Clinical trials play an important role in cancer care and research, yet participation rates remain low. We developed MSK-MATCH (Memorial Sloan Kettering Multi-Agent Trial Coordination Hub), an AI system for automated eligibility screening from clinical text. MSK-MATCH integrates a large language model with a curated oncology trial knowledge base and retrieval-augmented architecture providing explanations for all AI predictions grounded in source text. In a retrospective dataset of 88,518 clinical documents from 731 patients across six breast cancer trials, MSK-MATCH automatically resolved 61.9% of cases and triaged 38.1% for human review. This AI-assisted workflow achieved 98.6% accuracy, 98.4% sensitivity, and 98.7% specificity for patient-level eligibility classification, matching or exceeding performance of the human-only and AI-only comparisons. For the triaged cases requiring manual review, prepopulating eligibility screens with AI-generated explanations reduced screening time from 20 minutes to 43 seconds at an average cost of $0.96 per patient-trial pair.

In recent years, Electroencephalographic analysis has gained prominence in stress research when combined with AI and Machine Learning models for validation. In this study, a lightweight dynamic brain connectivity framework based on Time Varying Directed Transfer Function is proposed, where TV DTF features were validated through ML based stress classification. TV DTF estimates the directional information flow between brain regions across distinct EEG frequency bands, thereby capturing temporal and causal influences that are often overlooked by static functional connectivity measures. EEG recordings from the 32 channel SAM 40 dataset were employed, focusing on mental arithmetic task trials. The dynamic EEG-based TV-DTF features were validated through ML classifiers such as Support Vector Machine, Random Forest, Gradient Boosting, Adaptive Boosting, and Extreme Gradient Boosting. Experimental results show that alpha-TV-DTF provided the strongest discriminative power, with SVM achieving 89.73% accuracy in 3-class classification and with XGBoost achieving 93.69% accuracy in 2 class classification. Relative to absolute power and phase locking based functional connectivity features, alpha TV DTF and beta TV DTF achieved higher performance across the ML models, highlighting the advantages of dynamic over static measures. Feature importance analysis further highlighted dominant long-range frontal parietal and frontal occipital informational influences, emphasizing the regulatory role of frontal regions under stress. These findings validate the lightweight TV-DTF as a robust framework, revealing spatiotemporal brain dynamics and directional influences across different stress levels.

We introduce an explainability method for biomedical hypothesis generation systems, built on top of the novel Hypothesis Generation Context Retriever framework. Our approach combines semantic graph-based retrieval and relevant data-restrictive training to simulate real-world discovery constraints. Integrated with large language models (LLMs) via retrieval-augmented generation, the system explains hypotheses with contextual evidence using published scientific literature. We also propose a novel feedback loop approach, which iteratively identifies and corrects flawed parts of LLM-generated explanations, refining both the evidence paths and supporting context. We demonstrate the performance of our method with multiple large language models and evaluate the explanation and context retrieval quality through both expert-curated assessment and large-scale automated analysis.

Ultrasound imaging is one of the most widely used diagnostic modalities, offering real-time, radiation-free assessment across diverse clinical domains. However, interpretation of ultrasound images remains challenging due to high noise levels, operator dependence, and limited field of view, resulting in substantial inter-observer variability. Current Deep Learning approaches are hindered by the scarcity of large labeled datasets and the domain gap between general and sonographic images, which limits the transferability of models pretrained on non-medical data. To address these challenges, we introduce the Ultrasound Self-Supervised Foundation Model with Masked Autoencoding (USF-MAE), the first large-scale self-supervised MAE framework pretrained exclusively on ultrasound data. The model was pre-trained on 370,000 2D and 3D ultrasound images curated from 46 open-source datasets, collectively termed OpenUS-46, spanning over twenty anatomical regions. This curated dataset has been made publicly available to facilitate further research and reproducibility. Using a Vision Transformer encoder-decoder architecture, USF-MAE reconstructs masked image patches, enabling it to learn rich, modality-specific representations directly from unlabeled data. The pretrained encoder was fine-tuned on three public downstream classification benchmarks: BUS-BRA (breast cancer), MMOTU-2D (ovarian tumors), and GIST514-DB (gastrointestinal stromal tumors). Across all tasks, USF-MAE consistently outperformed conventional CNN and ViT baselines, achieving F1-scores of 81.6%, 79.6%, and 82.4%, respectively. Despite not using labels during pretraining, USF-MAE approached the performance of the supervised foundation model UltraSam on breast cancer classification and surpassed it on the other tasks, demonstrating strong cross-anatomical generalization.

With the emerging application of Federated Learning (FL) in decision-making scenarios, it is imperative to regulate model fairness to prevent disparities across sensitive groups (e.g., female, male). Current research predominantly focuses on two concepts of group fairness within FL: Global Fairness (overall model disparity across all clients) and Local Fairness (the disparity within each client). However, the non-decomposable, non-differentiable nature of fairness criteria poses two fundamental, unresolved challenges for fair FL: (i) Harmonizing global and local fairness, especially in multi-class setting; (ii) Enabling a controllable, optimal accuracy-fairness trade-off. To tackle these challenges, we propose a novel controllable federated group-fairness calibration framework, named FedFACT. FedFACT identifies the Bayes-optimal classifiers under both global and local fairness constraints, yielding models with minimal performance decline while guaranteeing fairness. Building on the characterization of the optimal fair classifiers, we reformulate fair federated learning as a personalized cost-sensitive learning problem for in-processing and a bi-level optimization for post-processing. Theoretically, we provide convergence and generalization guarantees for FedFACT to approach the near-optimal accuracy under given fairness levels. Extensive experiments on multiple datasets across various data heterogeneity demonstrate that FedFACT consistently outperforms baselines in balancing accuracy and global-local fairness.

Circuit discovery is a key step in many mechanistic interpretability pipelines. Current methods, such as Path Patching, are computationally expensive and have limited in-depth circuit analysis for smaller models. In this study, we propose Accelerated Path Patching (APP), a hybrid approach leveraging our novel contrastive attention head pruning method to drastically reduce the search space of circuit discovery methods. Our Contrastive-FLAP pruning algorithm uses techniques from causal mediation analysis to assign higher pruning scores to task-specific attention heads, leading to higher performing sparse models compared to traditional pruning techniques. Although Contrastive-FLAP is successful at preserving task-specific heads that existing pruning algorithms remove at low sparsity ratios, the circuits found by Contrastive-FLAP alone are too large to satisfy the minimality constraint required in circuit analysis. APP first applies Contrastive-FLAP to reduce the search space on required for circuit discovery algorithms by, on average, 56\%. Next, APP, applies traditional Path Patching on the remaining attention heads, leading to a speed up of 59.63\%-93.27\% compared to Path Patching applied to the dense model. Despite the substantial computational saving that APP provides, circuits obtained from APP exhibit substantial overlap and similar performance to previously established Path Patching circuits

Tokenization is an important first step in Natural Language Processing (NLP) pipelines because it decides how models learn and represent linguistic information. However, current subword tokenizers like SentencePiece or HuggingFace BPE are mostly designed for Latin or multilingual corpora and do not perform well on languages with rich morphology such as Bengali. To address this limitation, we present BengaliBPE, a Byte Pair Encoding (BPE) tokenizer specifically developed for the Bengali script. BengaliBPE applies Unicode normalization, grapheme-level initialization, and morphology-aware merge rules to maintain linguistic consistency and preserve subword integrity. We use a large-scale Bengali news classification dataset to compare BengaliBPE with three baselines: Whitespace, SentencePiece BPE, and HuggingFace BPE. The evaluation considers tokenization granularity, encoding speed, and downstream classification accuracy. While all methods perform reasonably well, BengaliBPE provides the most detailed segmentation and the best morphological interpretability, albeit with slightly higher computational cost. These findings highlight the importance of language-aware tokenization for morphologically rich scripts and establish BengaliBPE as a strong foundation for future Bengali NLP systems, including large-scale pretraining of contextual language models.

Balancing strong privacy guarantees with high predictive performance is critical for time series forecasting (TSF) tasks involving Electronic Health Records (EHR). In this study, we explore how data augmentation can mitigate Membership Inference Attacks (MIA) on TSF models. We show that retraining with synthetic data can substantially reduce the effectiveness of loss-based MIAs by reducing the attacker's true-positive to false-positive ratio. The key challenge is generating synthetic samples that closely resemble the original training data to confuse the attacker, while also introducing enough novelty to enhance the model's ability to generalize to unseen data. We examine multiple augmentation strategies -- Zeroth-Order Optimization (ZOO), a variant of ZOO constrained by Principal Component Analysis (ZOO-PCA), and MixUp -- to strengthen model resilience without sacrificing accuracy. Our experimental results show that ZOO-PCA yields the best reductions in TPR/FPR ratio for MIA attacks without sacrificing performance on test data.

As financial applications of large language models (LLMs) gain attention, accurate Information Retrieval (IR) remains crucial for reliable AI services. However, existing benchmarks fail to capture the complex and domain-specific information needs of real-world banking scenarios. Building domain-specific IR benchmarks is costly and constrained by legal restrictions on using real customer data. To address these challenges, we propose a systematic methodology for constructing domain-specific IR benchmarks through LLM-based query generation. As a concrete implementation of this methodology, our pipeline combines single and multi-document query generation with an enhanced and reasoning-augmented answerability assessment method, achieving stronger alignment with human judgments than prior approaches. Using this methodology, we construct KoBankIR, comprising 815 queries derived from 204 official banking documents. Our experiments show that existing retrieval models struggle with the complex multi-document queries in KoBankIR, demonstrating the value of our systematic approach for domain-specific benchmark construction and underscoring the need for improved retrieval techniques in financial domains.

Division of Clinical and Translational Cancer Research, University of Puerto Rico Comprehensive Cancer Center, San Juan, PR, 00921, USA Abstract Transformer-based deep learning models have shown promise for disease risk prediction using electronic health records (EHRs), but modeling temporal dependencies remains a key challenge due to irregular visit intervals and lack of uniform structure. We propose a Bi-Positional Embedding Transformer Encoder or BiPETE for single-disease prediction, which integrates rotary positional em-beddings to encode relative visit timing and sinusoidal embeddings to preserve visit order. Without relying on large-scale pretraining, BiPETE is trained on EHR data from two mental health cohorts-depressive disorder and post-traumatic stress disorder (PTSD)-to predict the risk of alcohol and substance use disorders (ASUD). BiPETE outperforms baseline models, improving the area under the precision-recall curve (AUPRC) by 34% and 50% in the depression and PTSD cohorts, respectively. An ablation study further confirms the effectiveness of the dual positional encoding strategy. We apply the Integrated Gradients method to interpret model predictions, identifying key clinical features associated with ASUD risk and protection, such as abnormal inflammatory, hematologic, and metabolic markers, as well as specific medications and comorbidities. Overall, these key clinical features identified by the attribution methods contribute to a deeper understanding of the risk assessment process and offer valuable clues for mitigating potential risks. In summary, our study presents a practical and interpretable framework for disease risk prediction using EHR data, which can achieve strong performance.