A Contrastive Variational AutoEncoder for NSCLC Survival Prediction with Missing Modalities

Predicting survival outcomes for non-small cell lung cancer (NSCLC) patients is challenging due to the different individual prognostic features. This task can benefit from the integration of whole-slide images, bulk transcriptomics, and DNA methylation, which offer complementary views of the patient's condition at diagnosis. However, real-world clinical datasets are often incomplete, with entire modalities missing for a significant fraction of patients. State-of-the-art models rely on available data to create patient-level representations or use generative models to infer missing modalities, but they lack robustness in cases of severe missingness. We propose a Multimodal Contrastive Variational AutoEncoder (MCVAE) to address this issue: modality-specific variational encoders capture the uncertainty in each data source, and a fusion bottleneck with learned gating mechanisms is introduced to normalize the contributions from present modalities. We propose a multi-task objective that combines survival loss and reconstruction loss to regularize patient representations, along with a cross-modal contrastive loss that enforces cross-modal alignment in the latent space. During training, we apply stochastic modality masking to improve the robustness to arbitrary missingness patterns. Extensive evaluations on the TCGA-LUAD (n=475) and TCGA-LUSC (n=446) datasets demonstrate the efficacy of our approach in predicting disease-specific survival (DSS) and its robustness to severe missingness scenarios compared to two state-of-the-art models. Finally, we bring some clarifications on multimodal integration by testing our model on all subsets of modalities, finding that integration is not always beneficial to the task.

A Hybrid Federated Learning Based Ensemble Approach for Lung Disease Diagnosis Leveraging Fusion of SWIN Transformer and CNN

The significant advancements in computational power cre- ate a vast opportunity for using Artificial Intelligence in different ap- plications of healthcare and medical science. A Hybrid FL-Enabled Ensemble Approach For Lung Disease Diagnosis Leveraging a Combination of SWIN Transformer and CNN is the combination of cutting-edge technology of AI and Federated Learning. Since, medi- cal specialists and hospitals will have shared data space, based on that data, with the help of Artificial Intelligence and integration of federated learning, we can introduce a secure and distributed system for medical data processing and create an efficient and reliable system. The proposed hybrid model enables the detection of COVID-19 and Pneumonia based on x-ray reports. We will use advanced and the latest available tech- nology offered by Tensorflow and Keras along with Microsoft-developed Vision Transformer, that can help to fight against the pandemic that the world has to fight together as a united. We focused on using the latest available CNN models (DenseNet201, Inception V3, VGG 19) and the Transformer model SWIN Transformer in order to prepare our hy- brid model that can provide a reliable solution as a helping hand for the physician in the medical field. In this research, we will discuss how the Federated learning-based Hybrid AI model can improve the accuracy of disease diagnosis and severity prediction of a patient using the real-time continual learning approach and how the integration of federated learn- ing can ensure hybrid model security and keep the authenticity of the information.

Parameter-free representations outperform single-cell foundation models on downstream benchmarks

Single-cell RNA sequencing (scRNA-seq) data exhibit strong and reproducible statistical structure. This has motivated the development of large-scale foundation models, such as TranscriptFormer, that use transformer-based architectures to learn a generative model for gene expression by embedding genes into a latent vector space. These embeddings have been used to obtain state-of-the-art (SOTA) performance on downstream tasks such as cell-type classification, disease-state prediction, and cross-species learning. Here, we ask whether similar performance can be achieved without utilizing computationally intensive deep learning-based representations. Using simple, interpretable pipelines that rely on careful normalization and linear methods, we obtain SOTA or near SOTA performance across multiple benchmarks commonly used to evaluate single-cell foundation models, including outperforming foundation models on out-of-distribution tasks involving novel cell types and organisms absent from the training data. Our findings highlight the need for rigorous benchmarking and suggest that the biology of cell identity can be captured by simple linear representations of single cell gene expression data.

HyPCA-Net: Advancing Multimodal Fusion in Medical Image Analysis

Multimodal fusion frameworks, which integrate diverse medical imaging modalities (e.g., MRI, CT), have shown great potential in applications such as skin cancer detection, dementia diagnosis, and brain tumor prediction. However, existing multimodal fusion methods face significant challenges. First, they often rely on computationally expensive models, limiting their applicability in low-resource environments. Second, they often employ cascaded attention modules, which potentially increase risk of information loss during inter-module transitions and hinder their capacity to effectively capture robust shared representations across modalities. This restricts their generalization in multi-disease analysis tasks. To address these limitations, we propose a Hybrid Parallel-Fusion Cascaded Attention Network (HyPCA-Net), composed of two core novel blocks: (a) a computationally efficient residual adaptive learning attention block for capturing refined modality-specific representations, and (b) a dual-view cascaded attention block aimed at learning robust shared representations across diverse modalities. Extensive experiments on ten publicly available datasets exhibit that HyPCA-Net significantly outperforms existing leading methods, with improvements of up to 5.2% in performance and reductions of up to 73.1% in computational cost. Code: https://github.com/misti1203/HyPCA-Net.

Effective and Robust Multimodal Medical Image Analysis

Multimodal Fusion Learning (MFL), leveraging disparate data from various imaging modalities (e.g., MRI, CT, SPECT), has shown great potential for addressing medical problems such as skin cancer and brain tumor prediction. However, existing MFL methods face three key limitations: a) they often specialize in specific modalities, and overlook effective shared complementary information across diverse modalities, hence limiting their generalizability for multi-disease analysis; b) they rely on computationally expensive models, restricting their applicability in resource-limited settings; and c) they lack robustness against adversarial attacks, compromising reliability in medical AI applications. To address these limitations, we propose a novel Multi-Attention Integration Learning (MAIL) network, incorporating two key components: a) an efficient residual learning attention block for capturing refined modality-specific multi-scale patterns and b) an efficient multimodal cross-attention module for learning enriched complementary shared representations across diverse modalities. Furthermore, to ensure adversarial robustness, we extend MAIL network to design Robust-MAIL by incorporating random projection filters and modulated attention noise. Extensive evaluations on 20 public datasets show that both MAIL and Robust-MAIL outperform existing methods, achieving performance gains of up to 9.34% while reducing computational costs by up to 78.3%. These results highlight the superiority of our approaches, ensuring more reliable predictions than top competitors. Code: https://github.com/misti1203/MAIL-Robust-MAIL.

Cardiac Output Prediction from Echocardiograms: Self-Supervised Learning with Limited Data

Cardiac Output (CO) is a key parameter in the diagnosis and management of cardiovascular diseases. However, its accurate measurement requires right-heart catheterization, an invasive and time-consuming procedure, motivating the development of reliable non-invasive alternatives using echocardiography. In this work, we propose a self-supervised learning (SSL) pretraining strategy based on SimCLR to improve CO prediction from apical four-chamber echocardiographic videos. The pretraining is performed using the same limited dataset available for the downstream task, demonstrating the potential of SSL even under data scarcity. Our results show that SSL mitigates overfitting and improves representation learning, achieving an average Pearson correlation of 0.41 on the test set and outperforming PanEcho, a model trained on over one million echocardiographic exams. Source code is available at https://github.com/EIDOSLAB/cardiac-output.

EVA: Towards a universal model of the immune system

The effective application of foundation models to translational research in immune-mediated diseases requires multimodal patient-level representations that can capture complex phenotypes emerging from multicellular interactions. Yet most current biological foundation models focus only on single-cell resolution and are evaluated on technical metrics often disconnected from actual drug development tasks and challenges. Here, we introduce EVA, the first cross-species, multimodal foundation model of immunology and inflammation, a therapeutic area where shared pathogenic mechanisms create unique opportunities for transfer learning. EVA harmonizes transcriptomics data across species, platforms, and resolutions, and integrates histology data to produce rich, unified patient representations. We establish clear scaling laws, demonstrating that increasing model size and compute translates to improvements in both pretraining and downstream tasks performance. We introduce a comprehensive evaluation suite of 39 tasks spanning the drug development pipeline: zero-shot target efficacy and gene function prediction for discovery, cross-species or cross-diseases molecular perturbations for preclinical development, and patient stratification with treatment response prediction or disease activity prediction for clinical trials applications. We benchmark EVA against several state-of-the-art biological foundation models and baselines on these tasks, and demonstrate state-of-the-art results on each task category. Using mechanistic interpretability, we further identify biological meaningful features, revealing intertwined representations across species and technologies. We release an open version of EVA for transcriptomics to accelerate research on immune-mediated diseases.

A Swap-Adversarial Framework for Improving Domain Generalization in Electroencephalography-Based Parkinson's Disease Prediction

Electroencephalography (ECoG) offers a promising alternative to conventional electrocorticography (EEG) for the early prediction of Parkinson's disease (PD), providing higher spatial resolution and a broader frequency range. However, reproducible comparisons has been limited by ethical constraints in human studies and the lack of open benchmark datasets. To address this gap, we introduce a new dataset, the first reproducible benchmark for PD prediction. It is constructed from long-term ECoG recordings of 6-hydroxydopamine (6-OHDA)-induced rat models and annotated with neural responses measured before and after electrical stimulation. In addition, we propose a Swap-Adversarial Framework (SAF) that mitigates high inter-subject variability and the high-dimensional low-sample-size (HDLSS) problem in ECoG data, while achieving robust domain generalization across ECoG and EEG-based Brain-Computer Interface (BCI) datasets. The framework integrates (1) robust preprocessing, (2) Inter-Subject Balanced Channel Swap (ISBCS) for cross-subject augmentation, and (3) domain-adversarial training to suppress subject-specific bias. ISBCS randomly swaps channels between subjects to reduce inter-subject variability, and domain-adversarial training jointly encourages the model to learn task-relevant shared features. We validated the effectiveness of the proposed method through extensive experiments under cross-subject, cross-session, and cross-dataset settings. Our method consistently outperformed all baselines across all settings, showing the most significant improvements in highly variable environments. Furthermore, the proposed method achieved superior cross-dataset performance between public EEG benchmarks, demonstrating strong generalization capability not only within ECoG but to EEG data. The new dataset and source code will be made publicly available upon publication.

Chain-of-Thought Reasoning with Large Language Models for Clinical Alzheimer's Disease Assessment and Diagnosis

Alzheimer's disease (AD) has become a prevalent neurodegenerative disease worldwide. Traditional diagnosis still relies heavily on medical imaging and clinical assessment by physicians, which is often time-consuming and resource-intensive in terms of both human expertise and healthcare resources. In recent years, large language models (LLMs) have been increasingly applied to the medical field using electronic health records (EHRs), yet their application in Alzheimer's disease assessment remains limited, particularly given that AD involves complex multifactorial etiologies that are difficult to observe directly through imaging modalities. In this work, we propose leveraging LLMs to perform Chain-of-Thought (CoT) reasoning on patients' clinical EHRs. Unlike direct fine-tuning of LLMs on EHR data for AD classification, our approach utilizes LLM-generated CoT reasoning paths to provide the model with explicit diagnostic rationale for AD assessment, followed by structured CoT-based predictions. This pipeline not only enhances the model's ability to diagnose intrinsically complex factors but also improves the interpretability of the prediction process across different stages of AD progression. Experimental results demonstrate that the proposed CoT-based diagnostic framework significantly enhances stability and diagnostic performance across multiple CDR grading tasks, achieving up to a 15% improvement in F1 score compared to the zero-shot baseline method.

Handling Supervision Scarcity in Chest X-ray Classification: Long-Tailed and Zero-Shot Learning

Chest X-ray (CXR) classification in clinical practice is often limited by imperfect supervision, arising from (i) extreme long-tailed multi-label disease distributions and (ii) missing annotations for rare or previously unseen findings. The CXR-LT 2026 challenge addresses these issues on a PadChest-based benchmark with a 36-class label space split into 30 in-distribution classes for training and 6 out-of-distribution (OOD) classes for zero-shot evaluation. We present task-specific solutions tailored to the distinct supervision regimes. For Task 1 (long-tailed multi-label classification), we adopt an imbalance-aware multi-label learning strategy to improve recognition of tail classes while maintaining stable performance on frequent findings. For Task 2 (zero-shot OOD recognition), we propose a prediction approach that produces scores for unseen disease categories without using any supervised labels or examples from the OOD classes during training. Evaluated with macro-averaged mean Average Precision (mAP), our method achieves strong performance on both tasks, ranking first on the public leaderboard of the development phase. Code and pre-trained models are available at https://github.com/hieuphamha19/CXR_LT.