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May 13

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.

  • 2 authors
·
Nov 27, 2020

Advancing Tabular Stroke Modelling Through a Novel Hybrid Architecture and Feature-Selection Synergy

Brain stroke remains one of the principal causes of death and disability worldwide, yet most tabular-data prediction models still hover below the 95% accuracy threshold, limiting real-world utility. Addressing this gap, the present work develops and validates a completely data-driven and interpretable machine-learning framework designed to predict strokes using ten routinely gathered demographic, lifestyle, and clinical variables sourced from a public cohort of 4,981 records. We employ a detailed exploratory data analysis (EDA) to understand the dataset's structure and distribution, followed by rigorous data preprocessing, including handling missing values, outlier removal, and class imbalance correction using Synthetic Minority Over-sampling Technique (SMOTE). To streamline feature selection, point-biserial correlation and random-forest Gini importance were utilized, and ten varied algorithms-encompassing tree ensembles, boosting, kernel methods, and a multilayer neural network-were optimized using stratified five-fold cross-validation. Their predictions based on probabilities helped us build the proposed model, which included Random Forest, XGBoost, LightGBM, and a support-vector classifier, with logistic regression acting as a meta-learner. The proposed model achieved an accuracy rate of 97.2% and an F1-score of 97.15%, indicating a significant enhancement compared to the leading individual model, LightGBM, which had an accuracy of 91.4%. Our study's findings indicate that rigorous preprocessing, coupled with a diverse hybrid model, can convert low-cost tabular data into a nearly clinical-grade stroke-risk assessment tool.

  • 3 authors
·
May 18, 2025

Active Sensing of Knee Osteoarthritis Progression with Reinforcement Learning

Osteoarthritis (OA) is the most common musculoskeletal disease, which has no cure. Knee OA (KOA) is one of the highest causes of disability worldwide, and it costs billions of United States dollars to the global community. Prediction of KOA progression has been of high interest to the community for years, as it can advance treatment development through more efficient clinical trials and improve patient outcomes through more efficient healthcare utilization. Existing approaches for predicting KOA, however, are predominantly static, i.e. consider data from a single time point to predict progression many years into the future, and knee level, i.e. consider progression in a single joint only. Due to these and related reasons, these methods fail to deliver the level of predictive performance, which is sufficient to result in cost savings and better patient outcomes. Collecting extensive data from all patients on a regular basis could address the issue, but it is limited by the high cost at a population level. In this work, we propose to go beyond static prediction models in OA, and bring a novel Active Sensing (AS) approach, designed to dynamically follow up patients with the objective of maximizing the number of informative data acquisitions, while minimizing their total cost over a period of time. Our approach is based on Reinforcement Learning (RL), and it leverages a novel reward function designed specifically for AS of disease progression in more than one part of a human body. Our method is end-to-end, relies on multi-modal Deep Learning, and requires no human input at inference time. Throughout an exhaustive experimental evaluation, we show that using RL can provide a higher monetary benefit when compared to state-of-the-art baselines.

  • 4 authors
·
Aug 5, 2024

Graph AI generates neurological hypotheses validated in molecular, organoid, and clinical systems

Neurological diseases are the leading global cause of disability, yet most lack disease-modifying treatments. We present PROTON, a heterogeneous graph transformer that generates testable hypotheses across molecular, organoid, and clinical systems. To evaluate PROTON, we apply it to Parkinson's disease (PD), bipolar disorder (BD), and Alzheimer's disease (AD). In PD, PROTON linked genetic risk loci to genes essential for dopaminergic neuron survival and predicted pesticides toxic to patient-derived neurons, including the insecticide endosulfan, which ranked within the top 1.29% of predictions. In silico screens performed by PROTON reproduced six genome-wide α-synuclein experiments, including a split-ubiquitin yeast two-hybrid system (normalized enrichment score [NES] = 2.30, FDR-adjusted p < 1 times 10^{-4}), an ascorbate peroxidase proximity labeling assay (NES = 2.16, FDR < 1 times 10^{-4}), and a high-depth targeted exome sequencing study in 496 synucleinopathy patients (NES = 2.13, FDR < 1 times 10^{-4}). In BD, PROTON predicted calcitriol as a candidate drug that reversed proteomic alterations observed in cortical organoids derived from BD patients. In AD, we evaluated PROTON predictions in health records from n = 610,524 patients at Mass General Brigham, confirming that five PROTON-predicted drugs were associated with reduced seven-year dementia risk (minimum hazard ratio = 0.63, 95% CI: 0.53-0.75, p < 1 times 10^{-7}). PROTON generated neurological hypotheses that were evaluated across molecular, organoid, and clinical systems, defining a path for AI-driven discovery in neurological disease.

  • 29 authors
·
Dec 13, 2025

MDD-Thinker: Towards Large Reasoning Models for Major Depressive Disorder Diagnosis

Background Major depressive disorder (MDD) is a leading cause of global disability, yet current diagnostic approaches often rely on subjective assessments and lack the ability to integrate multimodal clinical information. Large language models (LLMs) hold promise for enhancing diagnostic accuracy through advanced reasoning but face challenges in interpretability, hallucination, and reliance on synthetic data. Methods We developed MDD-Thinker, an LLM-based diagnostic framework that integrates supervised fine-tuning (SFT) with reinforcement learning (RL) to strengthen reasoning ability and interpretability. Using the UK Biobank dataset, we generated 40,000 reasoning samples, supplemented with 10,000 samples from publicly available mental health datasets. The model was fine-tuned on these reasoning corpora, and its diagnostic and reasoning performance was evaluated against machine learning, deep learning, and state-of-the-art LLM baselines. Findings MDD-Thinker achieved an accuracy of 0.8268 and F1-score of 0.8081, significantly outperforming traditional baselines such as SVM and MLP, as well as general-purpose LLMs. Incorporating both SFT and RL yielded the greatest improvements, with relative gains of 29.0% in accuracy, 38.1% in F1-score, and 34.8% in AUC. Moreover, the model demonstrated comparable reasoning performance compared to much larger LLMs, while maintaining computational efficiency. Interpretation This study presents the first reasoning-enhanced LLM framework for MDD diagnosis trained on large-scale real-world clinical data. By integrating SFT and RL, MDD-Thinker balances accuracy, interpretability, and efficiency, offering a scalable approach for intelligent psychiatric diagnostics. These findings suggest that reasoning-oriented LLMs can provide clinically reliable support for MDD detection and may inform broader applications in mental health care.

  • 6 authors
·
Sep 28, 2025

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.

  • 4 authors
·
Mar 4, 2020

SpineBench: A Clinically Salient, Level-Aware Benchmark Powered by the SpineMed-450k Corpus

Spine disorders affect 619 million people globally and are a leading cause of disability, yet AI-assisted diagnosis remains limited by the lack of level-aware, multimodal datasets. Clinical decision-making for spine disorders requires sophisticated reasoning across X-ray, CT, and MRI at specific vertebral levels. However, progress has been constrained by the absence of traceable, clinically-grounded instruction data and standardized, spine-specific benchmarks. To address this, we introduce SpineMed, an ecosystem co-designed with practicing spine surgeons. It features SpineMed-450k, the first large-scale dataset explicitly designed for vertebral-level reasoning across imaging modalities with over 450,000 instruction instances, and SpineBench, a clinically-grounded evaluation framework. SpineMed-450k is curated from diverse sources, including textbooks, guidelines, open datasets, and ~1,000 de-identified hospital cases, using a clinician-in-the-loop pipeline with a two-stage LLM generation method (draft and revision) to ensure high-quality, traceable data for question-answering, multi-turn consultations, and report generation. SpineBench evaluates models on clinically salient axes, including level identification, pathology assessment, and surgical planning. Our comprehensive evaluation of several recently advanced large vision-language models (LVLMs) on SpineBench reveals systematic weaknesses in fine-grained, level-specific reasoning. In contrast, our model fine-tuned on SpineMed-450k demonstrates consistent and significant improvements across all tasks. Clinician assessments confirm the diagnostic clarity and practical utility of our model's outputs.

  • 26 authors
·
Oct 3, 2025 2

Language Models as Inductive Reasoners

Inductive reasoning is a core component of human intelligence. In the past research of inductive reasoning within computer science, formal language is used as representations of knowledge (facts and rules, more specifically). However, formal language can cause systematic problems for inductive reasoning such as disability of handling raw input such as natural language, sensitiveness to mislabeled data, and incapacity to handle ambiguous input. To this end, we propose a new paradigm (task) for inductive reasoning, which is to induce natural language rules from natural language facts, and create a dataset termed DEER containing 1.2k rule-fact pairs for the task, where rules and facts are written in natural language. New automatic metrics are also proposed and analysed for the evaluation of this task. With DEER, we investigate a modern approach for inductive reasoning where we use natural language as representation for knowledge instead of formal language and use pretrained language models as ''reasoners''. Moreover, we provide the first and comprehensive analysis of how well pretrained language models can induce natural language rules from natural language facts. We also propose a new framework drawing insights from philosophy literature for this task, which we show in the experiment section that surpasses baselines in both automatic and human evaluations. We discuss about our future perspectives for inductive reasoning in Section 7. Dataset and code are available at https://github.com/ZonglinY/Inductive_Reasoning.

  • 8 authors
·
Dec 21, 2022

CIVICS: Building a Dataset for Examining Culturally-Informed Values in Large Language Models

This paper introduces the "CIVICS: Culturally-Informed & Values-Inclusive Corpus for Societal impacts" dataset, designed to evaluate the social and cultural variation of Large Language Models (LLMs) across multiple languages and value-sensitive topics. We create a hand-crafted, multilingual dataset of value-laden prompts which address specific socially sensitive topics, including LGBTQI rights, social welfare, immigration, disability rights, and surrogacy. CIVICS is designed to generate responses showing LLMs' encoded and implicit values. Through our dynamic annotation processes, tailored prompt design, and experiments, we investigate how open-weight LLMs respond to value-sensitive issues, exploring their behavior across diverse linguistic and cultural contexts. Using two experimental set-ups based on log-probabilities and long-form responses, we show social and cultural variability across different LLMs. Specifically, experiments involving long-form responses demonstrate that refusals are triggered disparately across models, but consistently and more frequently in English or translated statements. Moreover, specific topics and sources lead to more pronounced differences across model answers, particularly on immigration, LGBTQI rights, and social welfare. As shown by our experiments, the CIVICS dataset aims to serve as a tool for future research, promoting reproducibility and transparency across broader linguistic settings, and furthering the development of AI technologies that respect and reflect global cultural diversities and value pluralism. The CIVICS dataset and tools will be made available upon publication under open licenses; an anonymized version is currently available at https://huggingface.co/CIVICS-dataset.

  • 6 authors
·
May 22, 2024 1

SpiroLLM: Finetuning Pretrained LLMs to Understand Spirogram Time Series with Clinical Validation in COPD Reporting

Chronic Obstructive Pulmonary Disease (COPD), a major chronic respiratory disease with persistent airflow limitation, is a leading global cause of disability and mortality. Respiratory spirogram time series, routinely collected during pulmonary function tests (PFTs), play a critical role in the early detection of repsiratory diseases and in monitoring lung function over time. However, most current AI models for COPD diagnosis are limited to outputting classification results without providing a rationale for their diagnostic process, while current Large Language Models (LLMs) cannot understand spirograms yet, which severely limits their clinical trust and adoption. To tackle this challenge, we leverage a cohort of 234,028 individuals from the UK Biobank (UKB) to propose SpiroLLM, the first multimodal large language model that can understand spirogram. The model extracts morphological features from respiratory curves via a SpiroEncoder and aligns them with PFT numerical values in a unified latent space using a SpiroProjector, ultimately empowering a large language model to generate a comprehensive diagnostic report. Experimental results confirm that SpiroLLM achieved a diagnostic AUROC of 0.8980 (95% CI: 0.8820-0.9132). In a robustness test with missing core data, it maintained a 100% valid response rate, far surpassing the 13.4% of a text-only model and showcasing the superiority of its multimodal design. This work demonstrates the substantial potential of deeply fusing physiological signals with large language models, establishing a new paradigm for the next generation of interpretable and reliable clinical decision support tools.

  • 8 authors
·
Jul 21, 2025

Benchmarking the Pedagogical Knowledge of Large Language Models

Benchmarks like Massive Multitask Language Understanding (MMLU) have played a pivotal role in evaluating AI's knowledge and abilities across diverse domains. However, existing benchmarks predominantly focus on content knowledge, leaving a critical gap in assessing models' understanding of pedagogy - the method and practice of teaching. This paper introduces The Pedagogy Benchmark, a novel dataset designed to evaluate large language models on their Cross-Domain Pedagogical Knowledge (CDPK) and Special Education Needs and Disability (SEND) pedagogical knowledge. These benchmarks are built on a carefully curated set of questions sourced from professional development exams for teachers, which cover a range of pedagogical subdomains such as teaching strategies and assessment methods. Here we outline the methodology and development of these benchmarks. We report results for 97 models, with accuracies spanning a range from 28% to 89% on the pedagogical knowledge questions. We consider the relationship between cost and accuracy and chart the progression of the Pareto value frontier over time. We provide online leaderboards at https://rebrand.ly/pedagogy which are updated with new models and allow interactive exploration and filtering based on various model properties, such as cost per token and open-vs-closed weights, as well as looking at performance in different subjects. LLMs and generative AI have tremendous potential to influence education and help to address the global learning crisis. Education-focused benchmarks are crucial to measure models' capacities to understand pedagogical concepts, respond appropriately to learners' needs, and support effective teaching practices across diverse contexts. They are needed for informing the responsible and evidence-based deployment of LLMs and LLM-based tools in educational settings, and for guiding both development and policy decisions.

  • 10 authors
·
Jun 23, 2025

Nigerian Schizophrenia EEG Dataset (NSzED) Towards Data-Driven Psychiatry in Africa

This work has been carried out to improve the dearth of high-quality EEG datasets used for schizophrenia diagnostic tools development and studies from populations of developing and underdeveloped regions of the world. To this aim, the presented dataset contains international 10/20 system EEG recordings from West African subjects of Nigerian origin in restful states, mental arithmetic task execution states and while passively reacting to auditory stimuli, the first of its kind from the region and continent. The subjects are divided into patients and healthy controls and recorded from 37 patients and 22 healthy control subjects identified by the Mini International Schizophrenia Interview (MINI) and also assessed by the Positive and Negative Symptoms Scale (PANSS) and the World Health Organization Disability Assessment Schedule (WHODAS). All patients are admitted schizophrenia patients of the Mental Health Ward, Medical Outpatient Department of the Obafemi Awolowo University Teaching Hospital Complex (OAUTHC, Ile-Ife) and its subsidiary Wesley Guild Hospital Unit (OAUTHC, Ilesa). Controls are drawn from students and clinicians who volunteered to participate in the study at the Mental Health Ward of OAUTHC and the Wesley Guild Hospital Unit. This dataset is the first version of the Nigerian schizophrenia dataset (NSzED) and can be used by the neuroscience and computational psychiatry research community studying the diagnosis and prognosis of schizophrenia using the electroencephalogram signal modality.

  • 3 authors
·
Nov 30, 2023

SHINE: Deep Learning-Based Accessible Parking Management System

The ongoing expansion of urban areas facilitated by advancements in science and technology has resulted in a considerable increase in the number of privately owned vehicles worldwide, including in South Korea. However, this gradual increment in the number of vehicles has inevitably led to parking-related issues, including the abuse of disabled parking spaces (hereafter referred to as accessible parking spaces) designated for individuals with disabilities. Traditional license plate recognition (LPR) systems have proven inefficient in addressing such a problem in real-time due to the high frame rate of surveillance cameras, the presence of natural and artificial noise, and variations in lighting and weather conditions that impede detection and recognition by these systems. With the growing concept of parking 4.0, many sensors, IoT and deep learning-based approaches have been applied to automatic LPR and parking management systems. Nonetheless, the studies show a need for a robust and efficient model for managing accessible parking spaces in South Korea. To address this, we have proposed a novel system called, Shine, which uses the deep learning-based object detection algorithm for detecting the vehicle, license plate, and disability badges (referred to as cards, badges, or access badges hereafter) and verifies the rights of the driver to use accessible parking spaces by coordinating with the central server. Our model, which achieves a mean average precision of 92.16%, is expected to address the issue of accessible parking space abuse and contributes significantly towards efficient and effective parking management in urban environments.

  • 6 authors
·
Feb 1, 2023

DETONATE: A Benchmark for Text-to-Image Alignment and Kernelized Direct Preference Optimization

Alignment is crucial for text-to-image (T2I) models to ensure that generated images faithfully capture user intent while maintaining safety and fairness. Direct Preference Optimization (DPO), prominent in large language models (LLMs), is extending its influence to T2I systems. This paper introduces DPO-Kernels for T2I models, a novel extension enhancing alignment across three dimensions: (i) Hybrid Loss, integrating embedding-based objectives with traditional probability-based loss for improved optimization; (ii) Kernelized Representations, employing Radial Basis Function (RBF), Polynomial, and Wavelet kernels for richer feature transformations and better separation between safe and unsafe inputs; and (iii) Divergence Selection, expanding beyond DPO's default Kullback-Leibler (KL) regularizer by incorporating Wasserstein and R'enyi divergences for enhanced stability and robustness. We introduce DETONATE, the first large-scale benchmark of its kind, comprising approximately 100K curated image pairs categorized as chosen and rejected. DETONATE encapsulates three axes of social bias and discrimination: Race, Gender, and Disability. Prompts are sourced from hate speech datasets, with images generated by leading T2I models including Stable Diffusion 3.5 Large, Stable Diffusion XL, and Midjourney. Additionally, we propose the Alignment Quality Index (AQI), a novel geometric measure quantifying latent-space separability of safe/unsafe image activations, revealing hidden vulnerabilities. Empirically, we demonstrate that DPO-Kernels maintain strong generalization bounds via Heavy-Tailed Self-Regularization (HT-SR). DETONATE and complete code are publicly released.

  • 12 authors
·
Jun 16, 2025

Investigating Annotator Bias in Large Language Models for Hate Speech Detection

Data annotation, the practice of assigning descriptive labels to raw data, is pivotal in optimizing the performance of machine learning models. However, it is a resource-intensive process susceptible to biases introduced by annotators. The emergence of sophisticated Large Language Models (LLMs), like ChatGPT presents a unique opportunity to modernize and streamline this complex procedure. While existing research extensively evaluates the efficacy of LLMs, as annotators, this paper delves into the biases present in LLMs, specifically GPT 3.5 and GPT 4o when annotating hate speech data. Our research contributes to understanding biases in four key categories: gender, race, religion, and disability. Specifically targeting highly vulnerable groups within these categories, we analyze annotator biases. Furthermore, we conduct a comprehensive examination of potential factors contributing to these biases by scrutinizing the annotated data. We introduce our custom hate speech detection dataset, HateSpeechCorpus, to conduct this research. Additionally, we perform the same experiments on the ETHOS (Mollas et al., 2022) dataset also for comparative analysis. This paper serves as a crucial resource, guiding researchers and practitioners in harnessing the potential of LLMs for dataannotation, thereby fostering advancements in this critical field. The HateSpeechCorpus dataset is available here: https://github.com/AmitDasRup123/HateSpeechCorpus

  • 10 authors
·
Jun 16, 2024

PrivPAS: A real time Privacy-Preserving AI System and applied ethics

With 3.78 billion social media users worldwide in 2021 (48% of the human population), almost 3 billion images are shared daily. At the same time, a consistent evolution of smartphone cameras has led to a photography explosion with 85% of all new pictures being captured using smartphones. However, lately, there has been an increased discussion of privacy concerns when a person being photographed is unaware of the picture being taken or has reservations about the same being shared. These privacy violations are amplified for people with disabilities, who may find it challenging to raise dissent even if they are aware. Such unauthorized image captures may also be misused to gain sympathy by third-party organizations, leading to a privacy breach. Privacy for people with disabilities has so far received comparatively less attention from the AI community. This motivates us to work towards a solution to generate privacy-conscious cues for raising awareness in smartphone users of any sensitivity in their viewfinder content. To this end, we introduce PrivPAS (A real time Privacy-Preserving AI System) a novel framework to identify sensitive content. Additionally, we curate and annotate a dataset to identify and localize accessibility markers and classify whether an image is sensitive to a featured subject with a disability. We demonstrate that the proposed lightweight architecture, with a memory footprint of a mere 8.49MB, achieves a high mAP of 89.52% on resource-constrained devices. Furthermore, our pipeline, trained on face anonymized data, achieves an F1-score of 73.1%.

  • 6 authors
·
Feb 5, 2022

D-HUMOR: Dark Humor Understanding via Multimodal Open-ended Reasoning

Dark humor in online memes poses unique challenges due to its reliance on implicit, sensitive, and culturally contextual cues. To address the lack of resources and methods for detecting dark humor in multimodal content, we introduce a novel dataset of 4,379 Reddit memes annotated for dark humor, target category (gender, mental health, violence, race, disability, and other), and a three-level intensity rating (mild, moderate, severe). Building on this resource, we propose a reasoning-augmented framework that first generates structured explanations for each meme using a Large Vision-Language Model (VLM). Through a Role-Reversal Self-Loop, VLM adopts the author's perspective to iteratively refine its explanations, ensuring completeness and alignment. We then extract textual features from both the OCR transcript and the self-refined reasoning via a text encoder, while visual features are obtained using a vision transformer. A Tri-stream Cross-Reasoning Network (TCRNet) fuses these three streams, text, image, and reasoning, via pairwise attention mechanisms, producing a unified representation for classification. Experimental results demonstrate that our approach outperforms strong baselines across three tasks: dark humor detection, target identification, and intensity prediction. The dataset, annotations, and code are released to facilitate further research in multimodal humor understanding and content moderation. Code and Dataset are available at: https://github.com/Sai-Kartheek-Reddy/D-Humor-Dark-Humor-Understanding-via-Multimodal-Open-ended-Reasoning

  • 6 authors
·
Sep 8, 2025 2