Baradwaj Simha Sankar

John Rincon, Alexander R. Pelletier, Destiny Gilliland et al.

Objective: As AI becomes increasingly central to healthcare, there is a pressing need for bioinformatics and biomedical training systems that are personalized and adaptable. Materials and Methods: The NIH Bridge2AI Training, Recruitment, and Mentoring (TRM) Working Group developed a cross-disciplinary curriculum grounded in collaborative innovation, ethical data stewardship, and professional development within an adapted Learning Health System (LHS) framework. Results: The curriculum integrates foundational AI modules, real-world projects, and a structured mentee-mentor network spanning Bridge2AI Grand Challenges and the Bridge Center. Guided by six learner personas, the program tailors educational pathways to individual needs while supporting scalability. Discussion: Iterative refinement driven by continuous feedback ensures that content remains responsive to learner progress and emerging trends. Conclusion: With over 30 scholars and 100 mentors engaged across North America, the TRM model demonstrates how adaptive, persona-informed training can build interdisciplinary competencies and foster an integrative, ethically grounded AI education in biomedical contexts.

Erika Yilin Zheng, Yu Yan, Baradwaj Simha Sankar et al.

Existing machine learning methods for molecular (e.g., gene) embeddings are restricted to specific tasks or data modalities, limiting their effectiveness within narrow domains. As a result, they fail to capture the full breadth of gene functions and interactions across diverse biological contexts. In this study, we have systematically evaluated knowledge representations of biomolecules across multiple dimensions representing a task-agnostic manner spanning three major data sources, including omics experimental data, literature-derived text data, and knowledge graph-based representations. To distinguish between meaningful biological signals from chance correlations, we devised an adjusted variant of Singular Vector Canonical Correlation Analysis (SVCCA) that quantifies signal redundancy and complementarity across different data modalities and sources. These analyses reveal that existing embeddings capture largely non-overlapping molecular signals, highlighting the value of embedding integration. Building on this insight, we propose Platform for Representation and Integration of multimodal Molecular Embeddings (PRISME), a machine learning based workflow using an autoencoder to integrate these heterogeneous embeddings into a unified multimodal representation. We validated this approach across various benchmark tasks, where PRISME demonstrated consistent performance, and outperformed individual embedding methods in missing value imputations. This new framework supports comprehensive modeling of biomolecules, advancing the development of robust, broadly applicable multimodal embeddings optimized for downstream biomedical machine learning applications.