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Currently exploring offline reinforcement learning methods for learning a policy for sequentially designing crystal structures.
Designing novel deep graph generative model for generating new ligand molecules that can bind to a given target receptor binding site.
Computational methods to identify drug-gene correlations and molecules that can induce leukemic cell maturation.
Two ways to incorporate crystal symmetry information as an inductive bias into a generative model for crystal structure design.
Two ways for encoding visual inputs for navigation task using RL – pretraining a contrastive learning-based SimCLR model and VAE-based generative approach.
Evaluated state-of-the-art unsupervised deep learning techniques including variational autoencoders for single-cell gene expression data analysis.
Designed an attention-based transformer model for de novo generation of drug-like molecules that can induce a desired transcriptomic profile. Accepted as poster at MLCSB COSI, ISMB 2022.
CPU- and GPU-level parallelization of tensor decomposition algorithm using OpenMP and OpenACC.
Identified somatic mutations in RNA-sequencing data of human oral squamous cell carcinoma samples.
Published in ML4Materials Workshop at ICLR, 2023
Solid-state materials, which are made up of periodic 3D crystal structures, are particularly useful for a variety of real-world applications such as batteries, fuel cells and catalytic materials. Designing solid-state materials, especially in a robust and automated fashion, remains an ongoing challenge. To further the automated design of crystalline materials, we propose a method to learn to design valid crystal structures given a crystal skeleton. By incorporating Euclidean equivariance into a policy network, we portray the problem of designing new crystals as a sequential prediction task suited for imitation learning. At each step, given an incomplete graph of a crystal skeleton, an agent assigns an element to a specific node. We adopt a behavioral cloning strategy to train the policy network on data consisting of curated trajectories generated from known crystals.
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Published in Digital Discovery, 2024
Navigating through the exponentially large chemical space to search for desirable materials is an extremely challenging task in material discovery. Recent developments in generative and geometric deep learning have shown promising results in molecule and material discovery but often lack evaluation with high-accuracy computational methods. This work aims to design novel and stable crystalline materials conditioned on a desired band gap. To achieve conditional generation, we: 1. Formulate crystal design as a sequential decision-making problem, create relevant trajectories based on high-quality materials data, and use conservative Q-learning to learn a conditional policy from these trajectories. To do so, we formulate a reward function that incorporates constraints for energetic and electronic properties obtained directly from density functional theory (DFT) calculations; 2. Evaluate the generated materials from the policy using DFT calculations for both energy and band gap; 3. Compare our results to relevant baselines, including a random policy, behavioral cloning, and unconditioned policy learning. Our experiments show that conditioned policies achieve targeted crystal design and demonstrate the capability to perform crystal discovery evaluated with accurate and computationally expensive DFT calculations.
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Undergraduate course, University 1, Department, 2014
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Workshop, University 1, Department, 2015
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