity Grading from Plain Radiographs

Knee osteoarthritis (OA) is one of the highest disability factors in the world. This musculoskeletal disorder is assessed from clinical symptoms, and typically confirmed via radiographic assessment. This visual assessment done by a radiologist requires experience, and suffers from moderate to high inter-observer variability. The recent literature has shown that deep learning methods can reliably perform the OA severity assessment according to the gold standard Kellgren-Lawrence (KL) grading system. However, these methods require large amounts of labeled data, which are costly to obtain. In this study, we propose the Semixup algorithm, a semi-supervised learning (SSL) approach to leverage unlabeled data. Semixup relies on consistency regularization using in- and out-of-manifold samples, together with interpolated consistency. On an independent test set, our method significantly outperformed other state-of-the-art SSL methods in most cases. Finally, when compared to a well-tuned fully supervised baseline that yielded a balanced accuracy (BA) of 70.9pm0.8% on the test set, Semixup had comparable performance -- BA of 71pm0.8% (p=0.368) while requiring 6 times less labeled data. These results show that our proposed SSL method allows building fully automatic OA severity assessment tools with datasets that are available outside research settings.

Resources for Brewing BEIR: Reproducible Reference Models and an Official Leaderboard

BEIR is a benchmark dataset for zero-shot evaluation of information retrieval models across 18 different domain/task combinations. In recent years, we have witnessed the growing popularity of a representation learning approach to building retrieval models, typically using pretrained transformers in a supervised setting. This naturally begs the question: How effective are these models when presented with queries and documents that differ from the training data? Examples include searching in different domains (e.g., medical or legal text) and with different types of queries (e.g., keywords vs. well-formed questions). While BEIR was designed to answer these questions, our work addresses two shortcomings that prevent the benchmark from achieving its full potential: First, the sophistication of modern neural methods and the complexity of current software infrastructure create barriers to entry for newcomers. To this end, we provide reproducible reference implementations that cover the two main classes of approaches: learned dense and sparse models. Second, there does not exist a single authoritative nexus for reporting the effectiveness of different models on BEIR, which has led to difficulty in comparing different methods. To remedy this, we present an official self-service BEIR leaderboard that provides fair and consistent comparisons of retrieval models. By addressing both shortcomings, our work facilitates future explorations in a range of interesting research questions that BEIR enables.

Boosting EfficientNets Ensemble Performance via Pseudo-Labels and Synthetic Images by pix2pixHD for Infection and Ischaemia Classification in Diabetic Foot Ulcers

Diabetic foot ulcers are a common manifestation of lesions on the diabetic foot, a syndrome acquired as a long-term complication of diabetes mellitus. Accompanying neuropathy and vascular damage promote acquisition of pressure injuries and tissue death due to ischaemia. Affected areas are prone to infections, hindering the healing progress. The research at hand investigates an approach on classification of infection and ischaemia, conducted as part of the Diabetic Foot Ulcer Challenge (DFUC) 2021. Different models of the EfficientNet family are utilized in ensembles. An extension strategy for the training data is applied, involving pseudo-labeling for unlabeled images, and extensive generation of synthetic images via pix2pixHD to cope with severe class imbalances. The resulting extended training dataset features 8.68 times the size of the baseline and shows a real to synthetic image ratio of 1:3. Performances of models and ensembles trained on the baseline and extended training dataset are compared. Synthetic images featured a broad qualitative variety. Results show that models trained on the extended training dataset as well as their ensemble benefit from the large extension. F1-Scores for rare classes receive outstanding boosts, while those for common classes are either not harmed or boosted moderately. A critical discussion concretizes benefits and identifies limitations, suggesting improvements. The work concludes that classification performance of individual models as well as that of ensembles can be boosted utilizing synthetic images. Especially performance for rare classes benefits notably.

Explainable Depression Symptom Detection in Social Media

Users of social platforms often perceive these sites as supportive spaces to post about their mental health issues. Those conversations contain important traces about individuals' health risks. Recently, researchers have exploited this online information to construct mental health detection models, which aim to identify users at risk on platforms like Twitter, Reddit or Facebook. Most of these models are centred on achieving good classification results, ignoring the explainability and interpretability of the decisions. Recent research has pointed out the importance of using clinical markers, such as the use of symptoms, to improve trust in the computational models by health professionals. In this paper, we propose using transformer-based architectures to detect and explain the appearance of depressive symptom markers in the users' writings. We present two approaches: i) train a model to classify, and another one to explain the classifier's decision separately and ii) unify the two tasks simultaneously using a single model. Additionally, for this latter manner, we also investigated the performance of recent conversational LLMs when using in-context learning. Our natural language explanations enable clinicians to interpret the models' decisions based on validated symptoms, enhancing trust in the automated process. We evaluate our approach using recent symptom-based datasets, employing both offline and expert-in-the-loop metrics to assess the quality of the explanations generated by our models. The experimental results show that it is possible to achieve good classification results while generating interpretable symptom-based explanations.