Jathurshan Pradeepkumar

Jathurshan Pradeepkumar, Mithunjha Anandakumar, Vinith Kugathasan et al.

Accurate sleep stage classification is significant for sleep health assessment. In recent years, several machine-learning based sleep staging algorithms have been developed , and in particular, deep-learning based algorithms have achieved performance on par with human annotation. Despite improved performance, a limitation of most deep-learning based algorithms is their black-box behavior, which have limited their use in clinical settings. Here, we propose a cross-modal transformer, which is a transformer-based method for sleep stage classification. The proposed cross-modal transformer consists of a novel cross-modal transformer encoder architecture along with a multi-scale one-dimensional convolutional neural network for automatic representation learning. Our method outperforms the state-of-the-art methods and eliminates the black-box behavior of deep-learning models by utilizing the interpretability aspect of the attention modules. Furthermore, our method provides considerable reductions in the number of parameters and training time compared to the state-of-the-art methods. Our code is available at https://github.com/Jathurshan0330/Cross-Modal-Transformer. A demo of our work can be found at https://bit.ly/Cross_modal_transformer_demo.

Mithunjha Anandakumar, Jathurshan Pradeepkumar, Simon L. Kappel et al.

Sleep plays a crucial role in the well-being of human lives. Traditional sleep studies using Polysomnography are associated with discomfort and often lower sleep quality caused by the acquisition setup. Previous works have focused on developing less obtrusive methods to conduct high-quality sleep studies, and ear-EEG is among popular alternatives. However, the performance of sleep staging based on ear-EEG is still inferior to scalp-EEG based sleep staging. In order to address the performance gap between scalp-EEG and ear-EEG based sleep staging, we propose a cross-modal knowledge distillation strategy, which is a domain adaptation approach. Our experiments and analysis validate the effectiveness of the proposed approach with existing architectures, where it enhances the accuracy of the ear-EEG based sleep staging by 3.46% and Cohen's kappa coefficient by a margin of 0.038.

Nirhoshan Sivaroopan, Chamuditha Jayanga, Chalani Ekanayake et al.

Deep neural network models can learn clinically relevant features from millions of histopathology images. However generating high-quality annotations to train such models for each hospital, each cancer type, and each diagnostic task is prohibitively laborious. On the other hand, terabytes of training data -- while lacking reliable annotations -- are readily available in the public domain in some cases. In this work, we explore how these large datasets can be consciously utilized to pre-train deep networks to encode informative representations. We then fine-tune our pre-trained models on a fraction of annotated training data to perform specific downstream tasks. We show that our approach can reach the state-of-the-art (SOTA) for patch-level classification with only 1-10% randomly selected annotations compared to other SOTA approaches. Moreover, we propose an uncertainty-aware loss function, to quantify the model confidence during inference. Quantified uncertainty helps experts select the best instances to label for further training. Our uncertainty-aware labeling reaches the SOTA with significantly fewer annotations compared to random labeling. Last, we demonstrate how our pre-trained encoders can surpass current SOTA for whole-slide image classification with weak supervision. Our work lays the foundation for data and task-agnostic pre-trained deep networks with quantified uncertainty.

Abraham Francisco Arellano Tavara, Umesh Kumar, Jathurshan Pradeepkumar et al.

Variants of Uncertain Significance (VUS) limit the clinical utility of prostate cancer genomics by delaying diagnosis and therapy when evidence for pathogenicity or benignity is incomplete. Progress is further limited by inconsistent annotations across sources and the absence of a prostate-specific benchmark for fair comparison. We introduce Prostate-VarBench, a curated pipeline for creating prostate-specific benchmarks that integrates COSMIC (somatic cancer mutations), ClinVar (expert-curated clinical variants), and TCGA-PRAD (prostate tumor genomics from The Cancer Genome Atlas) into a harmonized dataset of 193,278 variants supporting patient- or gene-aware splits to prevent data leakage. To ensure data integrity, we corrected a Variant Effect Predictor (VEP) issue that merged multiple transcript records, introducing ambiguity in clinical significance fields. We then standardized 56 interpretable features across eight clinically relevant tiers, including population frequency, variant type, and clinical context. AlphaMissense pathogenicity scores were incorporated to enhance missense variant classification and reduce VUS uncertainty. Building on this resource, we trained an interpretable TabNet model to classify variant pathogenicity, whose step-wise sparse masks provide per-case rationales consistent with molecular tumor board review practices. On the held-out test set, the model achieved 89.9% accuracy with balanced class metrics, and the VEP correction yields an 6.5% absolute reduction in VUS.

Zifeng Wang, Qiao Jin, Jiacheng Lin et al.

Developing artificial intelligence (AI) for vertical domains requires a solid data foundation for both training and evaluation. In this work, we introduce TrialPanorama, a large-scale, structured database comprising 1,657,476 clinical trial records aggregated from 15 global sources. The database captures key aspects of trial design and execution, including trial setups, interventions, conditions, biomarkers, and outcomes, and links them to standard biomedical ontologies such as DrugBank and MedDRA. This structured and ontology-grounded design enables TrialPanorama to serve as a unified, extensible resource for a wide range of clinical trial tasks, including trial planning, design, and summarization. To demonstrate its utility, we derive a suite of benchmark tasks directly from the TrialPanorama database. The benchmark spans eight tasks across two categories: three for systematic review (study search, study screening, and evidence summarization) and five for trial design (arm design, eligibility criteria, endpoint selection, sample size estimation, and trial completion assessment). The experiments using five state-of-the-art large language models (LLMs) show that while general-purpose LLMs exhibit some zero-shot capability, their performance is still inadequate for high-stakes clinical trial workflows. We release TrialPanorama database and the benchmark to facilitate further research on AI for clinical trials.

Chufan Gao, Jathurshan Pradeepkumar, Trisha Das et al.

Background The cost of drug discovery and development is substantial, with clinical trial outcomes playing a critical role in regulatory approval and patient care. However, access to large-scale, high-quality clinical trial outcome data remains limited, hindering advancements in predictive modeling and evidence-based decision-making. Methods We present the Clinical Trial Outcome (CTO) benchmark, a fully reproducible, large-scale repository encompassing approximately 125,000 drug and biologics trials. CTO integrates large language model (LLM) interpretations of publications, trial phase progression tracking, sentiment analysis from news sources, stock price movements of trial sponsors, and additional trial-related metrics. Furthermore, we manually annotated a dataset of clinical trials conducted between 2020 and 2024 to enhance the quality and reliability of outcome labels. Results The trial outcome labels in the CTO benchmark agree strongly with expert annotations, achieving an F1 score of 94 for Phase 3 trials and 91 across all phases. Additionally, benchmarking standard machine learning models on our manually annotated dataset revealed distribution shifts in recent trials, underscoring the necessity of continuously updated labeling approaches. Conclusions By analyzing CTO's performance on recent clinical trials, we demonstrate the ongoing need for high-quality, up-to-date trial outcome labels. We publicly release the CTO knowledge base and annotated labels at https://chufangao.github.io/CTOD, with regular updates to support research on clinical trial outcomes and inform data-driven improvements in drug development.

Mohamed Afham, Udith Haputhanthri, Jathurshan Pradeepkumar et al.

Human behavioral monitoring during sleep is essential for various medical applications. Majority of the contactless human pose estimation algorithms are based on RGB modality, causing ineffectiveness in in-bed pose estimation due to occlusions by blankets and varying illumination conditions. Long-wavelength infrared (LWIR) modality based pose estimation algorithms overcome the aforementioned challenges; however, ground truth pose generations by a human annotator under such conditions are not feasible. A feasible solution to address this issue is to transfer the knowledge learned from images with pose labels and no occlusions, and adapt it towards real world conditions (occlusions due to blankets). In this paper, we propose a novel learning strategy comprises of two-fold data augmentation to reduce the cross-domain discrepancy and knowledge distillation to learn the distribution of unlabeled images in real world conditions. Our experiments and analysis show the effectiveness of our approach over multiple standard human pose estimation baselines.