Parthasarathy Suryanarayanan

Yoel Shoshan, Moshiko Raboh, Michal Ozery-Flato et al.

Large language models applied to vast biological datasets have the potential to transform biology by uncovering disease mechanisms and accelerating drug development. However, current models are often siloed, trained separately on small-molecules, proteins, or transcriptomic data, limiting their ability to capture complex, multi-modal interactions. Effective drug discovery requires computational tools that integrate multiple biological entities while supporting prediction and generation, a challenge existing models struggle to address. For this purpose, we present MAMMAL - Molecular Aligned Multi-Modal Architecture and Language - a versatile method applied to create a multi-task foundation model that learns from large-scale biological datasets across diverse modalities, including proteins, small-molecules, and omics. MAMMAL's structured prompt syntax supports classification, regression, and generation tasks while handling token and scalar inputs and outputs. Evaluated on eleven diverse downstream tasks, it reaches a new state of the art (SOTA) in nine tasks and is comparable to SOTA in two tasks, all within a unified architecture, unlike prior task-specific models. Additionally, we explored Alphafold 3 binding prediction capabilities on antibody-antigen and nanobody-antigen complexes showing significantly better classification performance of MAMMAL in 3 out of 4 targets. The model code and pretrained weights are publicly available at https://github.com/BiomedSciAI/biomed-multi-alignment and https://huggingface.co/ibm/biomed.omics.bl.sm.ma-ted-458m

Parthasarathy Suryanarayanan, Prithwish Chakraborty, Piyush Madan et al.

In this work we introduce Disease Progression Modeling workbench 360 (DPM360) opensource clinical informatics framework for collaborative research and delivery of healthcare AI. DPM360, when fully developed, will manage the entire modeling life cycle, from data analysis (e.g., cohort identification) to machine learning algorithm development and prototyping. DPM360 augments the advantages of data model standardization and tooling (OMOP-CDM, Athena, ATLAS) provided by the widely-adopted OHDSI initiative with a powerful machine learning training framework, and a mechanism for rapid prototyping through automatic deployment of models as containerized services to a cloud environment.

Bum Chul Kwon, Ben Shapira, Moshiko Raboh et al.

The chemical space of drug-like molecules is vast, motivating the development of generative models that must learn broad chemical distributions, enable conditional generation by capturing structure-property representations, and provide fast molecular generation. Meeting the objectives depends on modeling choices, including the probabilistic modeling approach, the conditional generative formulation, the architecture, and the molecular input representation. To address the challenges, we present STAR-VAE (Selfies-encoded, Transformer-based, AutoRegressive Variational Auto Encoder), a scalable latent-variable framework with a Transformer encoder and an autoregressive Transformer decoder. It is trained on 79 million drug-like molecules from PubChem, using SELFIES to guarantee syntactic validity. The latent-variable formulation enables conditional generation: a property predictor supplies a conditioning signal that is applied consistently to the latent prior, the inference network, and the decoder. Our contributions are: (i) a Transformer-based latent-variable encoder-decoder model trained on SELFIES representations; (ii) a principled conditional latent-variable formulation for property-guided generation; and (iii) efficient finetuning with low-rank adapters (LoRA) in both encoder and decoder, enabling fast adaptation with limited property and activity data. On the GuacaMol and MOSES benchmarks, our approach matches or exceeds baselines, and latent-space analyses reveal smooth, semantically structured representations that support both unconditional exploration and property-aware generation. On the Tartarus benchmarks, the conditional model shifts docking-score distributions toward stronger predicted binding. These results suggest that a modernized, scale-appropriate VAE remains competitive for molecular generation when paired with principled conditioning and parameter-efficient finetuning.

Parthasarathy Suryanarayanan, Yunguang Qiu, Shreyans Sethi et al. · ibm-research

Quality molecular representations are key to foundation model development in bio-medical research. Previous efforts have typically focused on a single representation or molecular view, which may have strengths or weaknesses on a given task. We develop Multi-view Molecular Embedding with Late Fusion (MMELON), an approach that integrates graph, image and text views in a foundation model setting and may be readily extended to additional representations. Single-view foundation models are each pre-trained on a dataset of up to 200M molecules. The multi-view model performs robustly, matching the performance of the highest-ranked single-view. It is validated on over 120 tasks, including molecular solubility, ADME properties, and activity against G Protein-Coupled receptors (GPCRs). We identify 33 GPCRs that are related to Alzheimer's disease and employ the multi-view model to select strong binders from a compound screen. Predictions are validated through structure-based modeling and identification of key binding motifs.

Parthasarathy Suryanarayanan, Sundar Saranathan, Shilpa Mahatma et al.

The evolution of AI is advancing rapidly, creating both challenges and opportunities for industry-community collaboration. In this work, we present a novel methodology aiming to facilitate this collaboration through crowdsourcing of AI models. Concretely, we have implemented a system and a process that any organization can easily adopt to host AI competitions. The system allows them to automatically harvest and evaluate the submitted models against in-house proprietary data and also to incorporate them as reusable services in a product.

Parthasarathy Suryanarayanan, Ching-Huei Tsou, Ananya Poddar et al.

The Coronavirus disease 2019 (COVID-19) global pandemic has transformed almost every facet of human society throughout the world. Against an emerging, highly transmissible disease with no definitive treatment or vaccine, governments worldwide have implemented non-pharmaceutical intervention (NPI) to slow the spread of the virus. Examples of such interventions include community actions (e.g. school closures, restrictions on mass gatherings), individual actions (e.g. mask wearing, self-quarantine), and environmental actions (e.g. public facility cleaning). We present the Worldwide Non-pharmaceutical Interventions Tracker for COVID-19 (WNTRAC), a comprehensive dataset consisting of over 6,000 NPIs implemented worldwide since the start of the pandemic. WNTRAC covers NPIs implemented across 261 countries and territories, and classifies NPI measures into a taxonomy of sixteen NPI types. NPI measures are automatically extracted daily from Wikipedia articles using natural language processing techniques and manually validated to ensure accuracy and veracity. We hope that the dataset is valuable for policymakers, public health leaders, and researchers in modeling and analysis efforts for controlling the spread of COVID-19.

Parthasarathy Suryanarayanan, Bhavani Iyer, Prithwish Chakraborty et al.

Many institutions within the healthcare ecosystem are making significant investments in AI technologies to optimize their business operations at lower cost with improved patient outcomes. Despite the hype with AI, the full realization of this potential is seriously hindered by several systemic problems, including data privacy, security, bias, fairness, and explainability. In this paper, we propose a novel canonical architecture for the development of AI models in healthcare that addresses these challenges. This system enables the creation and management of AI predictive models throughout all the phases of their life cycle, including data ingestion, model building, and model promotion in production environments. This paper describes this architecture in detail, along with a qualitative evaluation of our experience of using it on real world problems.