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Sally Turutov

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TMLR Journal 2026 Journal Article

Mechanism-Aware Prediction of Tissue-Specific Drug Activity via Multi-Modal Biological Graphs

Sally Turutov
Kira Radinsky

Predicting how small molecules behave across human tissues is essential for targeted therapy development. While some existing models incorporate tissue identity, they treat it as a label—ignoring the underlying biological mechanisms that differentiate tissues. We present Expresso, a multi-modal architecture that predicts tissue-contextual molecular activity as measured by the assay by modeling how compounds interact with transcriptomic and pathway-level tissue context. Expresso constructs heterogeneous graphs from GTEx data, linking samples, genes, and pathways to reflect expression profiles and curated biological relationships. These graphs are encoded using a hierarchical GNN and fused with frozen molecular embeddings to produce context-aware predictions. A multi-task pretraining strategy—spanning gene recovery, tissue classification, and pathway-level contrastive learning—guides the model to learn mechanistically grounded representations. On nine tissues, Expresso improves mean AUC by up to 27.9 points over molecule-only baselines. Our results demonstrate that incorporating biological structure—as defined by the assay—yields more accurate and interpretable models for tissue-specific drug behavior in human cell-based in vitro assay systems.

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AAAI Conference 2024 Conference Paper

Molecular Optimization Model with Patentability Constraint

Sally Turutov
Kira Radinsky

In drug development, molecular optimization is a crucial challenge that involves generating novel molecules given a lead molecule as input. The task requires maintaining molecular similarity to the original molecule while simultaneously optimizing multiple chemical attributes. To aid in this process, numerous generative models have been proposed. However, in practical applications, it is crucial for these models not only to generate novel molecules with the above constraints but also to generate molecules that significantly differ from any existing patented compounds. In this work, we present a multi-optimization molecular framework to address this challenge. Our framework trains a model to prioritize both enhanced properties and substantial dissimilarity from patented compounds. By jointly learning continuous representations of optimized and patentable molecules, we ensure that the generated molecules are significantly distant from any patented compounds while improving chemical properties. Through empirical evaluation, we demonstrate the superior performance of our approach compared to state-of-the-art molecular optimization methods both in chemical property optimization and patentability.

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