Author name cluster

Michael Sun

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6 papers

2 author rows

ICML Conference 2025 Conference Paper

Directed Graph Grammars for Sequence-based Learning

Michael Sun
Orion Foo
Gang Liu
Wojciech Matusik
Jie Chen 0007

Directed acyclic graphs (DAGs) are a class of graphs commonly used in practice, with examples that include electronic circuits, Bayesian networks, and neural architectures. While many effective encoders exist for DAGs, it remains challenging to decode them in a principled manner, because the nodes of a DAG can have many different topological orders. In this work, we propose a grammar-based approach to constructing a principled, compact and equivalent sequential representation of a DAG. Specifically, we view a graph as derivations over an unambiguous grammar, where the DAG corresponds to a unique sequence of production rules. Equivalently, the procedure to construct such a description can be viewed as a lossless compression of the data. Such a representation has many uses, including building a generative model for graph generation, learning a latent space for property prediction, and leveraging the sequence representational continuity for Bayesian Optimization over structured data.

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ICML Conference 2025 Conference Paper

Foundation Molecular Grammar: Multi-Modal Foundation Models Induce Interpretable Molecular Graph Languages

Michael Sun
Weize Yuan
Gang Liu
Wojciech Matusik
Jie Chen 0007

Recent data-efficient molecular generation approaches exploit graph grammars to introduce interpretability into the generative models. However, grammar learning therein relies on expert annotation or unreliable heuristics for algorithmic inference. We propose Foundation Molecular Grammar (FMG), which leverages multi-modal foundation models (MMFMs) to induce an interpretable molecular language. By exploiting the chemical knowledge of an MMFM, FMG renders molecules as images, describes them as text, and aligns information across modalities using prompt learning. FMG can be used as a drop-in replacement for the prior grammar learning approaches in molecular generation and property prediction. We show that FMG not only excels in synthesizability, diversity, and data efficiency but also offers built-in chemical interpretability for automated molecular discovery workflows. Code is available at https: //github. com/shiningsunnyday/induction.

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ICLR Conference 2025 Conference Paper

Multimodal Large Language Models for Inverse Molecular Design with Retrosynthetic Planning

Gang Liu
Michael Sun
Wojciech Matusik
Meng Jiang
Jie Chen 0007

While large language models (LLMs) have integrated images, adapting them to graphs remains challenging, limiting their applications in materials and drug design. This difficulty stems from the need for coherent autoregressive generation across texts and graphs. To address this, we introduce Llamole, the first multimodal LLM capable of interleaved text and graph generation, enabling molecular inverse design with retrosynthetic planning. Llamole integrates a base LLM with the Graph Diffusion Transformer and Graph Neural Networks for multi-conditional molecular generation and reaction inference within texts, while the LLM, with enhanced molecular understanding, flexibly controls activation among the different graph modules. Additionally, Llamole integrates A* search with LLM-based cost functions for efficient retrosynthetic planning. We create benchmarking datasets and conduct extensive experiments to evaluate Llamole against in-context learning and supervised fine-tuning. Llamole significantly outperforms 14 adapted LLMs across 12 metrics for controllable molecular design and retrosynthetic planning. Code and model at https://github.com/liugangcode/Llamole.

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NeurIPS Conference 2025 Conference Paper

Post Hoc Regression Refinement via Pairwise Rankings

Kevin Tirta Wijaya
Michael Sun
Minghao Guo
Hans-peter Seidel
Wojciech Matusik
Vahid Babaei

Accurate prediction of continuous properties is essential to many scientific and engineering tasks. Although deep-learning regressors excel with abundant labels, their accuracy deteriorates in data-scarce regimes. We introduce RankRefine, a model-agnostic, plug-and-play post-hoc refinement technique that injects expert knowledge through pairwise rankings. Given a query item and a small reference set with known properties, RankRefine combines the base regressor’s output with a rank-based estimate via inverse-variance weighting, requiring no retraining. In molecular property prediction task, RankRefine achieves up to 10\% relative reduction in mean absolute error using only 20 pairwise comparisons obtained through a general-purpose large language model (LLM) with no finetuning. As rankings provided by human experts or general-purpose LLMs are sufficient for improving regression across diverse domains, RankRefine offers practicality and broad applicability, especially in low-data settings.

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ICLR Conference 2025 Conference Paper

Procedural Synthesis of Synthesizable Molecules

Michael Sun
Alston Lo
Minghao Guo
Jie Chen 0007
Connor W. Coley
Wojciech Matusik

Designing synthetically accessible molecules and recommending analogs to unsynthesizable molecules are important problems for accelerating molecular discovery. We reconceptualize both problems using ideas from program synthesis. Drawing inspiration from syntax-guided synthesis approaches, we decouple the syntactic skeleton from the semantics of a synthetic tree to create a bilevel framework for reasoning about the combinatorial space of synthesis pathways. Given a molecule we aim to generate analogs for, we iteratively refine its skeletal characteristics via Markov Chain Monte Carlo simulations over the space of syntactic skeletons. Given a black-box oracle to optimize, we formulate a joint design space over syntactic templates and molecular descriptors and introduce evolutionary algorithms that optimize both syntactic and semantic dimensions synergistically. Our key insight is that once the syntactic skeleton is set, we can amortize over the search complexity of deriving the program's semantics by training policies to fully utilize the fixed horizon Markov Decision Process imposed by the syntactic template. We demonstrate performance advantages of our bilevel framework for synthesizable analog generation and synthesizable molecule design. Notably, our approach offers the user explicit control over the resources required to perform synthesis and biases the design space towards simpler solutions, making it particularly promising for autonomous synthesis platforms. Supporting code is at https://github.com/shiningsunnyday/SynthesisNet.

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ICML Conference 2024 Conference Paper

Representing Molecules as Random Walks Over Interpretable Grammars

Michael Sun
Minghao Guo
Weize Yuan
Veronika Thost
Crystal Elaine Owens
Aristotle Franklin Grosz
Sharvaa Selvan
Katelyn Zhou

Recent research in molecular discovery has primarily been devoted to small, drug-like molecules, leaving many similarly important applications in material design without adequate technology. These applications often rely on more complex molecular structures with fewer examples that are carefully designed using known substructures. We propose a data-efficient and interpretable model for representing and reasoning over such molecules in terms of graph grammars that explicitly describe the hierarchical design space featuring motifs to be the design basis. We present a novel representation in the form of random walks over the design space, which facilitates both molecule generation and property prediction. We demonstrate clear advantages over existing methods in terms of performance, efficiency, and synthesizability of predicted molecules, and we provide detailed insights into the method’s chemical interpretability.

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