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Chence Shi

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11 papers

2 author rows

ICLR Conference 2025 Conference Paper

Structure Language Models for Protein Conformation Generation

Jiarui Lu
Xiaoyin Chen
Stephen Zhewen Lu
Chence Shi
Hongyu Guo
Yoshua Bengio
Jian Tang 0005

Proteins adopt multiple structural conformations to perform their diverse biological functions, and understanding these conformations is crucial for advancing drug discovery. Traditional physics-based simulation methods often struggle with sampling equilibrium conformations and are computationally expensive. Recently, deep generative models have shown promise in generating protein conformations as a more efficient alternative. However, these methods predominantly rely on the diffusion process within a 3D geometric space, which typically centers around the vicinity of metastable states and is often inefficient in terms of runtime. In this paper, we introduce Structure Language Modeling (SLM) as a novel framework for efficient protein conformation generation. Specifically, the protein structures are first encoded into a compact latent space using a discrete variational auto-encoder, followed by conditional language modeling that effectively captures sequence-specific conformation distributions. This enables a more efficient and interpretable exploration of diverse ensemble modes compared to existing methods. Based on this general framework, we instantiate SLM with various popular LM architectures as well as proposing the ESMDiff, a novel BERT-like structure language model fine-tuned from ESM3 with masked diffusion. We verify our approach in various scenarios, including the equilibrium dynamics of BPTI, conformational change pairs, and intrinsically disordered proteins. SLM provides a highly efficient solution, offering a 20-100x speedup than existing methods in generating diverse conformations, shedding light on promising avenues for future research.

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ICLR Conference 2023 Conference Paper

E3Bind: An End-to-End Equivariant Network for Protein-Ligand Docking

Yangtian Zhang
Huiyu Cai
Chence Shi
Jian Tang 0005

In silico prediction of the ligand binding pose to a given protein target is a crucial but challenging task in drug discovery. This work focuses on blind flexible self-docking, where we aim to predict the positions, orientations and conformations of docked molecules. Traditional physics-based methods usually suffer from inaccurate scoring functions and high inference cost. Recently, data-driven methods based on deep learning techniques are attracting growing interest thanks to their efficiency during inference and promising performance. These methods usually either adopt a two-stage approach by first predicting the distances between proteins and ligands and then generating the final coordinates based on the predicted distances, or directly predicting the global roto-translation of ligands. In this paper, we take a different route. Inspired by the resounding success of AlphaFold2 for protein structure prediction, we propose E3Bind, an end-to-end equivariant network that iteratively updates the ligand pose. E3Bind models the protein-ligand interaction through careful consideration of the geometric constraints in docking and the local context of the binding site. Experiments on standard benchmark datasets demonstrate the superior performance of our end-to-end trainable model compared to traditional and recently-proposed deep learning methods.

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ICLR Conference 2023 Conference Paper

Protein Sequence and Structure Co-Design with Equivariant Translation

Chence Shi
Chuanrui Wang
Jiarui Lu
Bozitao Zhong
Jian Tang 0005

Proteins are macromolecules that perform essential functions in all living organisms. Designing novel proteins with specific structures and desired functions has been a long-standing challenge in the field of bioengineering. Existing approaches generate both protein sequence and structure using either autoregressive models or diffusion models, both of which suffer from high inference costs. In this paper, we propose a new approach capable of protein sequence and structure co-design, which iteratively translates both protein sequence and structure into the desired state from random initialization, based on context features given a priori. Our model consists of a trigonometry-aware encoder that reasons geometrical constraints and interactions from context features, and a roto-translation equivariant decoder that translates protein sequence and structure interdependently. Notably, all protein amino acids are updated in one shot in each translation step, which significantly accelerates the inference process. Experimental results across multiple tasks show that our model outperforms previous state-of-the-art baselines by a large margin, and is able to design proteins of high fidelity as regards both sequence and structure, with running time orders of magnitude less than sampling-based methods.

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ICLR Conference 2022 Conference Paper

GeoDiff: A Geometric Diffusion Model for Molecular Conformation Generation

Minkai Xu
Lantao Yu
Yang Song 0011
Chence Shi
Stefano Ermon
Jian Tang 0005

Predicting molecular conformations from molecular graphs is a fundamental problem in cheminformatics and drug discovery. Recently, significant progress has been achieved with machine learning approaches, especially with deep generative models. Inspired by the diffusion process in classical non-equilibrium thermodynamics where heated particles will diffuse from original states to a noise distribution, in this paper, we propose a novel generative model named GeoDiff for molecular conformation prediction. GeoDiff treats each atom as a particle and learns to directly reverse the diffusion process (i.e., transforming from a noise distribution to stable conformations) as a Markov chain. Modeling such a generation process is however very challenging as the likelihood of conformations should be roto-translational invariant. We theoretically show that Markov chains evolving with equivariant Markov kernels can induce an invariant distribution by design, and further propose building blocks for the Markov kernels to preserve the desirable equivariance property. The whole framework can be efficiently trained in an end-to-end fashion by optimizing a weighted variational lower bound to the (conditional) likelihood. Experiments on multiple benchmarks show that GeoDiff is superior or comparable to existing state-of-the-art approaches, especially on large molecules.

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ICML Conference 2021 Conference Paper

An End-to-End Framework for Molecular Conformation Generation via Bilevel Programming

Minkai Xu
Wujie Wang
Shitong Luo
Chence Shi
Yoshua Bengio
Rafael Gómez-Bombarelli
Jian Tang 0005

Predicting molecular conformations (or 3D structures) from molecular graphs is a fundamental problem in many applications. Most existing approaches are usually divided into two steps by first predicting the distances between atoms and then generating a 3D structure through optimizing a distance geometry problem. However, the distances predicted with such two-stage approaches may not be able to consistently preserve the geometry of local atomic neighborhoods, making the generated structures unsatisfying. In this paper, we propose an end-to-end solution for molecular conformation prediction called ConfVAE based on the conditional variational autoencoder framework. Specifically, the molecular graph is first encoded in a latent space, and then the 3D structures are generated by solving a principled bilevel optimization program. Extensive experiments on several benchmark data sets prove the effectiveness of our proposed approach over existing state-of-the-art approaches. Code is available at \url{https: //github. com/MinkaiXu/ConfVAE-ICML21}.

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ICML Conference 2021 Conference Paper

Learning Gradient Fields for Molecular Conformation Generation

Chence Shi
Shitong Luo
Minkai Xu
Jian Tang 0005

We study a fundamental problem in computational chemistry known as molecular conformation generation, trying to predict stable 3D structures from 2D molecular graphs. Existing machine learning approaches usually first predict distances between atoms and then generate a 3D structure satisfying the distances, where noise in predicted distances may induce extra errors during 3D coordinate generation. Inspired by the traditional force field methods for molecular dynamics simulation, in this paper, we propose a novel approach called ConfGF by directly estimating the gradient fields of the log density of atomic coordinates. The estimated gradient fields allow directly generating stable conformations via Langevin dynamics. However, the problem is very challenging as the gradient fields are roto-translation equivariant. We notice that estimating the gradient fields of atomic coordinates can be translated to estimating the gradient fields of interatomic distances, and hence develop a novel algorithm based on recent score-based generative models to effectively estimate these gradients. Experimental results across multiple tasks show that ConfGF outperforms previous state-of-the-art baselines by a significant margin.

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ICLR Conference 2021 Conference Paper

MARS: Markov Molecular Sampling for Multi-objective Drug Discovery

Yutong Xie 0007
Chence Shi
Hao Zhou 0012
Yuwei Yang
Weinan Zhang 0001
Yong Yu 0001
Lei Li 0005

Searching for novel molecules with desired chemical properties is crucial in drug discovery. Existing work focuses on developing neural models to generate either molecular sequences or chemical graphs. However, it remains a big challenge to find novel and diverse compounds satisfying several properties. In this paper, we propose MARS, a method for multi-objective drug molecule discovery. MARS is based on the idea of generating the chemical candidates by iteratively editing fragments of molecular graphs. To search for high-quality candidates, it employs Markov chain Monte Carlo sampling (MCMC) on molecules with an annealing scheme and an adaptive proposal. To further improve sample efficiency, MARS uses a graph neural network (GNN) to represent and select candidate edits, where the GNN is trained on-the-fly with samples from MCMC. Experiments show that MARS achieves state-of-the-art performance in various multi-objective settings where molecular bio-activity, drug-likeness, and synthesizability are considered. Remarkably, in the most challenging setting where all four objectives are simultaneously optimized, our approach outperforms previous methods significantly in comprehensive evaluations. The code is available at https://github.com/yutxie/mars.

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ICML Conference 2021 Conference Paper

Non-Autoregressive Electron Redistribution Modeling for Reaction Prediction

Hangrui Bi
Hengyi Wang
Chence Shi
Connor W. Coley
Jian Tang 0005
Hongyu Guo

Reliably predicting the products of chemical reactions presents a fundamental challenge in synthetic chemistry. Existing machine learning approaches typically produce a reaction product by sequentially forming its subparts or intermediate molecules. Such autoregressive methods, however, not only require a pre-defined order for the incremental construction but preclude the use of parallel decoding for efficient computation. To address these issues, we devise a non-autoregressive learning paradigm that predicts reaction in one shot. Leveraging the fact that chemical reactions can be described as a redistribution of electrons in molecules, we formulate a reaction as an arbitrary electron flow and predict it with a novel multi-pointer decoding network. Experiments on the USPTO-MIT dataset show that our approach has established a new state-of-the-art top-1 accuracy and achieves at least 27 times inference speedup over the state-of-the-art methods. Also, our predictions are easier for chemists to interpret owing to predicting the electron flows.

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NeurIPS Conference 2021 Conference Paper

Predicting Molecular Conformation via Dynamic Graph Score Matching

Shitong Luo
Chence Shi
Minkai Xu
Jian Tang

Predicting stable 3D conformations from 2D molecular graphs has been a long-standing challenge in computational chemistry. Recently, machine learning approaches have demonstrated very promising results compared to traditional experimental and physics-based simulation methods. These approaches mainly focus on modeling the local interactions between neighboring atoms on the molecular graphs and overlook the long-range interactions between non-bonded atoms. However, these non-bonded atoms may be proximal to each other in 3D space, and modeling their interactions is of crucial importance to accurately determine molecular conformations, especially for large molecules and multi-molecular complexes. In this paper, we propose a new approach called Dynamic Graph Score Matching (DGSM) for molecular conformation prediction, which models both the local and long-range interactions by dynamically constructing graph structures between atoms according to their spatial proximity during both training and inference. Specifically, the DGSM directly estimates the gradient fields of the logarithm density of atomic coordinates according to the dynamically constructed graphs using score matching methods. The whole framework can be efficiently trained in an end-to-end fashion. Experiments across multiple tasks show that the DGSM outperforms state-of-the-art baselines by a large margin, and it is capable of generating conformations for a broader range of systems such as proteins and multi-molecular complexes.

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ICML Conference 2020 Conference Paper

A Graph to Graphs Framework for Retrosynthesis Prediction

Chence Shi
Minkai Xu
Hongyu Guo
Ming Zhang 0004
Jian Tang 0005

A fundamental problem in computational chemistry is to find a set of reactants to synthesize a target molecule, a. k. a. retrosynthesis prediction. Existing state-of-the-art methods rely on matching the target molecule with a large set of reaction templates, which are very computationally expensive and also suffer from the problem of coverage. In this paper, we propose a novel template-free approach called G2Gs by transforming a target molecular graph into a set of reactant molecular graphs. G2Gs first splits the target molecular graph into a set of synthons by identifying the reaction centers, and then translates the synthons to the final reactant graphs via a variational graph translation framework. Experimental results show that G2Gs significantly outperforms existing template-free approaches by up to 63% in terms of the top-1 accuracy and achieves a performance close to that of state-of-the-art template-based approaches, but does not require domain knowledge and is much more scalable.

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ICLR Conference 2020 Conference Paper

GraphAF: a Flow-based Autoregressive Model for Molecular Graph Generation

Chence Shi
Minkai Xu
Zhaocheng Zhu
Weinan Zhang 0001
Ming Zhang 0004
Jian Tang 0005

Molecular graph generation is a fundamental problem for drug discovery and has been attracting growing attention. The problem is challenging since it requires not only generating chemically valid molecular structures but also optimizing their chemical properties in the meantime. Inspired by the recent progress in deep generative models, in this paper we propose a flow-based autoregressive model for graph generation called GraphAF. GraphAF combines the advantages of both autoregressive and flow-based approaches and enjoys: (1) high model flexibility for data density estimation; (2) efficient parallel computation for training; (3) an iterative sampling process, which allows leveraging chemical domain knowledge for valency checking. Experimental results show that GraphAF is able to generate 68\% chemically valid molecules even without chemical knowledge rules and 100\% valid molecules with chemical rules. The training process of GraphAF is two times faster than the existing state-of-the-art approach GCPN. After fine-tuning the model for goal-directed property optimization with reinforcement learning, GraphAF achieves state-of-the-art performance on both chemical property optimization and constrained property optimization.

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