Daily Papers

Medical report generation has achieved remarkable advancements yet has still been faced with several challenges. First, the inherent imbalance in the distribution of normal and abnormal cases may lead models to exhibit a biased focus on normal samples, resulting in unreliable diagnoses. Second, the frequent occurrence of common template sentences in the reports may overwhelm the critical abnormal information. Moreover, existing works focus on 2D chest X-rays, leaving CT report generation underexplored due to the high-dimensional nature of CT images and the limited availability of CT-report pairs. Recently, LLM has shown a great ability to generate reliable answers with appropriate prompts, which shed light on addressing the aforementioned challenges. In this paper, we propose Dia-LLaMA, a framework to adapt the LLaMA2-7B for CT report generation by incorporating diagnostic information as guidance prompts. Considering the high dimension of CT, we leverage a pre-trained ViT3D with perceiver to extract the visual information. To tailor the LLM for report generation and emphasize abnormality, we extract additional diagnostic information by referring to a disease prototype memory bank, which is updated during training to capture common disease representations. Furthermore, we introduce disease-aware attention to enable the model to adjust attention for different diseases. Experiments on the chest CT dataset demonstrated that our proposed method outperformed previous methods and achieved state-of-the-art on both clinical efficacy performance and natural language generation metrics. The code will be made publically available.

Alzheimer's disease (AD) constitutes a complex neurocognitive disease and is the main cause of dementia. Although many studies have been proposed targeting at diagnosing dementia through spontaneous speech, there are still limitations. Existing state-of-the-art approaches, which propose multimodal methods, train separately language and acoustic models, employ majority-vote approaches, and concatenate the representations of the different modalities either at the input level, i.e., early fusion, or during training. Also, some of them employ self-attention layers, which calculate the dependencies between representations without considering the contextual information. In addition, no prior work has taken into consideration the model calibration. To address these limitations, we propose some new methods for detecting AD patients, which capture the intra- and cross-modal interactions. First, we convert the audio files into log-Mel spectrograms, their delta, and delta-delta and create in this way an image per audio file consisting of three channels. Next, we pass each transcript and image through BERT and DeiT models respectively. After that, context-based self-attention layers, self-attention layers with a gate model, and optimal transport domain adaptation methods are employed for capturing the intra- and inter-modal interactions. Finally, we exploit two methods for fusing the self and cross-attended features. For taking into account the model calibration, we apply label smoothing. We use both performance and calibration metrics. Experiments conducted on the ADReSS Challenge dataset indicate the efficacy of our introduced approaches over existing research initiatives with our best performing model reaching Accuracy and F1-score up to 91.25% and 91.06% respectively.

Despite recent advances in medical vision-language pretraining, existing models still struggle to capture the diagnostic workflow: radiographs are typically treated as context-agnostic images, while radiologists' gaze -- a crucial cue for visual reasoning -- remains largely underexplored by existing methods. These limitations hinder the modeling of disease-specific patterns and weaken cross-modal alignment. To bridge this gap, we introduce CoGaze, a Context- and Gaze-guided vision-language pretraining framework for chest X-rays. We first propose a context-infused vision encoder that models how radiologists integrate clinical context -- including patient history, symptoms, and diagnostic intent -- to guide diagnostic reasoning. We then present a multi-level supervision paradigm that (1) enforces intra- and inter-modal semantic alignment through hybrid-positive contrastive learning, (2) injects diagnostic priors via disease-aware cross-modal representation learning, and (3) leverages radiologists' gaze as probabilistic priors to guide attention toward diagnostically salient regions. Extensive experiments demonstrate that CoGaze consistently outperforms state-of-the-art methods across diverse tasks, achieving up to +2.0% CheXbertF1 and +1.2% BLEU2 for free-text and structured report generation, +23.2% AUROC for zero-shot classification, and +12.2% Precision@1 for image-text retrieval. Code is available at https://github.com/mk-runner/CoGaze.

Medical image analysis continues to hold interesting challenges given the subtle characteristics of certain diseases and the significant overlap in appearance between diseases. In this work, we explore the concept of self-attention for tackling such subtleties in and between diseases. To this end, we introduce MEDUSA, a multi-scale encoder-decoder self-attention mechanism tailored for medical image analysis. While self-attention deep convolutional neural network architectures in existing literature center around the notion of multiple isolated lightweight attention mechanisms with limited individual capacities being incorporated at different points in the network architecture, MEDUSA takes a significant departure from this notion by possessing a single, unified self-attention mechanism with significantly higher capacity with multiple attention heads feeding into different scales in the network architecture. To the best of the authors' knowledge, this is the first "single body, multi-scale heads" realization of self-attention and enables explicit global context amongst selective attention at different levels of representational abstractions while still enabling differing local attention context at individual levels of abstractions. With MEDUSA, we obtain state-of-the-art performance on multiple challenging medical image analysis benchmarks including COVIDx, RSNA RICORD, and RSNA Pneumonia Challenge when compared to previous work. Our MEDUSA model is publicly available.

The medical domain is vast and diverse, with many existing embedding models focused on general healthcare applications. However, these models often struggle to capture a deep understanding of diseases due to their broad generalization across the entire medical field. To address this gap, I present DisEmbed, a disease-focused embedding model. DisEmbed is trained on a synthetic dataset specifically curated to include disease descriptions, symptoms, and disease-related Q\&A pairs, making it uniquely suited for disease-related tasks. For evaluation, I benchmarked DisEmbed against existing medical models using disease-specific datasets and the triplet evaluation method. My results demonstrate that DisEmbed outperforms other models, particularly in identifying disease-related contexts and distinguishing between similar diseases. This makes DisEmbed highly valuable for disease-specific use cases, including retrieval-augmented generation (RAG) tasks, where its performance is particularly robust.

Disease risk prediction has attracted increasing attention in the field of modern healthcare, especially with the latest advances in artificial intelligence (AI). Electronic health records (EHRs), which contain heterogeneous patient information, are widely used in disease risk prediction tasks. One challenge of applying AI models for risk prediction lies in generating interpretable evidence to support the prediction results while retaining the prediction ability. In order to address this problem, we propose the method of jointly embedding words and labels whereby attention modules learn the weights of words from medical notes according to their relevance to the names of risk prediction labels. This approach boosts interpretability by employing an attention mechanism and including the names of prediction tasks in the model. However, its application is only limited to the handling of textual inputs such as medical notes. In this paper, we propose a label dependent attention model LDAM to 1) improve the interpretability by exploiting Clinical-BERT (a biomedical language model pre-trained on a large clinical corpus) to encode biomedically meaningful features and labels jointly; 2) extend the idea of joint embedding to the processing of time-series data, and develop a multi-modal learning framework for integrating heterogeneous information from medical notes and time-series health status indicators. To demonstrate our method, we apply LDAM to the MIMIC-III dataset to predict different disease risks. We evaluate our method both quantitatively and qualitatively. Specifically, the predictive power of LDAM will be shown, and case studies will be carried out to illustrate its interpretability.

Healthcare data now span EHRs, medical imaging, genomics, and wearable sensors, but most diagnostic models still process these modalities in isolation. This limits their ability to capture early, cross-modal disease signatures. This paper introduces a multimodal foundation model built on a transformer architecture that integrates heterogeneous clinical data through modality-specific encoders and cross-modal attention. Each modality is mapped into a shared latent space and fused using multi-head attention with residual normalization. We implement the framework using a multimodal dataset that simulates early-stage disease patterns across EHR sequences, imaging patches, genomic profiles, and wearable signals, including missing-modality scenarios and label noise. The model is trained using supervised classification together with self-supervised reconstruction and contrastive alignment to improve robustness. Experimental evaluation demonstrates strong performance in early-detection settings, with stable classification metrics, reliable uncertainty estimates, and interpretable attention patterns. The approach moves toward a flexible, pretrain-and-fine-tune foundation model that supports precision diagnostics, handles incomplete inputs, and improves early disease detection across oncology, cardiology, and neurology applications.

In recent years, medical information technology has made it possible for electronic health record (EHR) to store fairly complete clinical data. This has brought health care into the era of "big data". However, medical data are often sparse and strongly correlated, which means that medical problems cannot be solved effectively. With the rapid development of deep learning in recent years, it has provided opportunities for the use of big data in healthcare. In this paper, we propose a temporal-saptial correlation attention network (TSCAN) to handle some clinical characteristic prediction problems, such as predicting death, predicting length of stay, detecting physiologic decline, and classifying phenotypes. Based on the design of the attention mechanism model, our approach can effectively remove irrelevant items in clinical data and irrelevant nodes in time according to different tasks, so as to obtain more accurate prediction results. Our method can also find key clinical indicators of important outcomes that can be used to improve treatment options. Our experiments use information from the Medical Information Mart for Intensive Care (MIMIC-IV) database, which is open to the public. Finally, we have achieved significant performance benefits of 2.0\% (metric) compared to other SOTA prediction methods. We achieved a staggering 90.7\% on mortality rate, 45.1\% on length of stay. The source code can be find: https://github.com/yuyuheintju/TSCAN.

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.

Alongside neuroimaging such as MRI scans and PET, Alzheimer's disease (AD) datasets contain valuable tabular data including AD biomarkers and clinical assessments. Existing computer vision approaches struggle to utilize this additional information. To address these needs, we propose a generalizable framework for multimodal contrastive learning of image data and tabular data, a novel tabular attention module for amplifying and ranking salient features in tables, and the application of these techniques onto Alzheimer's disease prediction. Experimental evaulations demonstrate the strength of our framework by detecting Alzheimer's disease (AD) from over 882 MR image slices from the ADNI database. We take advantage of the high interpretability of tabular data and our novel tabular attention approach and through attribution of the attention scores for each row of the table, we note and rank the most predominant features. Results show that the model is capable of an accuracy of over 83.8%, almost a 10% increase from previous state of the art.

Radiologists rely on eye movements to navigate and interpret medical images. A trained radiologist possesses knowledge about the potential diseases that may be present in the images and, when searching, follows a mental checklist to locate them using their gaze. This is a key observation, yet existing models fail to capture the underlying intent behind each fixation. In this paper, we introduce a deep learning-based approach, RadGazeIntent, designed to model this behavior: having an intention to find something and actively searching for it. Our transformer-based architecture processes both the temporal and spatial dimensions of gaze data, transforming fine-grained fixation features into coarse, meaningful representations of diagnostic intent to interpret radiologists' goals. To capture the nuances of radiologists' varied intention-driven behaviors, we process existing medical eye-tracking datasets to create three intention-labeled subsets: RadSeq (Systematic Sequential Search), RadExplore (Uncertainty-driven Exploration), and RadHybrid (Hybrid Pattern). Experimental results demonstrate RadGazeIntent's ability to predict which findings radiologists are examining at specific moments, outperforming baseline methods across all intention-labeled datasets.

Deep Learning based models are currently dominating most state-of-the-art solutions for disease prediction. Existing works employ RNNs along with multiple levels of attention mechanisms to provide interpretability. These deep learning models, with trainable parameters running into millions, require huge amounts of compute and data to train and deploy. These requirements are sometimes so huge that they render usage of such models as unfeasible. We address these challenges by developing a simpler yet interpretable non-deep learning based model for application to EHR data. We model and showcase our work's results on the task of predicting first occurrence of a diagnosis, often overlooked in existing works. We push the capabilities of a tree based model and come up with a strong baseline for more sophisticated models. Its performance shows an improvement over deep learning based solutions (both, with and without the first-occurrence constraint) all the while maintaining interpretability.

Deep learning has enabled the development of highly robust foundation models for various pathological tasks across diverse diseases and patient cohorts. Among these models, vision-language pre-training, which leverages large-scale paired data to align pathology image and text embedding spaces, and provides a novel zero-shot paradigm for downstream tasks. However, existing models have been primarily data-driven and lack the incorporation of domain-specific knowledge, which limits their performance in cancer diagnosis, especially for rare tumor subtypes. To address this limitation, we establish a Knowledge-enhanced Pathology (KEEP) foundation model that harnesses disease knowledge to facilitate vision-language pre-training. Specifically, we first construct a disease knowledge graph (KG) that covers 11,454 human diseases with 139,143 disease attributes, including synonyms, definitions, and hypernym relations. We then systematically reorganize the millions of publicly available noisy pathology image-text pairs, into 143K well-structured semantic groups linked through the hierarchical relations of the disease KG. To derive more nuanced image and text representations, we propose a novel knowledge-enhanced vision-language pre-training approach that integrates disease knowledge into the alignment within hierarchical semantic groups instead of unstructured image-text pairs. Validated on 18 diverse benchmarks with more than 14,000 whole slide images (WSIs), KEEP achieves state-of-the-art performance in zero-shot cancer diagnostic tasks. Notably, for cancer detection, KEEP demonstrates an average sensitivity of 89.8% at a specificity of 95.0% across 7 cancer types. For cancer subtyping, KEEP achieves a median balanced accuracy of 0.456 in subtyping 30 rare brain cancers, indicating strong generalizability for diagnosing rare tumors.

Deep learning brought boosts to auto diabetic retinopathy (DR) diagnosis, thus, greatly helping ophthalmologists for early disease detection, which contributes to preventing disease deterioration that may eventually lead to blindness. It has been proved that convolutional neural network (CNN)-aided lesion identifying or segmentation benefits auto DR screening. The key to fine-grained lesion tasks mainly lies in: (1) extracting features being both sensitive to tiny lesions and robust against DR-irrelevant interference, and (2) exploiting and re-using encoded information to restore lesion locations under extremely imbalanced data distribution. To this end, we propose a CNN-based DR diagnosis network with attention mechanism involved, termed lesion-aware network, to better capture lesion information from imbalanced data. Specifically, we design the lesion-aware module (LAM) to capture noise-like lesion areas across deeper layers, and the feature-preserve module (FPM) to assist shallow-to-deep feature fusion. Afterward, the proposed lesion-aware network (LANet) is constructed by embedding the LAM and FPM into the CNN decoders for DR-related information utilization. The proposed LANet is then further extended to a DR screening network by adding a classification layer. Through experiments on three public fundus datasets with pixel-level annotations, our method outperforms the mainstream methods with an area under curve of 0.967 in DR screening, and increases the overall average precision by 7.6%, 2.1%, and 1.2% in lesion segmentation on three datasets. Besides, the ablation study validates the effectiveness of the proposed sub-modules.

Effectively representing medical images, especially retinal images, presents a considerable challenge due to variations in appearance, size, and contextual information of pathological signs called lesions. Precise discrimination of these lesions is crucial for diagnosing vision-threatening issues such as diabetic retinopathy. While visual attention-based neural networks have been introduced to learn spatial context and channel correlations from retinal images, they often fall short in capturing localized lesion context. Addressing this limitation, we propose a novel attention mechanism called Guided Context Gating, an unique approach that integrates Context Formulation, Channel Correlation, and Guided Gating to learn global context, spatial correlations, and localized lesion context. Our qualitative evaluation against existing attention mechanisms emphasize the superiority of Guided Context Gating in terms of explainability. Notably, experiments on the Zenodo-DR-7 dataset reveal a substantial 2.63% accuracy boost over advanced attention mechanisms & an impressive 6.53% improvement over the state-of-the-art Vision Transformer for assessing the severity grade of retinopathy, even with imbalanced and limited training samples for each class.

Data scarcity is a common obstacle in medical research due to the high costs associated with data collection and the complexity of gaining access to and utilizing data. Synthesizing health data may provide an efficient and cost-effective solution to this shortage, enabling researchers to explore distributions and populations that are not represented in existing observations or difficult to access due to privacy considerations. To that end, we have developed a multi-task self-attention model that produces realistic wearable activity data. We examine the characteristics of the generated data and quantify its similarity to genuine samples with both quantitative and qualitative approaches.

Building AI models with trustworthiness is important especially in regulated areas such as healthcare. In tackling COVID-19, previous work uses convolutional neural networks as the backbone architecture, which has shown to be prone to over-caution and overconfidence in making decisions, rendering them less trustworthy -- a crucial flaw in the context of medical imaging. In this study, we propose a feature learning approach using Vision Transformers, which use an attention-based mechanism, and examine the representation learning capability of Transformers as a new backbone architecture for medical imaging. Through the task of classifying COVID-19 chest radiographs, we investigate into whether generalization capabilities benefit solely from Vision Transformers' architectural advances. Quantitative and qualitative evaluations are conducted on the trustworthiness of the models, through the use of "trust score" computation and a visual explainability technique. We conclude that the attention-based feature learning approach is promising in building trustworthy deep learning models for healthcare.

Automatic disease diagnosis has become increasingly valuable in clinical practice. The advent of large language models (LLMs) has catalyzed a paradigm shift in artificial intelligence, with growing evidence supporting the efficacy of LLMs in diagnostic tasks. Despite the increasing attention in this field, a holistic view is still lacking. Many critical aspects remain unclear, such as the diseases and clinical data to which LLMs have been applied, the LLM techniques employed, and the evaluation methods used. In this article, we perform a comprehensive review of LLM-based methods for disease diagnosis. Our review examines the existing literature across various dimensions, including disease types and associated clinical specialties, clinical data, LLM techniques, and evaluation methods. Additionally, we offer recommendations for applying and evaluating LLMs for diagnostic tasks. Furthermore, we assess the limitations of current research and discuss future directions. To our knowledge, this is the first comprehensive review for LLM-based disease diagnosis.

Attention Model has now become an important concept in neural networks that has been researched within diverse application domains. This survey provides a structured and comprehensive overview of the developments in modeling attention. In particular, we propose a taxonomy which groups existing techniques into coherent categories. We review salient neural architectures in which attention has been incorporated, and discuss applications in which modeling attention has shown a significant impact. We also describe how attention has been used to improve the interpretability of neural networks. Finally, we discuss some future research directions in attention. We hope this survey will provide a succinct introduction to attention models and guide practitioners while developing approaches for their applications.

Electronic Health Records (EHRs) contain rich temporal dynamics that conventional encoding approaches fail to adequately capture. While Large Language Models (LLMs) show promise for EHR modeling, they struggle to reason about sequential clinical events and temporal dependencies. We propose Next Event Prediction (NEP), a framework that enhances LLMs' temporal reasoning through autoregressive fine-tuning on clinical event sequences. By reformulating EHRs as timestamped event chains and predicting future medical events, NEP explicitly models disease progression patterns and causal relationships. Extensive evaluations across oncology survival prediction and clinical diagnosis tasks demonstrate NEP's superiority, outperforming specialized EHR models by 4.6% AUROC and general-purpose LLMs by 7.2% C-index in temporal reasoning tasks. Our analyses reveal dual benefits: state-of-the-art prediction accuracy combined with clinically interpretable attention patterns that align with known disease pathways.

Despite the outstanding performance of deep learning models in clinical prediction tasks, explainability remains a significant challenge. Inspired by transformer architectures, we introduce the Temporal-Feature Cross Attention Mechanism (TFCAM), a novel deep learning framework designed to capture dynamic interactions among clinical features across time, enhancing both predictive accuracy and interpretability. In an experiment with 1,422 patients with Chronic Kidney Disease, predicting progression to End-Stage Renal Disease, TFCAM outperformed LSTM and RETAIN baselines, achieving an AUROC of 0.95 and an F1-score of 0.69. Beyond performance gains, TFCAM provides multi-level explainability by identifying critical temporal periods, ranking feature importance, and quantifying how features influence each other across time before affecting predictions. Our approach addresses the "black box" limitations of deep learning in healthcare, offering clinicians transparent insights into disease progression mechanisms while maintaining state-of-the-art predictive performance.

Melanoma is the most lethal subtype of skin cancer, and early and accurate detection of this disease can greatly improve patients' outcomes. Although machine learning models, especially convolutional neural networks (CNNs), have shown great potential in automating melanoma classification, their diagnostic reliability still suffers due to inconsistent focus on lesion areas. In this study, we analyze the relationship between lesion attention and diagnostic performance, involving masked images, bounding box detection, and transfer learning. We used multiple explainability and sensitivity analysis approaches to investigate how well models aligned their attention with lesion areas and how this alignment correlated with precision, recall, and F1-score. Results showed that models with a higher focus on lesion areas achieved better diagnostic performance, suggesting the potential of interpretable AI in medical diagnostics. This study provides a foundation for developing more accurate and trustworthy melanoma classification models in the future.

Cancer has relational information residing at varying scales, modalities, and resolutions of the acquired data, such as radiology, pathology, genomics, proteomics, and clinical records. Integrating diverse data types can improve the accuracy and reliability of cancer diagnosis and treatment. There can be disease-related information that is too subtle for humans or existing technological tools to discern visually. Traditional methods typically focus on partial or unimodal information about biological systems at individual scales and fail to encapsulate the complete spectrum of the heterogeneous nature of data. Deep neural networks have facilitated the development of sophisticated multimodal data fusion approaches that can extract and integrate relevant information from multiple sources. Recent deep learning frameworks such as Graph Neural Networks (GNNs) and Transformers have shown remarkable success in multimodal learning. This review article provides an in-depth analysis of the state-of-the-art in GNNs and Transformers for multimodal data fusion in oncology settings, highlighting notable research studies and their findings. We also discuss the foundations of multimodal learning, inherent challenges, and opportunities for integrative learning in oncology. By examining the current state and potential future developments of multimodal data integration in oncology, we aim to demonstrate the promising role that multimodal neural networks can play in cancer prevention, early detection, and treatment through informed oncology practices in personalized settings.

This paper proposes joint attention estimation in a single image. Different from related work in which only the gaze-related attributes of people are independently employed, (I) their locations and actions are also employed as contextual cues for weighting their attributes, and (ii) interactions among all of these attributes are explicitly modeled in our method. For the interaction modeling, we propose a novel Transformer-based attention network to encode joint attention as low-dimensional features. We introduce a specialized MLP head with positional embedding to the Transformer so that it predicts pixelwise confidence of joint attention for generating the confidence heatmap. This pixelwise prediction improves the heatmap accuracy by avoiding the ill-posed problem in which the high-dimensional heatmap is predicted from the low-dimensional features. The estimated joint attention is further improved by being integrated with general image-based attention estimation. Our method outperforms SOTA methods quantitatively in comparative experiments. Code: https://anonymous.4open.science/r/anonymized_codes-ECA4.

In healthcare, medical image segmentation is crucial for accurate disease diagnosis and the development of effective treatment strategies. Early detection can significantly aid in managing diseases and potentially prevent their progression. Machine learning, particularly deep convolutional neural networks, has emerged as a promising approach to addressing segmentation challenges. Traditional methods like U-Net use encoding blocks for local representation modeling and decoding blocks to uncover semantic relationships. However, these models often struggle with multi-scale objects exhibiting significant variations in texture and shape, and they frequently fail to capture long-range dependencies in the input data. Transformers designed for sequence-to-sequence predictions have been proposed as alternatives, utilizing global self-attention mechanisms. Yet, they can sometimes lack precise localization due to insufficient granular details. To overcome these limitations, we introduce TransDAE: a novel approach that reimagines the self-attention mechanism to include both spatial and channel-wise associations across the entire feature space, while maintaining computational efficiency. Additionally, TransDAE enhances the skip connection pathway with an inter-scale interaction module, promoting feature reuse and improving localization accuracy. Remarkably, TransDAE outperforms existing state-of-the-art methods on the Synaps multi-organ dataset, even without relying on pre-trained weights.

In some medical imaging tasks and other settings where only small parts of the image are informative for the classification task, traditional CNNs can sometimes struggle to generalise. Manually annotated Regions of Interest (ROI) are sometimes used to isolate the most informative parts of the image. However, these are expensive to collect and may vary significantly across annotators. To overcome these issues, we propose a framework that employs saliency maps to obtain soft spatial attention masks that modulate the image features at different scales. We refer to our method as Adversarial Counterfactual Attention (ACAT). ACAT increases the baseline classification accuracy of lesions in brain CT scans from 71.39% to 72.55% and of COVID-19 related findings in lung CT scans from 67.71% to 70.84% and exceeds the performance of competing methods. We investigate the best way to generate the saliency maps employed in our architecture and propose a way to obtain them from adversarially generated counterfactual images. They are able to isolate the area of interest in brain and lung CT scans without using any manual annotations. In the task of localising the lesion location out of 6 possible regions, they obtain a score of 65.05% on brain CT scans, improving the score of 61.29% obtained with the best competing method.

Heart disease, also known as cardiovascular disease, is a prevalent and critical medical condition characterized by the impairment of the heart and blood vessels, leading to various complications such as coronary artery disease, heart failure, and myocardial infarction. The timely and accurate detection of heart disease is of paramount importance in clinical practice. Early identification of individuals at risk enables proactive interventions, preventive measures, and personalized treatment strategies to mitigate the progression of the disease and reduce adverse outcomes. In recent years, the field of heart disease detection has witnessed notable advancements due to the integration of sophisticated technologies and computational approaches. These include machine learning algorithms, data mining techniques, and predictive modeling frameworks that leverage vast amounts of clinical and physiological data to improve diagnostic accuracy and risk stratification. In this work, we propose to detect heart disease from ECG images using cutting-edge technologies, namely vision transformer models. These models are Google-Vit, Microsoft-Beit, and Swin-Tiny. To the best of our knowledge, this is the initial endeavor concentrating on the detection of heart diseases through image-based ECG data by employing cuttingedge technologies namely, transformer models. To demonstrate the contribution of the proposed framework, the performance of vision transformer models are compared with state-of-the-art studies. Experiment results show that the proposed framework exhibits remarkable classification results.

International Classification of Disease (ICD) coding procedure which refers to tagging medical notes with diagnosis codes has been shown to be effective and crucial to the billing system in medical sector. Currently, ICD codes are assigned to a clinical note manually which is likely to cause many errors. Moreover, training skilled coders also requires time and human resources. Therefore, automating the ICD code determination process is an important task. With the advancement of artificial intelligence theory and computational hardware, machine learning approach has emerged as a suitable solution to automate this process. In this project, we apply a transformer-based architecture to capture the interdependence among the tokens of a document and then use a code-wise attention mechanism to learn code-specific representations of the entire document. Finally, they are fed to separate dense layers for corresponding code prediction. Furthermore, to handle the imbalance in the code frequency of clinical datasets, we employ a label distribution aware margin (LDAM) loss function. The experimental results on the MIMIC-III dataset show that our proposed model outperforms other baselines by a significant margin. In particular, our best setting achieves a micro-AUC score of 0.923 compared to 0.868 of bidirectional recurrent neural networks. We also show that by using the code-wise attention mechanism, the model can provide more insights about its prediction, and thus it can support clinicians to make reliable decisions. Our code is available online (https://github.com/biplob1ly/TransICD)

In recent years, Deep Learning (DL) models are becoming important due to their demonstrated success at overcoming complex learning problems. DL models have been applied effectively for different Natural Language Processing (NLP) tasks such as part-of-Speech (PoS) tagging and Machine Translation (MT). Disease Named Entity Recognition (Disease-NER) is a crucial task which aims at extracting disease Named Entities (NEs) from text. In this paper, a DL model for Disease-NER using dictionary information is proposed and evaluated on National Center for Biotechnology Information (NCBI) disease corpus and BC5CDR dataset. Word embeddings trained over general domain texts as well as biomedical texts have been used to represent input to the proposed model. This study also compares two different Segment Representation (SR) schemes, namely IOB2 and IOBES for Disease-NER. The results illustrate that using dictionary information, pre-trained word embeddings, character embeddings and CRF with global score improves the performance of Disease-NER system.

Clinical diagnosis is a highly specialized discipline requiring both domain expertise and strict adherence to rigorous guidelines. While current AI-driven medical research predominantly focuses on knowledge graphs or natural text pretraining paradigms to incorporate medical knowledge, these approaches primarily rely on implicitly encoded knowledge within model parameters, neglecting task-specific knowledge required by diverse downstream tasks. To address this limitation, we propose Retrieval-Augmented Diagnosis (RAD), a novel framework that explicitly injects external knowledge into multimodal models directly on downstream tasks. Specifically, RAD operates through three key mechanisms: retrieval and refinement of disease-centered knowledge from multiple medical sources, a guideline-enhanced contrastive loss that constrains the latent distance between multi-modal features and guideline knowledge, and the dual transformer decoder that employs guidelines as queries to steer cross-modal fusion, aligning the models with clinical diagnostic workflows from guideline acquisition to feature extraction and decision-making. Moreover, recognizing the lack of quantitative evaluation of interpretability for multimodal diagnostic models, we introduce a set of criteria to assess the interpretability from both image and text perspectives. Extensive evaluations across four datasets with different anatomies demonstrate RAD's generalizability, achieving state-of-the-art performance. Furthermore, RAD enables the model to concentrate more precisely on abnormal regions and critical indicators, ensuring evidence-based, trustworthy diagnosis. Our code is available at https://github.com/tdlhl/RAD.

Generalist Large Language Models (LLMs), such as GPT-4, have shown considerable promise in various domains, including medical diagnosis. Rare diseases, affecting approximately 300 million people worldwide, often have unsatisfactory clinical diagnosis rates primarily due to a lack of experienced physicians and the complexity of differentiating among many rare diseases. In this context, recent news such as "ChatGPT correctly diagnosed a 4-year-old's rare disease after 17 doctors failed" underscore LLMs' potential, yet underexplored, role in clinically diagnosing rare diseases. To bridge this research gap, we introduce RareBench, a pioneering benchmark designed to systematically evaluate the capabilities of LLMs on 4 critical dimensions within the realm of rare diseases. Meanwhile, we have compiled the largest open-source dataset on rare disease patients, establishing a benchmark for future studies in this domain. To facilitate differential diagnosis of rare diseases, we develop a dynamic few-shot prompt methodology, leveraging a comprehensive rare disease knowledge graph synthesized from multiple knowledge bases, significantly enhancing LLMs' diagnostic performance. Moreover, we present an exhaustive comparative study of GPT-4's diagnostic capabilities against those of specialist physicians. Our experimental findings underscore the promising potential of integrating LLMs into the clinical diagnostic process for rare diseases. This paves the way for exciting possibilities in future advancements in this field.

The World Health Organization added Disease X to their shortlist of blueprint priority diseases to represent a hypothetical, unknown pathogen that could cause a future epidemic. During different virus outbreaks of the past, such as COVID-19, Influenza, Lyme Disease, and Zika virus, researchers from various disciplines utilized Google Trends to mine multimodal components of web behavior to study, investigate, and analyze the global awareness, preparedness, and response associated with these respective virus outbreaks. As the world prepares for Disease X, a dataset on web behavior related to Disease X would be crucial to contribute towards the timely advancement of research in this field. Furthermore, none of the prior works in this field have focused on the development of a dataset to compile relevant web behavior data, which would help to prepare for Disease X. To address these research challenges, this work presents a dataset of web behavior related to Disease X, which emerged from different geographic regions of the world, between February 2018 and August 2023. Specifically, this dataset presents the search interests related to Disease X from 94 geographic regions. The dataset was developed by collecting data using Google Trends. The relevant search interests for all these regions for each month in this time range are available in this dataset. This paper also discusses the compliance of this dataset with the FAIR principles of scientific data management. Finally, an analysis of this dataset is presented to uphold the applicability, relevance, and usefulness of this dataset for the investigation of different research questions in the interrelated fields of Big Data, Data Mining, Healthcare, Epidemiology, and Data Analysis with a specific focus on Disease X.

Millions of users share their experiences on social media sites, such as Twitter, which in turn generate valuable data for public health monitoring, digital epidemiology, and other analyses of population health at global scale. The first, critical, task for these applications is classifying whether a personal health event was mentioned, which we call the (PHM) problem. This task is challenging for many reasons, including typically short length of social media posts, inventive spelling and lexicons, and figurative language, including hyperbole using diseases like "heart attack" or "cancer" for emphasis, and not as a health self-report. This problem is even more challenging for rarely reported, or frequent but ambiguously expressed conditions, such as "stroke". To address this problem, we propose a general, robust method for detecting PHMs in social media, which we call WESPAD, that combines lexical, syntactic, word embedding-based, and context-based features. WESPAD is able to generalize from few examples by automatically distorting the word embedding space to most effectively detect the true health mentions. Unlike previously proposed state-of-the-art supervised and deep-learning techniques, WESPAD requires relatively little training data, which makes it possible to adapt, with minimal effort, to each new disease and condition. We evaluate WESPAD on both an established publicly available Flu detection benchmark, and on a new dataset that we have constructed with mentions of multiple health conditions. Our experiments show that WESPAD outperforms the baselines and state-of-the-art methods, especially in cases when the number and proportion of true health mentions in the training data is small.

Even though convolutional neural networks (CNNs) are driving progress in medical image segmentation, standard models still have some drawbacks. First, the use of multi-scale approaches, i.e., encoder-decoder architectures, leads to a redundant use of information, where similar low-level features are extracted multiple times at multiple scales. Second, long-range feature dependencies are not efficiently modeled, resulting in non-optimal discriminative feature representations associated with each semantic class. In this paper we attempt to overcome these limitations with the proposed architecture, by capturing richer contextual dependencies based on the use of guided self-attention mechanisms. This approach is able to integrate local features with their corresponding global dependencies, as well as highlight interdependent channel maps in an adaptive manner. Further, the additional loss between different modules guides the attention mechanisms to neglect irrelevant information and focus on more discriminant regions of the image by emphasizing relevant feature associations. We evaluate the proposed model in the context of semantic segmentation on three different datasets: abdominal organs, cardiovascular structures and brain tumors. A series of ablation experiments support the importance of these attention modules in the proposed architecture. In addition, compared to other state-of-the-art segmentation networks our model yields better segmentation performance, increasing the accuracy of the predictions while reducing the standard deviation. This demonstrates the efficiency of our approach to generate precise and reliable automatic segmentations of medical images. Our code is made publicly available at https://github.com/sinAshish/Multi-Scale-Attention

General-purpose Large Vision-Language Models (LVLMs), despite their massive scale, often falter in dermatology due to "diffuse attention" - the inability to disentangle subtle pathological lesions from background noise. In this paper, we challenge the assumption that parameter scaling is the only path to medical precision. We introduce SkinFlow, a framework that treats diagnosis as an optimization of visual information transmission efficiency. Our approach utilizes a Virtual-Width Dynamic Vision Encoder (DVE) to "unfold" complex pathological manifolds without physical parameter expansion, coupled with a two-stage Reinforcement Learning strategy. This strategy sequentially aligns explicit medical descriptions (Stage I) and reconstructs implicit diagnostic textures (Stage II) within a constrained semantic space. Furthermore, we propose a clinically grounded evaluation protocol that prioritizes diagnostic safety and hierarchical relevance over rigid label matching. Empirical results are compelling: our 7B model establishes a new state-of-the-art on the Fitzpatrick17k benchmark, achieving a +12.06% gain in Top-1 accuracy and a +28.57% boost in Top-6 accuracy over the massive general-purpose models (e.g., Qwen3VL-235B and GPT-5.2). These findings demonstrate that optimizing geometric capacity and information flow yields superior diagnostic reasoning compared to raw parameter scaling.

Attention mechanisms are a central property of cognitive systems allowing them to selectively deploy cognitive resources in a flexible manner. Attention has been long studied in the neurosciences and there are numerous phenomenological models that try to capture its core properties. Recently attentional mechanisms have become a dominating architectural choice of machine learning and are the central innovation of Transformers. The dominant intuition and formalism underlying their development has drawn on ideas of keys and queries in database management systems. In this work, we propose an alternative Bayesian foundation for attentional mechanisms and show how this unifies different attentional architectures in machine learning. This formulation allows to to identify commonality across different attention ML architectures as well as suggest a bridge to those developed in neuroscience. We hope this work will guide more sophisticated intuitions into the key properties of attention architectures and suggest new ones.

Accurate and interpretable multi-disease diagnosis remains a critical challenge in medical research, particularly when leveraging heterogeneous multimodal medical data. Current approaches often rely on single-modal data, limiting their ability to comprehensively understand complex diseases. To address this, we propose MedTVT-R1, a novel Multimodal Large Language Model (MLLM) framework designed to integrate clinical multimodal data for reasoning and diagnosing multiple diseases. We construct MedTVT-QA, a curated instruction dataset that provides question-answer pairs for physiological-level interpretations and disease-level diagnoses with a Chain of Evidence approach. MedTVT-R1 incorporates a modality perception layer to capture inter-modal dependencies and adaptively weight modality contributions. Additionally, we employ Group Relative Policy Optimization (GRPO)-based Reinforcement Fine-Tuning with a Jaccard Reward function to enhance diagnostic reasoning. Experimental results demonstrate MedTVT-R1's superiority in multimodal feature utilization and multi-disease diagnosis, offering significant potential for clinical applications such as diagnostic report generation and comorbidity reasoning. The dataset and code are available at https://github.com/keke-nice/MedTVT-R1.

The rapid increase in the number of Computed Tomography (CT) scan examinations has created an urgent need for automated tools, such as organ segmentation, anomaly classification, and report generation, to assist radiologists with their growing workload. Multi-label classification of Three-Dimensional (3D) CT scans is a challenging task due to the volumetric nature of the data and the variety of anomalies to be detected. Existing deep learning methods based on Convolutional Neural Networks (CNNs) struggle to capture long-range dependencies effectively, while Vision Transformers require extensive pre-training, posing challenges for practical use. Additionally, these existing methods do not explicitly model the radiologist's navigational behavior while scrolling through CT scan slices, which requires both global context understanding and local detail awareness. In this study, we present CT-Scroll, a novel global-local attention model specifically designed to emulate the scrolling behavior of radiologists during the analysis of 3D CT scans. Our approach is evaluated on two public datasets, demonstrating its efficacy through comprehensive experiments and an ablation study that highlights the contribution of each model component.

Automatic radiology report generation is booming due to its huge application potential for the healthcare industry. However, existing computer vision and natural language processing approaches to tackle this problem are limited in two aspects. First, when extracting image features, most of them neglect multi-view reasoning in vision and model single-view structure of medical images, such as space-view or channel-view. However, clinicians rely on multi-view imaging information for comprehensive judgment in daily clinical diagnosis. Second, when generating reports, they overlook context reasoning with multi-modal information and focus on pure textual optimization utilizing retrieval-based methods. We aim to address these two issues by proposing a model that better simulates clinicians' perspectives and generates more accurate reports. Given the above limitation in feature extraction, we propose a Globally-intensive Attention (GIA) module in the medical image encoder to simulate and integrate multi-view vision perception. GIA aims to learn three types of vision perception: depth view, space view, and pixel view. On the other hand, to address the above problem in report generation, we explore how to involve multi-modal signals to generate precisely matched reports, i.e., how to integrate previously predicted words with region-aware visual content in next word prediction. Specifically, we design a Visual Knowledge-guided Decoder (VKGD), which can adaptively consider how much the model needs to rely on visual information and previously predicted text to assist next word prediction. Hence, our final Intensive Vision-guided Network (IVGN) framework includes a GIA-guided Visual Encoder and the VKGD. Experiments on two commonly-used datasets IU X-Ray and MIMIC-CXR demonstrate the superior ability of our method compared with other state-of-the-art approaches.

A user-generated text on social media enables health workers to keep track of information, identify possible outbreaks, forecast disease trends, monitor emergency cases, and ascertain disease awareness and response to official health correspondence. This exchange of health information on social media has been regarded as an attempt to enhance public health surveillance (PHS). Despite its potential, the technology is still in its early stages and is not ready for widespread application. Advancements in pretrained language models (PLMs) have facilitated the development of several domain-specific PLMs and a variety of downstream applications. However, there are no PLMs for social media tasks involving PHS. We present and release PHS-BERT, a transformer-based PLM, to identify tasks related to public health surveillance on social media. We compared and benchmarked the performance of PHS-BERT on 25 datasets from different social medial platforms related to 7 different PHS tasks. Compared with existing PLMs that are mainly evaluated on limited tasks, PHS-BERT achieved state-of-the-art performance on all 25 tested datasets, showing that our PLM is robust and generalizable in the common PHS tasks. By making PHS-BERT available, we aim to facilitate the community to reduce the computational cost and introduce new baselines for future works across various PHS-related tasks.

Detecting and delineating tiny targets in 3D brain scans is a central yet under-addressed challenge in medical imaging.In ischemic stroke, for instance, the culprit thrombus is small, low-contrast, and variably expressed across modalities(e.g., susceptibility-weighted T2 blooming, diffusion restriction on DWI/ADC), while real-world multi-center dataintroduce domain shifts, anisotropy, and frequent missing sequences. We introduce a methodology that couples an attention-based recurrent segmentation network (UpAttLLSTM), a training schedule that progressively increases the difficulty of hetero-modal learning, with gradual modality dropout, UpAttLLSTM aggregates context across slices via recurrent units (2.5D) and uses attention gates to fuse complementary cues across available sequences, making it robust to anisotropy and class imbalance. Gradual modality dropout systematically simulates site heterogeneity,noise, and missing modalities during training, acting as both augmentation and regularization to improve multi-center generalization. On a monocentric cohort, our approach detects thrombi in >90% of cases with a Dice score of 0.65. In a multi-center setting with missing modalities, it achieves-80% detection with a Dice score around 0.35. Beyond stroke, the proposed methodology directly transfers to other small-lesion tasks in 3D medical imaging where targets are scarce, subtle, and modality-dependent

Recent Multimodal Large Language Models (MLLMs) have demonstrated significant progress in perceiving and reasoning over multimodal inquiries, ushering in a new research era for foundation models. However, vision-language misalignment in MLLMs has emerged as a critical challenge, where the textual responses generated by these models are not factually aligned with the given text-image inputs. Existing efforts to address vision-language misalignment have focused on developing specialized vision-language connectors or leveraging visual instruction tuning from diverse domains. In this paper, we tackle this issue from a fundamental yet unexplored perspective by revisiting the core architecture of MLLMs. Most MLLMs are typically built on decoder-only LLMs consisting of a causal attention mechanism, which limits the ability of earlier modalities (e.g., images) to incorporate information from later modalities (e.g., text). To address this problem, we propose AKI, a novel MLLM that unlocks causal attention into modality-mutual attention (MMA) to enable image tokens to attend to text tokens. This simple yet effective design allows AKI to achieve superior performance in 12 multimodal understanding benchmarks (+7.2% on average) without introducing additional parameters and increasing training time. Our MMA design is intended to be generic, allowing for application across various modalities, and scalable to accommodate diverse multimodal scenarios. The code is publicly available at https://github.com/sony/aki, and we will release our AKI-4B model to encourage further advancements in MLLMs across various directions.

Large language models (LLMs) offer a promising pre-screening tool, improving early disease detection and providing enhanced healthcare access for underprivileged communities. The early diagnosis of various diseases continues to be a significant challenge in healthcare, primarily due to the nonspecific nature of early symptoms, the shortage of expert medical practitioners, and the need for prolonged clinical evaluations, all of which can delay treatment and adversely affect patient outcomes. With impressive accuracy in prediction across a range of diseases, LLMs have the potential to revolutionize clinical pre-screening and decision-making for various medical conditions. In this work, we study the diagnostic capability of LLMs for Rheumatoid Arthritis (RA) with real world patients data. Patient data was collected alongside diagnoses from medical experts, and the performance of LLMs was evaluated in comparison to expert diagnoses for RA disease prediction. We notice an interesting pattern in disease diagnosis and find an unexpected misalignment between prediction and explanation. We conduct a series of multi-round analyses using different LLM agents. The best-performing model accurately predicts rheumatoid arthritis (RA) diseases approximately 95\% of the time. However, when medical experts evaluated the reasoning generated by the model, they found that nearly 68\% of the reasoning was incorrect. This study highlights a clear misalignment between LLMs high prediction accuracy and its flawed reasoning, raising important questions about relying on LLM explanations in clinical settings. LLMs provide incorrect reasoning to arrive at the correct answer for RA disease diagnosis.

Artificial intelligence has significantly impacted medical applications, particularly with the advent of Medical Large Vision Language Models (Med-LVLMs), sparking optimism for the future of automated and personalized healthcare. However, the trustworthiness of Med-LVLMs remains unverified, posing significant risks for future model deployment. In this paper, we introduce CARES and aim to comprehensively evaluate the Trustworthiness of Med-LVLMs across the medical domain. We assess the trustworthiness of Med-LVLMs across five dimensions, including trustfulness, fairness, safety, privacy, and robustness. CARES comprises about 41K question-answer pairs in both closed and open-ended formats, covering 16 medical image modalities and 27 anatomical regions. Our analysis reveals that the models consistently exhibit concerns regarding trustworthiness, often displaying factual inaccuracies and failing to maintain fairness across different demographic groups. Furthermore, they are vulnerable to attacks and demonstrate a lack of privacy awareness. We publicly release our benchmark and code in https://github.com/richard-peng-xia/CARES.

In this paper, we introduce a novel Multi-Modal Contrastive Pre-training Framework that synergistically combines X-rays, electrocardiograms (ECGs), and radiology/cardiology reports. Our approach leverages transformers to encode these diverse modalities into a unified representation space, aiming to enhance diagnostic accuracy and facilitate comprehensive patient assessments. We utilize LoRA-Peft to significantly reduce trainable parameters in the LLM and incorporate recent linear attention dropping strategy in the Vision Transformer(ViT) for smoother attention. Furthermore, we provide novel multimodal attention explanations and retrieval for our model. To the best of our knowledge, we are the first to propose an integrated model that combines X-ray, ECG, and Radiology/Cardiology Report with this approach. By utilizing contrastive loss, MoRE effectively aligns modality-specific features into a coherent embedding, which supports various downstream tasks such as zero-shot classification and multimodal retrieval. Employing our proposed methodology, we achieve state-of-the-art (SOTA) on the Mimic-IV, CheXpert, Edema Severity, and PtbXl downstream datasets, surpassing existing multimodal approaches. Our proposed framework shows significant improvements in capturing intricate inter-modal relationships and its robustness in medical diagnosis that establishes a framework for future research in multimodal learning in the healthcare sector.

Our research is motivated by the urgent global issue of a large population affected by retinal diseases, which are evenly distributed but underserved by specialized medical expertise, particularly in non-urban areas. Our primary objective is to bridge this healthcare gap by developing a comprehensive diagnostic system capable of accurately predicting retinal diseases solely from fundus images. However, we faced significant challenges due to limited, diverse datasets and imbalanced class distributions. To overcome these issues, we have devised innovative strategies. Our research introduces novel approaches, utilizing hybrid models combining deeper Convolutional Neural Networks (CNNs), Transformer encoders, and ensemble architectures sequentially and in parallel to classify retinal fundus images into 20 disease labels. Our overarching goal is to assess these advanced models' potential in practical applications, with a strong focus on enhancing retinal disease diagnosis accuracy across a broader spectrum of conditions. Importantly, our efforts have surpassed baseline model results, with the C-Tran ensemble model emerging as the leader, achieving a remarkable model score of 0.9166, surpassing the baseline score of 0.9. Additionally, experiments with the IEViT model showcased equally promising outcomes with improved computational efficiency. We've also demonstrated the effectiveness of dynamic patch extraction and the integration of domain knowledge in computer vision tasks. In summary, our research strives to contribute significantly to retinal disease diagnosis, addressing the critical need for accessible healthcare solutions in underserved regions while aiming for comprehensive and accurate disease prediction.

Vision Transformers (ViTs) have recently taken computer vision by storm. However, the softmax attention underlying ViTs comes with a quadratic complexity in time and memory, hindering the application of ViTs to high-resolution images. We revisit the attention design and propose a linear attention method to address the limitation, which doesn't sacrifice ViT's core advantage of capturing global representation like existing methods (e.g. local window attention of Swin). We further investigate the key difference between linear attention and softmax attention. Our empirical results suggest that linear attention lacks a fundamental property of concentrating the distribution of the attention matrix. Inspired by this observation, we introduce a local concentration module to enhance linear attention. By incorporating enhanced linear global attention and local window attention, we propose a new ViT architecture, dubbed L^2ViT. Notably, L^2ViT can effectively capture both global interactions and local representations while enjoying linear computational complexity. Extensive experiments demonstrate the strong performance of L^2ViT. On image classification, L^2ViT achieves 84.4% Top-1 accuracy on ImageNet-1K without any extra training data or label. By further pre-training on ImageNet-22k, it attains 87.0% when fine-tuned with resolution 384^2. For downstream tasks, L^2ViT delivers favorable performance as a backbone on object detection as well as semantic segmentation.

Rare diseases affect hundreds of millions worldwide, yet diagnosis often spans years. Convectional pipelines decouple noisy evidence extraction from downstream inferential diagnosis, and general/medical large language models (LLMs) face scarce real world electronic health records (EHRs), stale domain knowledge, and hallucinations. We assemble a large, domain specialized clinical corpus and a clinician validated reasoning set, and develop RareSeek R1 via staged instruction tuning, chain of thought learning, and graph grounded retrieval. Across multicenter EHR narratives and public benchmarks, RareSeek R1 attains state of the art accuracy, robust generalization, and stability under noisy or overlapping phenotypes. Augmented retrieval yields the largest gains when narratives pair with prioritized variants by resolving ambiguity and aligning candidates to mechanisms. Human studies show performance on par with experienced physicians and consistent gains in assistive use. Notably, transparent reasoning highlights decisive non phenotypic evidence (median 23.1%, such as imaging, interventions, functional tests) underpinning many correct diagnoses. This work advances a narrative first, knowledge integrated reasoning paradigm that shortens the diagnostic odyssey and enables auditable, clinically translatable decision support.

Convolutional networks, transformers, hybrid models, and Mamba-based architectures have demonstrated strong performance across various medical image classification tasks. However, these methods were primarily designed to classify clean images using labeled data. In contrast, real-world clinical data often involve image corruptions that are unique to multi-center studies and stem from variations in imaging equipment across manufacturers. In this paper, we introduce the Medical Vision Transformer (MedViTV2), a novel architecture incorporating Kolmogorov-Arnold Network (KAN) layers into the transformer architecture for the first time, aiming for generalized medical image classification. We have developed an efficient KAN block to reduce computational load while enhancing the accuracy of the original MedViT. Additionally, to counteract the fragility of our MedViT when scaled up, we propose an enhanced Dilated Neighborhood Attention (DiNA), an adaptation of the efficient fused dot-product attention kernel capable of capturing global context and expanding receptive fields to scale the model effectively and addressing feature collapse issues. Moreover, a hierarchical hybrid strategy is introduced to stack our Local Feature Perception and Global Feature Perception blocks in an efficient manner, which balances local and global feature perceptions to boost performance. Extensive experiments on 17 medical image classification datasets and 12 corrupted medical image datasets demonstrate that MedViTV2 achieved state-of-the-art results in 27 out of 29 experiments with reduced computational complexity. MedViTV2 is 44\% more computationally efficient than the previous version and significantly enhances accuracy, achieving improvements of 4.6\% on MedMNIST, 5.8\% on NonMNIST, and 13.4\% on the MedMNIST-C benchmark.

As the global burden of Alzheimer's disease (AD) continues to grow, early and accurate detection has become increasingly critical, especially in regions with limited access to advanced diagnostic tools. We propose BRAINS (Biomedical Retrieval-Augmented Intelligence for Neurodegeneration Screening) to address this challenge. This novel system harnesses the powerful reasoning capabilities of Large Language Models (LLMs) for Alzheimer's detection and monitoring. BRAINS features a dual-module architecture: a cognitive diagnostic module and a case-retrieval module. The Diagnostic Module utilizes LLMs fine-tuned on cognitive and neuroimaging datasets -- including MMSE, CDR scores, and brain volume metrics -- to perform structured assessments of Alzheimer's risk. Meanwhile, the Case Retrieval Module encodes patient profiles into latent representations and retrieves similar cases from a curated knowledge base. These auxiliary cases are fused with the input profile via a Case Fusion Layer to enhance contextual understanding. The combined representation is then processed with clinical prompts for inference. Evaluations on real-world datasets demonstrate BRAINS effectiveness in classifying disease severity and identifying early signs of cognitive decline. This system not only shows strong potential as an assistive tool for scalable, explainable, and early-stage Alzheimer's disease detection, but also offers hope for future applications in the field.

Mental health disorders are one of the most serious diseases in the world. Most people with such a disease lack access to adequate care, which highlights the importance of training models for the diagnosis and treatment of mental health disorders. However, in the mental health domain, privacy concerns limit the accessibility of personalized treatment data, making it challenging to build powerful models. In this paper, we introduce MentalArena, a self-play framework to train language models by generating domain-specific personalized data, where we obtain a better model capable of making a personalized diagnosis and treatment (as a therapist) and providing information (as a patient). To accurately model human-like mental health patients, we devise Symptom Encoder, which simulates a real patient from both cognition and behavior perspectives. To address intent bias during patient-therapist interactions, we propose Symptom Decoder to compare diagnosed symptoms with encoded symptoms, and dynamically manage the dialogue between patient and therapist according to the identified deviations. We evaluated MentalArena against 6 benchmarks, including biomedicalQA and mental health tasks, compared to 6 advanced models. Our models, fine-tuned on both GPT-3.5 and Llama-3-8b, significantly outperform their counterparts, including GPT-4o. We hope that our work can inspire future research on personalized care. Code is available in https://github.com/Scarelette/MentalArena/tree/main

Alzheimer's disease (AD) is a common neurodegenerative disease among the elderly. Early prediction and timely intervention of its prodromal stage, mild cognitive impairment (MCI), can decrease the risk of advancing to AD. Combining information from various modalities can significantly improve predictive accuracy. However, challenges such as missing data and heterogeneity across modalities complicate multimodal learning methods as adding more modalities can worsen these issues. Current multimodal fusion techniques often fail to adapt to the complexity of medical data, hindering the ability to identify relationships between modalities. To address these challenges, we propose an innovative multimodal approach for predicting MCI conversion, focusing specifically on the issues of missing positron emission tomography (PET) data and integrating diverse medical information. The proposed incomplete triple-modal MCI conversion prediction network is tailored for this purpose. Through the missing modal generation module, we synthesize the missing PET data from the magnetic resonance imaging and extract features using specifically designed encoders. We also develop a channel aggregation module and a triple-modal co-attention fusion module to reduce feature redundancy and achieve effective multimodal data fusion. Furthermore, we design a loss function to handle missing modality issues and align cross-modal features. These components collectively harness multimodal data to boost network performance. Experimental results on the ADNI1 and ADNI2 datasets show that our method significantly surpasses existing unimodal and other multimodal models. Our code is available at https://github.com/justinhxy/ITFC.

Medical images and radiology reports are crucial for diagnosing medical conditions, highlighting the importance of quantitative analysis for clinical decision-making. However, the diversity and cross-source heterogeneity of these data challenge the generalizability of current data-mining methods. Multimodal large language models (MLLMs) have recently transformed many domains, significantly affecting the medical field. Notably, Gemini-Vision-series (Gemini) and GPT-4-series (GPT-4) models have epitomized a paradigm shift in Artificial General Intelligence (AGI) for computer vision, showcasing their potential in the biomedical domain. In this study, we evaluated the performance of the Gemini, GPT-4, and 4 popular large models for an exhaustive evaluation across 14 medical imaging datasets, including 5 medical imaging categories (dermatology, radiology, dentistry, ophthalmology, and endoscopy), and 3 radiology report datasets. The investigated tasks encompass disease classification, lesion segmentation, anatomical localization, disease diagnosis, report generation, and lesion detection. Our experimental results demonstrated that Gemini-series models excelled in report generation and lesion detection but faces challenges in disease classification and anatomical localization. Conversely, GPT-series models exhibited proficiency in lesion segmentation and anatomical localization but encountered difficulties in disease diagnosis and lesion detection. Additionally, both the Gemini series and GPT series contain models that have demonstrated commendable generation efficiency. While both models hold promise in reducing physician workload, alleviating pressure on limited healthcare resources, and fostering collaboration between clinical practitioners and artificial intelligence technologies, substantial enhancements and comprehensive validations remain imperative before clinical deployment.

Recent medical vision-language models have shown promise on tasks such as VQA, report generation, and anomaly detection. However, most are adapted to structured adult imaging and underperform in fetal ultrasound, which poses challenges of multi-view image reasoning, numerous diseases, and image diversity. To bridge this gap, we introduce FetalMind, a medical AI system tailored to fetal ultrasound for both report generation and diagnosis. Guided by clinical workflow, we propose Salient Epistemic Disentanglement (SED), which injects an expert-curated bipartite graph into the model to decouple view-disease associations and to steer preference selection along clinically faithful steps via reinforcement learning. This design mitigates variability across diseases and heterogeneity across views, reducing learning bottlenecks while aligning the model's inference with obstetric practice. To train FetalMind at scale, we curate FetalSigma-1M dataset, the first large-scale fetal ultrasound report corpus, comprising 20K reports from twelve medical centers, addressing the scarcity of domain data. Extensive experiments show that FetalMind outperforms open- and closed-source baselines across all gestational stages, achieving +14% average gains and +61.2% higher accuracy on critical conditions while remaining efficient, stable, and scalable. Project Page: https://hexiao0275.github.io/FetalMind.

Recent large language models (LLMs) offer the potential to support public health monitoring by facilitating health disclosure through open-ended conversations but rarely preserve the knowledge gained about individuals across repeated interactions. Augmenting LLMs with long-term memory (LTM) presents an opportunity to improve engagement and self-disclosure, but we lack an understanding of how LTM impacts people's interaction with LLM-driven chatbots in public health interventions. We examine the case of CareCall -- an LLM-driven voice chatbot with LTM -- through the analysis of 1,252 call logs and interviews with nine users. We found that LTM enhanced health disclosure and fostered positive perceptions of the chatbot by offering familiarity. However, we also observed challenges in promoting self-disclosure through LTM, particularly around addressing chronic health conditions and privacy concerns. We discuss considerations for LTM integration in LLM-driven chatbots for public health monitoring, including carefully deciding what topics need to be remembered in light of public health goals.

Automatic diabetic retinopathy (DR) lesions segmentation makes great sense of assisting ophthalmologists in diagnosis. Although many researches have been conducted on this task, most prior works paid too much attention to the designs of networks instead of considering the pathological association for lesions. Through investigating the pathogenic causes of DR lesions in advance, we found that certain lesions are closed to specific vessels and present relative patterns to each other. Motivated by the observation, we propose a relation transformer block (RTB) to incorporate attention mechanisms at two main levels: a self-attention transformer exploits global dependencies among lesion features, while a cross-attention transformer allows interactions between lesion and vessel features by integrating valuable vascular information to alleviate ambiguity in lesion detection caused by complex fundus structures. In addition, to capture the small lesion patterns first, we propose a global transformer block (GTB) which preserves detailed information in deep network. By integrating the above blocks of dual-branches, our network segments the four kinds of lesions simultaneously. Comprehensive experiments on IDRiD and DDR datasets well demonstrate the superiority of our approach, which achieves competitive performance compared to state-of-the-arts.

Zero-shot medical detection can further improve detection performance without relying on annotated medical images even upon the fine-tuned model, showing great clinical value. Recent studies leverage grounded vision-language models (GLIP) to achieve this by using detailed disease descriptions as prompts for the target disease name during the inference phase. However, these methods typically treat prompts as equivalent context to the target name, making it difficult to assign specific disease knowledge based on visual information, leading to a coarse alignment between images and target descriptions. In this paper, we propose StructuralGLIP, which introduces an auxiliary branch to encode prompts into a latent knowledge bank layer-by-layer, enabling more context-aware and fine-grained alignment. Specifically, in each layer, we select highly similar features from both the image representation and the knowledge bank, forming structural representations that capture nuanced relationships between image patches and target descriptions. These features are then fused across modalities to further enhance detection performance. Extensive experiments demonstrate that StructuralGLIP achieves a +4.1\% AP improvement over prior state-of-the-art methods across seven zero-shot medical detection benchmarks, and consistently improves fine-tuned models by +3.2\% AP on endoscopy image datasets.

Infodemics and health misinformation have significant negative impact on individuals and society, exacerbating confusion and increasing hesitancy in adopting recommended health measures. Recent advancements in generative AI, capable of producing realistic, human like text and images, have significantly accelerated the spread and expanded the reach of health misinformation, resulting in an alarming surge in its dissemination. To combat the infodemics, most existing work has focused on developing misinformation datasets from social media and fact checking platforms, but has faced limitations in topical coverage, inclusion of AI generation, and accessibility of raw content. To address these issues, we present MM Health, a large scale multimodal misinformation dataset in the health domain consisting of 34,746 news article encompassing both textual and visual information. MM Health includes human-generated multimodal information (5,776 articles) and AI generated multimodal information (28,880 articles) from various SOTA generative AI models. Additionally, We benchmarked our dataset against three tasks (reliability checks, originality checks, and fine-grained AI detection) demonstrating that existing SOTA models struggle to accurately distinguish the reliability and origin of information. Our dataset aims to support the development of misinformation detection across various health scenarios, facilitating the detection of human and machine generated content at multimodal levels.

Clinical diagnosis prediction models, when provided with a patient's medical history, aim to detect potential diseases early, facilitating timely intervention and improving prognostic outcomes. However, the inherent scarcity of patient data and large disease candidate space often pose challenges in developing satisfactory models for this intricate task. The exploration of leveraging Large Language Models (LLMs) for encapsulating clinical decision processes has been limited. We introduce MERA, a clinical diagnosis prediction model that bridges pertaining natural language knowledge with medical practice. We apply hierarchical contrastive learning on a disease candidate ranking list to alleviate the large decision space issue. With concept memorization through fine-tuning, we bridge the natural language clinical knowledge with medical codes. Experimental results on MIMIC-III and IV datasets show that MERA achieves the state-of-the-art diagnosis prediction performance and dramatically elevates the diagnosis prediction capabilities of generative LMs.

The long-term effects of Postacute Sequelae of SARS-CoV-2, known as PASC, pose a significant challenge to healthcare systems worldwide. Accurate identification of progression events, such as hospitalization and reinfection, is essential for effective patient management and resource allocation. However, traditional models trained on structured data struggle to capture the nuanced progression of PASC. In this study, we introduce the first publicly available cohort of 18 PASC patients, with text time series features based on Large Language Model Llama-3.1-70B-Instruct and clinical risk annotated by clinical expert. We propose an Active Attention Network to predict the clinical risk and identify progression events related to the risk. By integrating human expertise with active learning, we aim to enhance clinical risk prediction accuracy and enable progression events identification with fewer number of annotation. The ultimate goal is to improves patient care and decision-making for SARS-CoV-2 patient.

The prevalence of vision-threatening eye diseases is a significant global burden, with many cases remaining undiagnosed or diagnosed too late for effective treatment. Large vision-language models (LVLMs) have the potential to assist in understanding anatomical information, diagnosing eye diseases, and drafting interpretations and follow-up plans, thereby reducing the burden on clinicians and improving access to eye care. However, limited benchmarks are available to assess LVLMs' performance in ophthalmology-specific applications. In this study, we introduce LMOD, a large-scale multimodal ophthalmology benchmark consisting of 21,993 instances across (1) five ophthalmic imaging modalities: optical coherence tomography, color fundus photographs, scanning laser ophthalmoscopy, lens photographs, and surgical scenes; (2) free-text, demographic, and disease biomarker information; and (3) primary ophthalmology-specific applications such as anatomical information understanding, disease diagnosis, and subgroup analysis. In addition, we benchmarked 13 state-of-the-art LVLM representatives from closed-source, open-source, and medical domains. The results demonstrate a significant performance drop for LVLMs in ophthalmology compared to other domains. Systematic error analysis further identified six major failure modes: misclassification, failure to abstain, inconsistent reasoning, hallucination, assertions without justification, and lack of domain-specific knowledge. In contrast, supervised neural networks specifically trained on these tasks as baselines demonstrated high accuracy. These findings underscore the pressing need for benchmarks in the development and validation of ophthalmology-specific LVLMs.

Convolutional Neural Networks (CNNs) have advanced existing medical systems for automatic disease diagnosis. However, there are still concerns about the reliability of deep medical diagnosis systems against the potential threats of adversarial attacks since inaccurate diagnosis could lead to disastrous consequences in the safety realm. In this study, we propose a highly robust yet efficient CNN-Transformer hybrid model which is equipped with the locality of CNNs as well as the global connectivity of vision Transformers. To mitigate the high quadratic complexity of the self-attention mechanism while jointly attending to information in various representation subspaces, we construct our attention mechanism by means of an efficient convolution operation. Moreover, to alleviate the fragility of our Transformer model against adversarial attacks, we attempt to learn smoother decision boundaries. To this end, we augment the shape information of an image in the high-level feature space by permuting the feature mean and variance within mini-batches. With less computational complexity, our proposed hybrid model demonstrates its high robustness and generalization ability compared to the state-of-the-art studies on a large-scale collection of standardized MedMNIST-2D datasets.

Rare diseases collectively affect over 300 million individuals worldwide, yet timely and accurate diagnosis remains a pervasive challenge. This is largely due to their clinical heterogeneity, low individual prevalence, and the limited familiarity most clinicians have with rare conditions. Here, we introduce DeepRare, the first rare disease diagnosis agentic system powered by a large language model (LLM), capable of processing heterogeneous clinical inputs. The system generates ranked diagnostic hypotheses for rare diseases, each accompanied by a transparent chain of reasoning that links intermediate analytic steps to verifiable medical evidence. DeepRare comprises three key components: a central host with a long-term memory module; specialized agent servers responsible for domain-specific analytical tasks integrating over 40 specialized tools and web-scale, up-to-date medical knowledge sources, ensuring access to the most current clinical information. This modular and scalable design enables complex diagnostic reasoning while maintaining traceability and adaptability. We evaluate DeepRare on eight datasets. The system demonstrates exceptional diagnostic performance among 2,919 diseases, achieving 100% accuracy for 1013 diseases. In HPO-based evaluations, DeepRare significantly outperforms other 15 methods, like traditional bioinformatics diagnostic tools, LLMs, and other agentic systems, achieving an average Recall@1 score of 57.18% and surpassing the second-best method (Reasoning LLM) by a substantial margin of 23.79 percentage points. For multi-modal input scenarios, DeepRare achieves 70.60% at Recall@1 compared to Exomiser's 53.20% in 109 cases. Manual verification of reasoning chains by clinical experts achieves 95.40% agreements. Furthermore, the DeepRare system has been implemented as a user-friendly web application http://raredx.cn/doctor.

We introduce Adaptive Filter Attention (AFA), a novel attention mechanism that incorporates a learnable dynamics model directly into the computation of attention weights. Rather than comparing queries and keys directly, we model the input sequence as discrete observations of a linear stochastic differential equation (SDE). By imposing a linear dynamics model with simultaneously diagonalizable state matrices and noise covariances, we can make use of a closed-form solution to the differential Lyapunov equation to efficiently propagate pairwise uncertainties through the dynamics. Attention naturally arises as the maximum likelihood solution for this linear SDE, with attention weights corresponding to robust residual-based reweightings of the propagated pairwise precisions. Imposing an additional constraint on the state matrix's eigenvalues leads to a simplified variant with the same computational and memory complexity as standard attention. In the limit of vanishing dynamics and process noise, and using a small-angle approximation, we recover ordinary dot-product attention.

To overcome the limitations of manual administrative coding in geriatric Cardiovascular Risk Management, this study introduces an automated classification framework leveraging unstructured Electronic Health Records (EHRs). Using a dataset of 3,482 patients, we benchmarked three distinct modeling paradigms on longitudinal Dutch clinical narratives: classical machine learning baselines, specialized deep learning architectures optimized for large-context sequences, and general-purpose generative Large Language Models (LLMs) in a zero-shot setting. Additionally, we evaluated a late fusion strategy to integrate unstructured text with structured medication embeddings and anthropometric data. Our analysis reveals that the custom Transformer architecture outperforms both traditional methods and generative llms, achieving the highest F1-scores and Matthews Correlation Coefficients. These findings underscore the critical role of specialized hierarchical attention mechanisms in capturing long-range dependencies within medical texts, presenting a robust, automated alternative to manual workflows for clinical risk stratification.

Survival prediction is a complicated ordinal regression task that aims to predict the ranking risk of death, which generally benefits from the integration of histology and genomic data. Despite the progress in joint learning from pathology and genomics, existing methods still suffer from challenging issues: 1) Due to the large size of pathological images, it is difficult to effectively represent the gigapixel whole slide images (WSIs). 2) Interactions within tumor microenvironment (TME) in histology are essential for survival analysis. Although current approaches attempt to model these interactions via co-attention between histology and genomic data, they focus on only dense local similarity across modalities, which fails to capture global consistency between potential structures, i.e. TME-related interactions of histology and co-expression of genomic data. To address these challenges, we propose a Multimodal Optimal Transport-based Co-Attention Transformer framework with global structure consistency, in which optimal transport (OT) is applied to match patches of a WSI and genes embeddings for selecting informative patches to represent the gigapixel WSI. More importantly, OT-based co-attention provides a global awareness to effectively capture structural interactions within TME for survival prediction. To overcome high computational complexity of OT, we propose a robust and efficient implementation over micro-batch of WSI patches by approximating the original OT with unbalanced mini-batch OT. Extensive experiments show the superiority of our method on five benchmark datasets compared to the state-of-the-art methods. The code is released.

To mitigate the computational complexity in the self-attention mechanism on long sequences, linear attention utilizes computation tricks to achieve linear complexity, while state space models (SSMs) popularize a favorable practice of using non-data-dependent memory pattern, i.e., emphasize the near and neglect the distant, to processing sequences. Recent studies have shown the priorities by combining them as one. However, the efficiency of linear attention remains only at the theoretical level in a causal setting, and SSMs require various designed constraints to operate effectively on specific data. Therefore, in order to unveil the true power of the hybrid design, the following two issues need to be addressed: (1) hardware-efficient implementation for linear attention and (2) stabilization of SSMs. To achieve this, we leverage the thought of tiling and hierarchy to propose CHELA (short-long Convolutions with Hardware-Efficient Linear Attention), which replaces SSMs with short-long convolutions and implements linear attention in a divide-and-conquer manner. This approach enjoys global abstraction and data-dependent selection from stable SSM and linear attention while maintaining real linear complexity. Our comprehensive experiments on the Long Range Arena benchmark and language modeling tasks demonstrate the effectiveness of the proposed method.

Vision Transformers (ViT) have shown their competitive advantages performance-wise compared to convolutional neural networks (CNNs) though they often come with high computational costs. To this end, previous methods explore different attention patterns by limiting a fixed number of spatially nearby tokens to accelerate the ViT's multi-head self-attention (MHSA) operations. However, such structured attention patterns limit the token-to-token connections to their spatial relevance, which disregards learned semantic connections from a full attention mask. In this work, we propose a novel approach to learn instance-dependent attention patterns, by devising a lightweight connectivity predictor module to estimate the connectivity score of each pair of tokens. Intuitively, two tokens have high connectivity scores if the features are considered relevant either spatially or semantically. As each token only attends to a small number of other tokens, the binarized connectivity masks are often very sparse by nature and therefore provide the opportunity to accelerate the network via sparse computations. Equipped with the learned unstructured attention pattern, sparse attention ViT (Sparsifiner) produces a superior Pareto-optimal trade-off between FLOPs and top-1 accuracy on ImageNet compared to token sparsity. Our method reduces 48% to 69% FLOPs of MHSA while the accuracy drop is within 0.4%. We also show that combining attention and token sparsity reduces ViT FLOPs by over 60%.

Artificial intelligence (AI) is vital in ophthalmology, tackling tasks like diagnosis, classification, and visual question answering (VQA). However, existing AI models in this domain often require extensive annotation and are task-specific, limiting their clinical utility. While recent developments have brought about foundation models for ophthalmology, they are limited by the need to train separate weights for each imaging modality, preventing a comprehensive representation of multi-modal features. This highlights the need for versatile foundation models capable of handling various tasks and modalities in ophthalmology. To address this gap, we present EyeFound, a multimodal foundation model for ophthalmic images. Unlike existing models, EyeFound learns generalizable representations from unlabeled multimodal retinal images, enabling efficient model adaptation across multiple applications. Trained on 2.78 million images from 227 hospitals across 11 ophthalmic modalities, EyeFound facilitates generalist representations and diverse multimodal downstream tasks, even for detecting challenging rare diseases. It outperforms previous work RETFound in diagnosing eye diseases, predicting systemic disease incidents, and zero-shot multimodal VQA. EyeFound provides a generalizable solution to improve model performance and lessen the annotation burden on experts, facilitating widespread clinical AI applications for retinal imaging.

Linear attention mechanisms have gained prominence in causal language models due to their linear computational complexity and enhanced speed. However, the inherent decay mechanism in linear attention presents challenges when applied to multi-dimensional sequence modeling tasks, such as image processing and multi-modal learning. In these scenarios, the utilization of sequential scanning to establish a global receptive field necessitates multiple scans for multi-dimensional data, thereby leading to inefficiencies. This paper identifies the inefficiency caused by a multiplicative linear recurrence and proposes an efficient alternative additive linear recurrence to avoid the issue, as it can handle multi-dimensional data within a single scan. We further develop an efficient multi-dimensional sequential modeling framework called LightNet based on the new recurrence. Moreover, we present two new multi-dimensional linear relative positional encoding methods, MD-TPE and MD-LRPE to enhance the model's ability to discern positional information in multi-dimensional scenarios. Our empirical evaluations across various tasks, including image classification, image generation, bidirectional language modeling, and autoregressive language modeling, demonstrate the efficacy of LightNet, showcasing its potential as a versatile and efficient solution for multi-dimensional sequential modeling.

Conventional medical image segmentation methods have been found inadequate in facilitating physicians with the identification of specific lesions for diagnosis and treatment. Given the utility of text as an instructional format, we introduce a novel task termed Medical Image Referring Segmentation (MIRS), which requires segmenting specified lesions in images based on the given language expressions. Due to the varying object scales in medical images, MIRS demands robust vision-language modeling and comprehensive multi-scale interaction for precise localization and segmentation under linguistic guidance. However, existing medical image segmentation methods fall short in meeting these demands, resulting in insufficient segmentation accuracy. In response, we propose an approach named Language-guided Scale-aware MedSegmentor (LSMS), incorporating two appealing designs: (1)~a Scale-aware Vision-Language Attention module that leverages diverse convolutional kernels to acquire rich visual knowledge and interact closely with linguistic features, thereby enhancing lesion localization capability; (2)~a Full-Scale Decoder that globally models multi-modal features across various scales, capturing complementary information between scales to accurately outline lesion boundaries. Addressing the lack of suitable datasets for MIRS, we constructed a vision-language medical dataset called Reference Hepatic Lesion Segmentation (RefHL-Seg). This dataset comprises 2,283 abdominal CT slices from 231 cases, with corresponding textual annotations and segmentation masks for various liver lesions in images. We validated the performance of LSMS for MIRS and conventional medical image segmentation tasks across various datasets. Our LSMS consistently outperforms on all datasets with lower computational costs. The code and datasets will be released.

Medical vision-language models (VLMs) excel at image-text understanding but typically rely on a single-pass reasoning that neglects localized visual cues. In clinical practice, however, human experts iteratively scan, focus, and refine the regions of interest before reaching a final diagnosis. To narrow this machine-human perception gap, we introduce ViTAR, a novel VLM framework that emulates the iterative reasoning process of human experts through a cognitive chain of "think-act-rethink-answer". ViTAR treats medical images as interactive objects, enabling models to engage multi-step visual reasoning. To support this approach, we curate a high-quality instruction dataset comprising 1K interactive examples that encode expert-like diagnostic behaviors. In addition, a 16K visual question answering training data has been curated towards fine-grained visual diagnosis. We introduce a two-stage training strategy that begins with supervised fine-tuning to guide cognitive trajectories, followed by the reinforcement learning to optimize decision-making. Extensive evaluations demonstrate that ViTAR outperforms strong state-of-the-art models. Visual attention analysis reveals that from the "think" to "rethink" rounds, ViTAR increasingly anchors visual grounding to clinically critical regions and maintains high attention allocation to visual tokens during reasoning, providing mechanistic insight into its improved performance. These findings demonstrate that embedding expert-style iterative thinking chains into VLMs enhances both performance and trustworthiness of medical AI.

Predicting high-dimensional or extreme multilabels, such as in medical coding, requires both accuracy and interpretability. Existing works often rely on local interpretability methods, failing to provide comprehensive explanations of the overall mechanism behind each label prediction within a multilabel set. We propose a mechanistic interpretability module called DIctionary Label Attention (\method) that disentangles uninterpretable dense embeddings into a sparse embedding space, where each nonzero element (a dictionary feature) represents a globally learned medical concept. Through human evaluations, we show that our sparse embeddings are more human understandable than its dense counterparts by at least 50 percent. Our automated dictionary feature identification pipeline, leveraging large language models (LLMs), uncovers thousands of learned medical concepts by examining and summarizing the highest activating tokens for each dictionary feature. We represent the relationships between dictionary features and medical codes through a sparse interpretable matrix, enhancing the mechanistic and global understanding of the model's predictions while maintaining competitive performance and scalability without extensive human annotation.

Soft attention is a critical mechanism powering LLMs to locate relevant parts within a given context. However, individual attention weights are determined by the similarity of only a single query and key token vector. This "single token attention" bottlenecks the amount of information used in distinguishing a relevant part from the rest of the context. To address this issue, we propose a new attention method, Multi-Token Attention (MTA), which allows LLMs to condition their attention weights on multiple query and key vectors simultaneously. This is achieved by applying convolution operations over queries, keys and heads, allowing nearby queries and keys to affect each other's attention weights for more precise attention. As a result, our method can locate relevant context using richer, more nuanced information that can exceed a single vector's capacity. Through extensive evaluations, we demonstrate that MTA achieves enhanced performance on a range of popular benchmarks. Notably, it outperforms Transformer baseline models on standard language modeling tasks, and on tasks that require searching for information within long contexts, where our method's ability to leverage richer information proves particularly beneficial.

When reading books, humans focus primarily on the current page, flipping back to recap prior context only when necessary. Similarly, we demonstrate that Large Language Models (LLMs) can learn to dynamically determine when to attend to global context. We propose All-or-Here Attention (AHA), which utilizes a binary router per attention head to dynamically toggle between full attention and local sliding window attention for each token. Our results indicate that with a window size of 256 tokens, up to 93\% of the original full attention operations can be replaced by sliding window attention without performance loss. Furthermore, by evaluating AHA across various window sizes, we identify a long-tail distribution in context dependency, where the necessity for full attention decays rapidly as the local window expands. By decoupling local processing from global access, AHA reveals that full attention is largely redundant, and that efficient inference requires only on-demand access to the global context.

While deep networks have achieved broad success in analyzing natural images, when applied to medical scans, they often fail in unexcepted situations. We investigate this challenge and focus on model sensitivity to domain shifts, such as data sampled from different hospitals or data confounded by demographic variables such as sex, race, etc, in the context of chest X-rays and skin lesion images. A key finding we show empirically is that existing visual backbones lack an appropriate prior from the architecture for reliable generalization in these settings. Taking inspiration from medical training, we propose giving deep networks a prior grounded in explicit medical knowledge communicated in natural language. To this end, we introduce Knowledge-enhanced Bottlenecks (KnoBo), a class of concept bottleneck models that incorporates knowledge priors that constrain it to reason with clinically relevant factors found in medical textbooks or PubMed. KnoBo uses retrieval-augmented language models to design an appropriate concept space paired with an automatic training procedure for recognizing the concept. We evaluate different resources of knowledge and recognition architectures on a broad range of domain shifts across 20 datasets. In our comprehensive evaluation with two imaging modalities, KnoBo outperforms fine-tuned models on confounded datasets by 32.4% on average. Finally, evaluations reveal that PubMed is a promising resource for making medical models less sensitive to domain shift, outperforming other resources on both diversity of information and final prediction performance.

Biomedical data is inherently multimodal, consisting of electronic health records, medical imaging, digital pathology, genome sequencing, wearable sensors, and more. The application of artificial intelligence tools to these multifaceted sensing technologies has the potential to revolutionize the prognosis, diagnosis, and management of human health and disease. However, current approaches to biomedical AI typically only train and evaluate with one or a small set of medical modalities and tasks. This limitation hampers the development of comprehensive tools that can leverage the rich interconnected information across many heterogeneous biomedical sensors. To address this challenge, we present MultiMed, a benchmark designed to evaluate and enable large-scale learning across a wide spectrum of medical modalities and tasks. MultiMed consists of 2.56 million samples across ten medical modalities such as medical reports, pathology, genomics, and protein data, and is structured into eleven challenging tasks, including disease prognosis, protein structure prediction, and medical question answering. Using MultiMed, we conduct comprehensive experiments benchmarking state-of-the-art unimodal, multimodal, and multitask models. Our analysis highlights the advantages of training large-scale medical models across many related modalities and tasks. Moreover, MultiMed enables studies of generalization across related medical concepts, robustness to real-world noisy data and distribution shifts, and novel modality combinations to improve prediction performance. MultiMed will be publicly available and regularly updated and welcomes inputs from the community.

Automatic medical report generation (MRG), which possesses significant research value as it can aid radiologists in clinical diagnosis and report composition, has garnered increasing attention. Despite recent progress, generating accurate reports remains arduous due to the requirement for precise clinical comprehension and disease diagnosis inference. Furthermore, owing to the limited accessibility of medical data and the imbalanced distribution of diseases, the underrepresentation of rare diseases in training data makes large-scale medical visual language models (LVLMs) prone to hallucinations, such as omissions or fabrications, severely undermining diagnostic performance and further intensifying the challenges for MRG in practice. In this study, to effectively mitigate hallucinations in medical report generation, we propose a chain-of-medical-thought approach (CoMT), which intends to imitate the cognitive process of human doctors by decomposing diagnostic procedures. The radiological features with different importance are structured into fine-grained medical thought chains to enhance the inferential ability during diagnosis, thereby alleviating hallucination problems and enhancing the diagnostic accuracy of MRG. The code and dataset have been released at https://github.com/FRENKIE-CHIANG/CoMT.

We introduce three new attention mechanisms that outperform standard multi-head attention in terms of efficiency and learning capabilities, thereby improving the performance and broader deployability of Transformer models. Our first contribution is Optimised Attention, which performs similarly to standard attention, but has 3/4 as many parameters and one matrix multiplication fewer per head. Next, we introduce Efficient Attention, which performs on par with standard attention with only 1/2 as many parameters as many parameters and two matrix multiplications fewer per head and is up to twice as fast as standard attention. Lastly, we introduce Super Attention, which surpasses standard attention by a significant margin in both vision and natural language processing tasks while having fewer parameters and matrix multiplications. In addition to providing rigorous mathematical comparisons, we evaluate the presented attention mechanisms on MNIST, CIFAR100, IMDB Movie Reviews, and Amazon Reviews datasets.

Feature selection is the problem of selecting a subset of features for a machine learning model that maximizes model quality subject to a budget constraint. For neural networks, prior methods, including those based on ell_1 regularization, attention, and other techniques, typically select the entire feature subset in one evaluation round, ignoring the residual value of features during selection, i.e., the marginal contribution of a feature given that other features have already been selected. We propose a feature selection algorithm called Sequential Attention that achieves state-of-the-art empirical results for neural networks. This algorithm is based on an efficient one-pass implementation of greedy forward selection and uses attention weights at each step as a proxy for feature importance. We give theoretical insights into our algorithm for linear regression by showing that an adaptation to this setting is equivalent to the classical Orthogonal Matching Pursuit (OMP) algorithm, and thus inherits all of its provable guarantees. Our theoretical and empirical analyses offer new explanations towards the effectiveness of attention and its connections to overparameterization, which may be of independent interest.

An efficient attention implementation is essential for large models due to its quadratic time complexity. Fortunately, attention commonly exhibits sparsity, i.e., many values in the attention map are near zero, allowing for the omission of corresponding computations. Many studies have utilized the sparse pattern to accelerate attention. However, most existing works focus on optimizing attention within specific models by exploiting certain sparse patterns of the attention map. A universal sparse attention that guarantees both the speedup and end-to-end performance of diverse models remains elusive. In this paper, we propose SpargeAttn, a universal sparse and quantized attention for any model. Our method uses a two-stage online filter: in the first stage, we rapidly and accurately predict the attention map, enabling the skip of some matrix multiplications in attention. In the second stage, we design an online softmax-aware filter that incurs no extra overhead and further skips some matrix multiplications. Experiments show that our method significantly accelerates diverse models, including language, image, and video generation, without sacrificing end-to-end metrics. The codes are available at https://github.com/thu-ml/SpargeAttn.

Attention is a powerful and ubiquitous mechanism for allowing neural models to focus on particular salient pieces of information by taking their weighted average when making predictions. In particular, multi-headed attention is a driving force behind many recent state-of-the-art NLP models such as Transformer-based MT models and BERT. These models apply multiple attention mechanisms in parallel, with each attention "head" potentially focusing on different parts of the input, which makes it possible to express sophisticated functions beyond the simple weighted average. In this paper we make the surprising observation that even if models have been trained using multiple heads, in practice, a large percentage of attention heads can be removed at test time without significantly impacting performance. In fact, some layers can even be reduced to a single head. We further examine greedy algorithms for pruning down models, and the potential speed, memory efficiency, and accuracy improvements obtainable therefrom. Finally, we analyze the results with respect to which parts of the model are more reliant on having multiple heads, and provide precursory evidence that training dynamics play a role in the gains provided by multi-head attention.

Efficiently capturing multi-scale information and building long-range dependencies among pixels are essential for medical image segmentation because of the various sizes and shapes of the lesion regions or organs. In this paper, we present Multi-scale Cross-axis Attention (MCA) to solve the above challenging issues based on the efficient axial attention. Instead of simply connecting axial attention along the horizontal and vertical directions sequentially, we propose to calculate dual cross attentions between two parallel axial attentions to capture global information better. To process the significant variations of lesion regions or organs in individual sizes and shapes, we also use multiple convolutions of strip-shape kernels with different kernel sizes in each axial attention path to improve the efficiency of the proposed MCA in encoding spatial information. We build the proposed MCA upon the MSCAN backbone, yielding our network, termed MCANet. Our MCANet with only 4M+ parameters performs even better than most previous works with heavy backbones (e.g., Swin Transformer) on four challenging tasks, including skin lesion segmentation, nuclei segmentation, abdominal multi-organ segmentation, and polyp segmentation. Code is available at https://github.com/haoshao-nku/medical_seg.

Scalp disorders are highly prevalent worldwide, yet remain underdiagnosed due to limited access to expert evaluation and the high cost of annotation. Although AI-based approaches hold great promise, their practical deployment is hindered by challenges such as severe data imbalance and the absence of pixel-level segmentation labels. To address these issues, we propose ScalpVision, an AI-driven system for the holistic diagnosis of scalp diseases. In ScalpVision, effective hair segmentation is achieved using pseudo image-label pairs and an innovative prompting method in the absence of traditional hair masking labels. Additionally, ScalpVision introduces DiffuseIT-M, a generative model adopted for dataset augmentation while maintaining hair information, facilitating improved predictions of scalp disease severity. Our experimental results affirm ScalpVision's efficiency in diagnosing a variety of scalp conditions, showcasing its potential as a valuable tool in dermatological care. Our code is available at https://github.com/winston1214/ScalpVision.

Large language models (LLMs) have shown great promise in the medical domain, achieving strong performance on several benchmarks. However, they continue to underperform in real-world medical scenarios, which often demand stronger context-awareness, i.e., the ability to recognize missing or critical details (e.g., user identity, medical history, risk factors) and provide safe, helpful, and contextually appropriate responses. To address this issue, we propose Multifaceted Self-Refinement (MuSeR), a data-driven approach that enhances LLMs' context-awareness along three key facets (decision-making, communication, and safety) through self-evaluation and refinement. Specifically, we first design a attribute-conditioned query generator that simulates diverse real-world user contexts by varying attributes such as role, geographic region, intent, and degree of information ambiguity. An LLM then responds to these queries, self-evaluates its answers along three key facets, and refines its responses to better align with the requirements of each facet. Finally, the queries and refined responses are used for supervised fine-tuning to reinforce the model's context-awareness ability. Evaluation results on the latest HealthBench dataset demonstrate that our method significantly improves LLM performance across multiple aspects, with particularly notable gains in the context-awareness axis. Furthermore, by incorporating knowledge distillation with the proposed method, the performance of a smaller backbone LLM (e.g., Qwen3-32B) surpasses its teacher model, achieving a new SOTA across all open-source LLMs on HealthBench (63.8%) and its hard subset (43.1%). Code and dataset will be released at https://muser-llm.github.io.

Large language models (LLMs) have demonstrated impressive capabilities in disease diagnosis. However, their effectiveness in identifying rarer diseases, which are inherently more challenging to diagnose, remains an open question. Rare disease performance is critical with the increasing use of LLMs in healthcare settings. This is especially true if a primary care physician needs to make a rarer prognosis from only a patient conversation so that they can take the appropriate next step. To that end, several clinical decision support systems are designed to support providers in rare disease identification. Yet their utility is limited due to their lack of knowledge of common disorders and difficulty of use. In this paper, we propose RareScale to combine the knowledge LLMs with expert systems. We use jointly use an expert system and LLM to simulate rare disease chats. This data is used to train a rare disease candidate predictor model. Candidates from this smaller model are then used as additional inputs to black-box LLM to make the final differential diagnosis. Thus, RareScale allows for a balance between rare and common diagnoses. We present results on over 575 rare diseases, beginning with Abdominal Actinomycosis and ending with Wilson's Disease. Our approach significantly improves the baseline performance of black-box LLMs by over 17% in Top-5 accuracy. We also find that our candidate generation performance is high (e.g. 88.8% on gpt-4o generated chats).

Many sparse attention mechanisms such as Neighborhood Attention have typically failed to consistently deliver speedup over the self attention baseline. This is largely due to the level of complexity in attention infrastructure, and the rapid evolution of AI hardware architecture. At the same time, many state-of-the-art foundational models, particularly in computer vision, are heavily bound by attention, and need reliable sparsity to escape the O(n^2) complexity. In this paper, we study a class of promising sparse attention mechanisms that focus on locality, and aim to develop a better analytical model of their performance improvements. We first introduce Generalized Neighborhood Attention (GNA), which can describe sliding window, strided sliding window, and blocked attention. We then consider possible design choices in implementing these approaches, and create a simulator that can provide much more realistic speedup upper bounds for any given setting. Finally, we implement GNA on top of a state-of-the-art fused multi-headed attention (FMHA) kernel designed for the NVIDIA Blackwell architecture in CUTLASS. Our implementation can fully realize the maximum speedup theoretically possible in many perfectly block-sparse cases, and achieves an effective utilization of 1.3 petaFLOPs/second in FP16. In addition, we plug various GNA configurations into off-the-shelf generative models, such as Cosmos-7B, HunyuanVideo, and FLUX, and show that it can deliver 28% to 46% end-to-end speedup on B200 without any fine-tuning. We will open source our simulator and Blackwell kernels directly through the NATTEN project.

Learning medical visual representations directly from paired radiology reports has become an emerging topic in representation learning. However, existing medical image-text joint learning methods are limited by instance or local supervision analysis, ignoring disease-level semantic correspondences. In this paper, we present a novel Multi-Granularity Cross-modal Alignment (MGCA) framework for generalized medical visual representation learning by harnessing the naturally exhibited semantic correspondences between medical image and radiology reports at three different levels, i.e., pathological region-level, instance-level, and disease-level. Specifically, we first incorporate the instance-wise alignment module by maximizing the agreement between image-report pairs. Further, for token-wise alignment, we introduce a bidirectional cross-attention strategy to explicitly learn the matching between fine-grained visual tokens and text tokens, followed by contrastive learning to align them. More important, to leverage the high-level inter-subject relationship semantic (e.g., disease) correspondences, we design a novel cross-modal disease-level alignment paradigm to enforce the cross-modal cluster assignment consistency. Extensive experimental results on seven downstream medical image datasets covering image classification, object detection, and semantic segmentation tasks demonstrate the stable and superior performance of our framework.

The favorable performance of Vision Transformers (ViTs) is often attributed to the multi-head self-attention (MSA). The MSA enables global interactions at each layer of a ViT model, which is a contrasting feature against Convolutional Neural Networks (CNNs) that gradually increase the range of interaction across multiple layers. We study the role of the density of the attention. Our preliminary analyses suggest that the spatial interactions of attention maps are close to dense interactions rather than sparse ones. This is a curious phenomenon, as dense attention maps are harder for the model to learn due to steeper softmax gradients around them. We interpret this as a strong preference for ViT models to include dense interaction. We thus manually insert the uniform attention to each layer of ViT models to supply the much needed dense interactions. We call this method Context Broadcasting, CB. We observe that the inclusion of CB reduces the degree of density in the original attention maps and increases both the capacity and generalizability of the ViT models. CB incurs negligible costs: 1 line in your model code, no additional parameters, and minimal extra operations.

Large multimodal models (LMMs) "see" images by leveraging the attention mechanism between text and visual tokens in the transformer decoder. Ideally, these models should focus on key visual information relevant to the text token. However, recent findings indicate that LMMs have an extraordinary tendency to consistently allocate high attention weights to specific visual tokens, even when these tokens are irrelevant to the corresponding text. In this study, we investigate the property behind the appearance of these irrelevant visual tokens and examine their characteristics. Our findings show that this behavior arises due to the massive activation of certain hidden state dimensions, which resembles the attention sink found in language models. Hence, we refer to this phenomenon as the visual attention sink. In particular, our analysis reveals that removing the irrelevant visual sink tokens does not impact model performance, despite receiving high attention weights. Consequently, we recycle the attention to these tokens as surplus resources, redistributing the attention budget to enhance focus on the image. To achieve this, we introduce Visual Attention Redistribution (VAR), a method that redistributes attention in image-centric heads, which we identify as innately focusing on visual information. VAR can be seamlessly applied across different LMMs to improve performance on a wide range of tasks, including general vision-language tasks, visual hallucination tasks, and vision-centric tasks, all without the need for additional training, models, or inference steps. Experimental results demonstrate that VAR enables LMMs to process visual information more effectively by adjusting their internal attention mechanisms, offering a new direction to enhancing the multimodal capabilities of LMMs.

Vision transformer (ViT) expands the success of transformer models from sequential data to images. The model decomposes an image into many smaller patches and arranges them into a sequence. Multi-head self-attentions are then applied to the sequence to learn the attention between patches. Despite many successful interpretations of transformers on sequential data, little effort has been devoted to the interpretation of ViTs, and many questions remain unanswered. For example, among the numerous attention heads, which one is more important? How strong are individual patches attending to their spatial neighbors in different heads? What attention patterns have individual heads learned? In this work, we answer these questions through a visual analytics approach. Specifically, we first identify what heads are more important in ViTs by introducing multiple pruning-based metrics. Then, we profile the spatial distribution of attention strengths between patches inside individual heads, as well as the trend of attention strengths across attention layers. Third, using an autoencoder-based learning solution, we summarize all possible attention patterns that individual heads could learn. Examining the attention strengths and patterns of the important heads, we answer why they are important. Through concrete case studies with experienced deep learning experts on multiple ViTs, we validate the effectiveness of our solution that deepens the understanding of ViTs from head importance, head attention strength, and head attention pattern.

Large language models (LLMs) have the potential to transform medicine, but real-world clinical scenarios contain extraneous information that can hinder performance. The rise of assistive technologies like ambient dictation, which automatically generates draft notes from live patient encounters, has the potential to introduce additional noise making it crucial to assess the ability of LLM's to filter relevant data. To investigate this, we developed MedDistractQA, a benchmark using USMLE-style questions embedded with simulated real-world distractions. Our findings show that distracting statements (polysemous words with clinical meanings used in a non-clinical context or references to unrelated health conditions) can reduce LLM accuracy by up to 17.9%. Commonly proposed solutions to improve model performance such as retrieval-augmented generation (RAG) and medical fine-tuning did not change this effect and in some cases introduced their own confounders and further degraded performance. Our findings suggest that LLMs natively lack the logical mechanisms necessary to distinguish relevant from irrelevant clinical information, posing challenges for real-world applications. MedDistractQA and our results highlights the need for robust mitigation strategies to enhance LLM resilience to extraneous information.

Traditionally, AI research in medical diagnosis has largely centered on image analysis. While this has led to notable advancements, the absence of patient-reported symptoms continues to hinder diagnostic accuracy. To address this, we propose a Pre-Consultation Dialogue Framework (PCDF) that mimics real-world diagnostic procedures, where doctors iteratively query patients before reaching a conclusion. Specifically, we simulate diagnostic dialogues between two vision-language models (VLMs): a DocVLM, which generates follow-up questions based on the image and dialogue history, and a PatientVLM, which responds using a symptom profile derived from the ground-truth diagnosis. We additionally conducted a small-scale clinical validation of the synthetic symptoms generated by our framework, with licensed clinicians confirming their clinical relevance, symptom coverage, and overall realism. These findings indicate that the resulting DocVLM-PatientVLM interactions form coherent, multi-turn consultations paired with images and diagnoses, which we then use to fine-tune the DocVLM. This dialogue-based supervision leads to substantial gains over image-only training, highlighting the value of realistic symptom elicitation for diagnosis.

Despite the impressive capabilities of Large Language Models (LLMs) in general medical domains, questions remain about their performance in diagnosing rare diseases. To answer this question, we aim to assess the diagnostic performance of LLMs in rare diseases, and explore methods to enhance their effectiveness in this area. In this work, we introduce a rare disease question-answering (ReDis-QA) dataset to evaluate the performance of LLMs in diagnosing rare diseases. Specifically, we collected 1360 high-quality question-answer pairs within the ReDis-QA dataset, covering 205 rare diseases. Additionally, we annotated meta-data for each question, facilitating the extraction of subsets specific to any given disease and its property. Based on the ReDis-QA dataset, we benchmarked several open-source LLMs, revealing that diagnosing rare diseases remains a significant challenge for these models. To facilitate retrieval augmentation generation for rare disease diagnosis, we collect the first rare diseases corpus (ReCOP), sourced from the National Organization for Rare Disorders (NORD) database. Specifically, we split the report of each rare disease into multiple chunks, each representing a different property of the disease, including their overview, symptoms, causes, effects, related disorders, diagnosis, and standard therapies. This structure ensures that the information within each chunk aligns consistently with a question. Experiment results demonstrate that ReCOP can effectively improve the accuracy of LLMs on the ReDis-QA dataset by an average of 8%. Moreover, it significantly guides LLMs to generate trustworthy answers and explanations that can be traced back to existing literature.

We revisit the relationship between attention mechanisms and large kernel ConvNets in visual transformers and propose a new spatial attention named Large Kernel Convolutional Attention (LKCA). It simplifies the attention operation by replacing it with a single large kernel convolution. LKCA combines the advantages of convolutional neural networks and visual transformers, possessing a large receptive field, locality, and parameter sharing. We explained the superiority of LKCA from both convolution and attention perspectives, providing equivalent code implementations for each view. Experiments confirm that LKCA implemented from both the convolutional and attention perspectives exhibit equivalent performance. We extensively experimented with the LKCA variant of ViT in both classification and segmentation tasks. The experiments demonstrated that LKCA exhibits competitive performance in visual tasks. Our code will be made publicly available at https://github.com/CatworldLee/LKCA.

Medical imaging plays a pivotal role in modern healthcare, with computed tomography pulmonary angiography (CTPA) being a critical tool for diagnosing pulmonary embolism and other thoracic conditions. However, the complexity of interpreting CTPA scans and generating accurate radiology reports remains a significant challenge. This paper introduces Abn-BLIP (Abnormality-aligned Bootstrapping Language-Image Pretraining), an advanced diagnosis model designed to align abnormal findings to generate the accuracy and comprehensiveness of radiology reports. By leveraging learnable queries and cross-modal attention mechanisms, our model demonstrates superior performance in detecting abnormalities, reducing missed findings, and generating structured reports compared to existing methods. Our experiments show that Abn-BLIP outperforms state-of-the-art medical vision-language models and 3D report generation methods in both accuracy and clinical relevance. These results highlight the potential of integrating multimodal learning strategies for improving radiology reporting. The source code is available at https://github.com/zzs95/abn-blip.

For the early identification, diagnosis, and treatment of mental health illnesses, the integration of deep learning (DL) and machine learning (ML) has started playing a significant role. By evaluating complex data from imaging, genetics, and behavioral assessments, these technologies have the potential to significantly improve clinical outcomes. However, they also present unique challenges related to data integration and ethical issues. This survey reviews the development of ML and DL methods for the early diagnosis and treatment of mental health issues. It examines a range of applications, with a particular emphasis on behavioral assessments, genetic and biomarker analysis, and medical imaging for diagnosing diseases like depression, bipolar disorder, and schizophrenia. Predictive modeling for illness progression is further discussed, focusing on the role of risk prediction models and longitudinal studies. Key findings highlight how ML and DL can improve diagnostic accuracy and treatment outcomes while addressing methodological inconsistencies, data integration challenges, and ethical concerns. The study emphasizes the importance of building real-time monitoring systems for individualized treatment, enhancing data fusion techniques, and fostering interdisciplinary collaboration. Future research should focus on overcoming these obstacles to ensure the valuable and ethical application of ML and DL in mental health services.

The rapid advancement of large language models (LLMs) has significantly impacted various domains, including healthcare and biomedicine. However, the phenomenon of hallucination, where LLMs generate outputs that deviate from factual accuracy or context, poses a critical challenge, especially in high-stakes domains. This paper conducts a scoping study of existing techniques for mitigating hallucinations in knowledge-based task in general and especially for medical domains. Key methods covered in the paper include Retrieval-Augmented Generation (RAG)-based techniques, iterative feedback loops, supervised fine-tuning, and prompt engineering. These techniques, while promising in general contexts, require further adaptation and optimization for the medical domain due to its unique demands for up-to-date, specialized knowledge and strict adherence to medical guidelines. Addressing these challenges is crucial for developing trustworthy AI systems that enhance clinical decision-making and patient safety as well as accuracy of biomedical scientific research.

Identifying disease phenotypes from electronic health records (EHRs) is critical for numerous secondary uses. Manually encoding physician knowledge into rules is particularly challenging for rare diseases due to inadequate EHR coding, necessitating review of clinical notes. Large language models (LLMs) offer promise in text understanding but may not efficiently handle real-world clinical documentation. We propose a zero-shot LLM-based method enriched by retrieval-augmented generation and MapReduce, which pre-identifies disease-related text snippets to be used in parallel as queries for the LLM to establish diagnosis. We show that this method as applied to pulmonary hypertension (PH), a rare disease characterized by elevated arterial pressures in the lungs, significantly outperforms physician logic rules (F_1 score of 0.62 vs. 0.75). This method has the potential to enhance rare disease cohort identification, expanding the scope of robust clinical research and care gap identification.

Alzheimer's disease (AD) is a degenerative brain disease impairing a person's ability to perform day to day activities. The clinical manifestations of Alzheimer's disease are characterized by heterogeneity in age, disease span, progression rate, impairment of memory and cognitive abilities. Due to these variabilities, personalized care and treatment planning, as well as patient counseling about their individual progression is limited. Recent developments in machine learning to detect hidden patterns in complex, multi-dimensional datasets provides significant opportunities to address this critical need. In this work, we use unsupervised and supervised machine learning approaches for subtype identification and prediction. We apply machine learning methods to the extensive clinical observations available at the Alzheimer's Disease Neuroimaging Initiative (ADNI) data set to identify patient subtypes and to predict disease progression. Our analysis depicts the progression space for the Alzheimer's disease into low, moderate and high disease progression zones. The proposed work will enable early detection and characterization of distinct disease subtypes based on clinical heterogeneity. We anticipate that our models will enable patient counseling, clinical trial design, and ultimately individualized clinical care.

WHO has declared that more than 2.2 billion people worldwide are suffering from visual disorders, such as media haze, glaucoma, and drusen. At least 1 billion of these cases could have been either prevented or successfully treated, yet they remain unaddressed due to poverty, a lack of specialists, inaccurate ocular fundus diagnoses by ophthalmologists, or the presence of a rare disease. To address this, the research has developed the Hybrid Trio-Network Model Algorithm for accurately diagnosing 12 distinct common and rare eye diseases. This algorithm utilized the RFMiD dataset of 3,200 fundus images and the Binary Relevance Method to detect diseases separately, ensuring expandability and avoiding incorrect correlations. Each detector, incorporating finely tuned hyperparameters to optimize performance, consisted of three feature components: A classical transfer learning CNN model, a two-stage CNN model, and a Siamese Network. The diagnosis was made using features extracted through this Trio-Model with Ensembled Machine Learning algorithms. The proposed model achieved an average accuracy of 97% and an AUC score of 0.96. Compared to past benchmark studies, an increase of over 10% in the F1-score was observed for most diseases. Furthermore, using the Siamese Network, the model successfully made predictions in diseases like optic disc pallor, which past studies failed to predict due to low confidence. This diagnostic tool presents a stable, adaptive, cost-effective, efficient, accessible, and fast solution for globalizing early detection of both common and rare diseases.

In the era of modern healthcare, swiftly generating medical question summaries is crucial for informed and timely patient care. Despite the increasing complexity and volume of medical data, existing studies have focused solely on text-based summarization, neglecting the integration of visual information. Recognizing the untapped potential of combining textual queries with visual representations of medical conditions, we introduce the Multimodal Medical Question Summarization (MMQS) Dataset. This dataset, a major contribution to our work, pairs medical queries with visual aids, facilitating a richer and more nuanced understanding of patient needs. We also propose a framework, utilizing the power of Contrastive Language Image Pretraining(CLIP) and Large Language Models(LLMs), consisting of four modules that identify medical disorders, generate relevant context, filter medical concepts, and craft visually aware summaries. Our comprehensive framework harnesses the power of CLIP, a multimodal foundation model, and various general-purpose LLMs, comprising four main modules: the medical disorder identification module, the relevant context generation module, the context filtration module for distilling relevant medical concepts and knowledge, and finally, a general-purpose LLM to generate visually aware medical question summaries. Leveraging our MMQS dataset, we showcase how visual cues from images enhance the generation of medically nuanced summaries. This multimodal approach not only enhances the decision-making process in healthcare but also fosters a more nuanced understanding of patient queries, laying the groundwork for future research in personalized and responsive medical care

In large language models, the demand for modeling long contexts is constantly increasing, but the quadratic complexity of the standard self-attention mechanism often becomes a bottleneck. Although existing sparse attention mechanisms have improved efficiency, they may still encounter issues such as static patterns or information loss. We introduce a trainable dynamic mask sparse attention mechanism, Dynamic Mask Attention, which effectively utilizes content-aware and position-aware sparsity. DMA achieves this through two key innovations: First, it dynamically generates content-aware sparse masks from value representations, enabling the model to identify and focus on critical information adaptively. Second, it implements position-aware sparse attention computation that effectively skips unnecessary calculation regions. This dual-sparsity design allows the model to significantly reduce the computational complexity of important information while retaining complete information, achieving an excellent balance between information fidelity and computational efficiency. We have verified the performance of DMA through comprehensive experiments. Comparative studies show that DMA outperforms multi-head attention, sliding window attention, multi-head latent attention, and native sparse attention in terms of perplexity under Chinchilla Scaling Law settings. Moreover, in challenging multi-query associative recall tasks, DMA also demonstrates superior performance and efficiency compared to these methods. Crucially, in the evaluation of a 1.7B parameter model, DMA significantly outperforms multi-head attention in both standard benchmark performance and the challenging needle-in-a-haystack task. These experimental results highlight its capability to balance model efficiency and long-context modeling ability effectively.

The quadratic cost of attention hinders the scalability of long-context LLMs, especially in resource-constrained settings. Existing static sparse methods such as sliding windows or global tokens utilizes the sparsity of attention to reduce the cost of attention, but poorly adapts to the content-dependent variations in attention due to their staticity. While previous work has proposed several dynamic approaches to improve flexibility, they still depend on predefined templates or heuristic mechanisms. Such strategies reduce generality and prune tokens that remain contextually important, limiting their accuracy across diverse tasks. To tackle these bottlenecks of existing methods for long-context modeling, we introduce Dynamic Hierarchical Sparse Attention (DHSA), a data-driven framework that dynamically predicts attention sparsity online without retraining. Our proposed DHSA adaptively segments sequences into variable-length chunks, then computes chunk representations by aggregating the token embeddings within each chunk. To avoid the bias introduced by varying chunk lengths, we apply length-normalized aggregation that scales the averaged embeddings by the square root of the chunk size. Finally, DHSA upsamples the chunk-level similarity scores to token level similarities to calculate importance scores that determine which token-level interactions should be preserved. Our experiments on Gemma2 with Needle-in-a-Haystack Test and LongBench show that DHSA matches dense attention in accuracy, while reducing prefill latency by 20-60% and peak memory usage by 35%. Compared to other representative baselines such as block sparse attention, DHSA achieves consistently higher accuracy (6-18% relative gains) with comparable or lower cost, offering an efficient and adaptable solution for long-context on-device LLMs.

In the field of chest X-ray (CXR) diagnosis, existing works often focus solely on determining where a radiologist looks, typically through tasks such as detection, segmentation, or classification. However, these approaches are often designed as black-box models, lacking interpretability. In this paper, we introduce Interpretable Artificial Intelligence (I-AI) a novel and unified controllable interpretable pipeline for decoding the intense focus of radiologists in CXR diagnosis. Our I-AI addresses three key questions: where a radiologist looks, how long they focus on specific areas, and what findings they diagnose. By capturing the intensity of the radiologist's gaze, we provide a unified solution that offers insights into the cognitive process underlying radiological interpretation. Unlike current methods that rely on black-box machine learning models, which can be prone to extracting erroneous information from the entire input image during the diagnosis process, we tackle this issue by effectively masking out irrelevant information. Our proposed I-AI leverages a vision-language model, allowing for precise control over the interpretation process while ensuring the exclusion of irrelevant features. To train our I-AI model, we utilize an eye gaze dataset to extract anatomical gaze information and generate ground truth heatmaps. Through extensive experimentation, we demonstrate the efficacy of our method. We showcase that the attention heatmaps, designed to mimic radiologists' focus, encode sufficient and relevant information, enabling accurate classification tasks using only a portion of CXR. The code, checkpoints, and data are at https://github.com/UARK-AICV/IAI

Since the beginning of world-wide COVID-19 pandemic, facial masks have been recommended to limit the spread of the disease. However, these masks hide certain facial attributes. Hence, it has become difficult for existing face recognition systems to perform identity verification on masked faces. In this context, it is necessary to develop masked Face Recognition (MFR) for contactless biometric recognition systems. Thus, in this paper, we propose Complementary Attention Learning and Multi-Focal Spatial Attention that precisely removes masked region by training complementary spatial attention to focus on two distinct regions: masked regions and backgrounds. In our method, standard spatial attention and networks focus on unmasked regions, and extract mask-invariant features while minimizing the loss of the conventional Face Recognition (FR) performance. For conventional FR, we evaluate the performance on the IJB-C, Age-DB, CALFW, and CPLFW datasets. We evaluate the MFR performance on the ICCV2021-MFR/Insightface track, and demonstrate the improved performance on the both MFR and FR datasets. Additionally, we empirically verify that spatial attention of proposed method is more precisely activated in unmasked regions.

We present a novel approach for the prediction of anticancer compound sensitivity by means of multi-modal attention-based neural networks (PaccMann). In our approach, we integrate three key pillars of drug sensitivity, namely, the molecular structure of compounds, transcriptomic profiles of cancer cells as well as prior knowledge about interactions among proteins within cells. Our models ingest a drug-cell pair consisting of SMILES encoding of a compound and the gene expression profile of a cancer cell and predicts an IC50 sensitivity value. Gene expression profiles are encoded using an attention-based encoding mechanism that assigns high weights to the most informative genes. We present and study three encoders for SMILES string of compounds: 1) bidirectional recurrent 2) convolutional 3) attention-based encoders. We compare our devised models against a baseline model that ingests engineered fingerprints to represent the molecular structure. We demonstrate that using our attention-based encoders, we can surpass the baseline model. The use of attention-based encoders enhance interpretability and enable us to identify genes, bonds and atoms that were used by the network to make a prediction.

Medical imaging is widely used in clinical practice for diagnosis and treatment. Report-writing can be error-prone for unexperienced physicians, and time- consuming and tedious for experienced physicians. To address these issues, we study the automatic generation of medical imaging reports. This task presents several challenges. First, a complete report contains multiple heterogeneous forms of information, including findings and tags. Second, abnormal regions in medical images are difficult to identify. Third, the re- ports are typically long, containing multiple sentences. To cope with these challenges, we (1) build a multi-task learning framework which jointly performs the pre- diction of tags and the generation of para- graphs, (2) propose a co-attention mechanism to localize regions containing abnormalities and generate narrations for them, (3) develop a hierarchical LSTM model to generate long paragraphs. We demonstrate the effectiveness of the proposed methods on two publicly available datasets.

Retinal imaging has emerged as a powerful, non-invasive modality for detecting and quantifying biomarkers of systemic diseases-ranging from diabetes and hypertension to Alzheimer's disease and cardiovascular disorders but current insights remain dispersed across platforms and specialties. Recent technological advances in optical coherence tomography (OCT/OCTA) and adaptive optics (AO) now deliver ultra-high-resolution scans (down to 5 {\mu}m ) with superior contrast and spatial integration, allowing early identification of microvascular abnormalities and neurodegenerative changes. At the same time, AI-driven and machine learning (ML) algorithms have revolutionized the analysis of large-scale retinal datasets, increasing sensitivity and specificity; for example, deep learning models achieve > 90 \% sensitivity for diabetic retinopathy and AUC = 0.89 for the prediction of cardiovascular risk from fundus photographs. The proliferation of mobile health technologies and telemedicine platforms further extends access, reduces costs, and facilitates community-based screening and longitudinal monitoring. Despite these breakthroughs, translation into routine practice is hindered by heterogeneous imaging protocols, limited external validation of AI models, and integration challenges within clinical workflows. In this review, we systematically synthesize the latest OCT/OCT and AO developments, AI/ML approaches, and mHealth/Tele-ophthalmology initiatives and quantify their diagnostic performance across disease domains. Finally, we propose a roadmap for multicenter protocol standardization, prospective validation trials, and seamless incorporation of retinal screening into primary and specialty care pathways-paving the way for precision prevention, early intervention, and ongoing treatment of life-threatening systemic diseases.

We propose the Multi-Head Gaussian Adaptive Attention Mechanism (GAAM), a novel probabilistic attention framework, and the Gaussian Adaptive Transformer (GAT), designed to enhance information aggregation across multiple modalities, including Speech, Text and Vision. GAAM integrates learnable mean and variance into its attention mechanism, implemented in a Multi-Headed framework enabling it to collectively model any Probability Distribution for dynamic recalibration of feature significance. This method demonstrates significant improvements, especially with highly non-stationary data, surpassing the state-of-the-art attention techniques in model performance (up to approximately +20% in accuracy) by identifying key elements within the feature space. GAAM's compatibility with dot-product-based attention models and relatively low number of parameters showcases its adaptability and potential to boost existing attention frameworks. Empirically, GAAM exhibits superior adaptability and efficacy across a diverse range of tasks, including emotion recognition in speech, image classification, and text classification, thereby establishing its robustness and versatility in handling multi-modal data. Furthermore, we introduce the Importance Factor (IF), a new learning-based metric that enhances the explainability of models trained with GAAM-based methods. Overall, GAAM represents an advancement towards development of better performing and more explainable attention models across multiple modalities.

Visual search is important in our daily life. The efficient allocation of visual attention is critical to effectively complete visual search tasks. Prior research has predominantly modelled the spatial allocation of visual attention in images at the pixel level, e.g. using a saliency map. However, emerging evidence shows that visual attention is guided by objects rather than pixel intensities. This paper introduces the Object-level Attention Transformer (OAT), which predicts human scanpaths as they search for a target object within a cluttered scene of distractors. OAT uses an encoder-decoder architecture. The encoder captures information about the position and appearance of the objects within an image and about the target. The decoder predicts the gaze scanpath as a sequence of object fixations, by integrating output features from both the encoder and decoder. We also propose a new positional encoding that better reflects spatial relationships between objects. We evaluated OAT on the Amazon book cover dataset and a new dataset for visual search that we collected. OAT's predicted gaze scanpaths align more closely with human gaze patterns, compared to predictions by algorithms based on spatial attention on both established metrics and a novel behavioural-based metric. Our results demonstrate the generalization ability of OAT, as it accurately predicts human scanpaths for unseen layouts and target objects.

While Attention has come to be an important mechanism in deep learning, there remains limited intuition for why it works so well. Here, we show that Transformer Attention can be closely related under certain data conditions to Kanerva's Sparse Distributed Memory (SDM), a biologically plausible associative memory model. We confirm that these conditions are satisfied in pre-trained GPT2 Transformer models. We discuss the implications of the Attention-SDM map and provide new computational and biological interpretations of Attention.

Recent advances in large language models highlighted the excessive quadratic cost of self-attention. Despite the significant research efforts, subquadratic attention methods still suffer from inferior performance in practice. We hypothesize that dynamic, learned content-based sparsity can lead to more efficient attention mechanisms. We present Mixture of Sparse Attention (MoSA), a novel approach inspired by Mixture of Experts (MoE) with expert choice routing. MoSA dynamically selects tokens for each attention head, allowing arbitrary sparse attention patterns. By selecting k tokens from a sequence of length T, MoSA reduces the computational complexity of each attention head from O(T^2) to O(k^2 + T). This enables using more heads within the same computational budget, allowing higher specialization. We show that among the tested sparse attention variants, MoSA is the only one that can outperform the dense baseline, sometimes with up to 27% better perplexity for an identical compute budget. MoSA can also reduce the resource usage compared to dense self-attention. Despite using torch implementation without an optimized kernel, perplexity-matched MoSA models are simultaneously faster in wall-clock time, require less memory for training, and drastically reduce the size of the KV-cache compared to the dense transformer baselines.

The drug development pipeline for a new compound can last 10-20 years and cost over 10 billion. Drug repurposing offers a more time- and cost-effective alternative. Computational approaches based on biomedical knowledge graph representations have recently yielded new drug repurposing hypotheses. In this study, we present a novel, disease-specific hypergraph representation learning technique to derive contextual embeddings of biological pathways of various lengths but that all start at any given drug and all end at the disease of interest. Further, we extend this method to multi-disease hypergraphs. To determine the repurposing potential of each of the 1,522 drugs, we derive drug-specific distributions of cosine similarity values and ultimately consider the median for ranking. Cosine similarity values are computed between (1) all biological pathways starting at the considered drug and ending at the disease of interest and (2) all biological pathways starting at drugs currently prescribed against that disease and ending at the disease of interest. We illustrate our approach with Alzheimer's disease (AD) and two of its risk factors: hypertension (HTN) and type 2 diabetes (T2D). We compare each drug's rank across four hypergraph settings (single- or multi-disease): AD only, AD + HTN, AD + T2D, and AD + HTN + T2D. Notably, our framework led to the identification of two promising drugs whose repurposing potential was significantly higher in hypergraphs combining two diseases: dapagliflozin (antidiabetic; moved up, from top 32% to top 7%, across all considered drugs) and debrisoquine (antihypertensive; moved up, from top 76% to top 23%). Our approach serves as a hypothesis generation tool, to be paired with a validation pipeline relying on laboratory experiments and semi-automated parsing of the biomedical literature.

Artificial intelligence is revealing what medicine never intended to encode. Deep vision models, trained on chest X-rays, can now detect not only disease but also invisible traces of social inequality. In this study, we show that state-of-the-art architectures (DenseNet121, SwinV2-B, MedMamba) can predict a patient's health insurance type, a strong proxy for socioeconomic status, from normal chest X-rays with significant accuracy (AUC around 0.70 on MIMIC-CXR-JPG, 0.68 on CheXpert). The signal was unlikely contributed by demographic features by our machine learning study combining age, race, and sex labels to predict health insurance types; it also remains detectable when the model is trained exclusively on a single racial group. Patch-based occlusion reveals that the signal is diffuse rather than localized, embedded in the upper and mid-thoracic regions. This suggests that deep networks may be internalizing subtle traces of clinical environments, equipment differences, or care pathways; learning socioeconomic segregation itself. These findings challenge the assumption that medical images are neutral biological data. By uncovering how models perceive and exploit these hidden social signatures, this work reframes fairness in medical AI: the goal is no longer only to balance datasets or adjust thresholds, but to interrogate and disentangle the social fingerprints embedded in clinical data itself.

People are increasingly seeking healthcare information from large language models (LLMs) via interactive chatbots, yet the nature and inherent risks of these conversations remain largely unexplored. In this paper, we filter large-scale conversational AI datasets to achieve HealthChat-11K, a curated dataset of 11K real-world conversations composed of 25K user messages. We use HealthChat-11K and a clinician-driven taxonomy for how users interact with LLMs when seeking healthcare information in order to systematically study user interactions across 21 distinct health specialties. Our analysis reveals insights into the nature of how and why users seek health information, such as common interactions, instances of incomplete context, affective behaviors, and interactions (e.g., leading questions) that can induce sycophancy, underscoring the need for improvements in the healthcare support capabilities of LLMs deployed as conversational AI. Code and artifacts to retrieve our analyses and combine them into a curated dataset can be found here: https://github.com/yahskapar/HealthChat

Recently computer-aided diagnosis has demonstrated promising performance, effectively alleviating the workload of clinicians. However, the inherent sample imbalance among different diseases leads algorithms biased to the majority categories, leading to poor performance for rare categories. Existing works formulated this challenge as a long-tailed problem and attempted to tackle it by decoupling the feature representation and classification. Yet, due to the imbalanced distribution and limited samples from tail classes, these works are prone to biased representation learning and insufficient classifier calibration. To tackle these problems, we propose a new Long-tailed Medical Diagnosis (LMD) framework for balanced medical image classification on long-tailed datasets. In the initial stage, we develop a Relation-aware Representation Learning (RRL) scheme to boost the representation ability by encouraging the encoder to capture intrinsic semantic features through different data augmentations. In the subsequent stage, we propose an Iterative Classifier Calibration (ICC) scheme to calibrate the classifier iteratively. This is achieved by generating a large number of balanced virtual features and fine-tuning the encoder using an Expectation-Maximization manner. The proposed ICC compensates for minority categories to facilitate unbiased classifier optimization while maintaining the diagnostic knowledge in majority classes. Comprehensive experiments on three public long-tailed medical datasets demonstrate that our LMD framework significantly surpasses state-of-the-art approaches. The source code can be accessed at https://github.com/peterlipan/LMD.

The rapid evolution of artificial intelligence (AI), together with the increased availability of social media and news for epidemiological surveillance, are marking a pivotal moment in epidemiology and public health research. Leveraging the power of generative AI, we use an ensemble approach which incorporates multiple Large Language Models (LLMs) to extract valuable actionable epidemiological information from the World Health Organization (WHO) Disease Outbreak News (DONs). DONs is a collection of regular reports on global outbreaks curated by the WHO and the adopted decision-making processes to respond to them. The extracted information is made available in a daily-updated dataset and a knowledge graph, referred to as eKG, derived to provide a nuanced representation of the public health domain knowledge. We provide an overview of this new dataset and describe the structure of eKG, along with the services and tools used to access and utilize the data that we are building on top. These innovative data resources open altogether new opportunities for epidemiological research, and the analysis and surveillance of disease outbreaks.

Attention mechanisms are ubiquitous components in neural architectures applied to natural language processing. In addition to yielding gains in predictive accuracy, attention weights are often claimed to confer interpretability, purportedly useful both for providing insights to practitioners and for explaining why a model makes its decisions to stakeholders. We call the latter use of attention mechanisms into question by demonstrating a simple method for training models to produce deceptive attention masks. Our method diminishes the total weight assigned to designated impermissible tokens, even when the models can be shown to nevertheless rely on these features to drive predictions. Across multiple models and tasks, our approach manipulates attention weights while paying surprisingly little cost in accuracy. Through a human study, we show that our manipulated attention-based explanations deceive people into thinking that predictions from a model biased against gender minorities do not rely on the gender. Consequently, our results cast doubt on attention's reliability as a tool for auditing algorithms in the context of fairness and accountability.

Softmax attention is the principle backbone of foundation models for various artificial intelligence applications, yet its quadratic complexity in sequence length can limit its inference throughput in long-context settings. To address this challenge, alternative architectures such as linear attention, State Space Models (SSMs), and Recurrent Neural Networks (RNNs) have been considered as more efficient alternatives. While connections between these approaches exist, such models are commonly developed in isolation and there is a lack of theoretical understanding of the shared principles underpinning these architectures and their subtle differences, greatly influencing performance and scalability. In this paper, we introduce the Dynamical Systems Framework (DSF), which allows a principled investigation of all these architectures in a common representation. Our framework facilitates rigorous comparisons, providing new insights on the distinctive characteristics of each model class. For instance, we compare linear attention and selective SSMs, detailing their differences and conditions under which both are equivalent. We also provide principled comparisons between softmax attention and other model classes, discussing the theoretical conditions under which softmax attention can be approximated. Additionally, we substantiate these new insights with empirical validations and mathematical arguments. This shows the DSF's potential to guide the systematic development of future more efficient and scalable foundation models.