arXiv subjects

Shuan Chen

Publications and source records attributed to Shuan Chen.

8 recordsLinked to original sources

arXiv2026

Compiling Chemical Knowledge into Executable Descriptors for Materials Prediction

Materials prediction depends critically on how scientific knowledge is represented, yet many governing considerations exist only as natural-language heuristics that conventional learners cannot use. We introduce CRISP, a large language model-assisted framework that treats representation construction as a rule-space exploration and compilation problem: it repeatedly samples target-relevant chemical rules without access to structures, labels or data splits, consolidates related concepts, and compiles each into an executable scalar descriptor supplied to a conventional learner. For positive-unlabeled inorganic-crystal synthesizability, CRISP outperformed expert-curated and generic structural representations under a shared learner and surpassed purpose-built synthesizability models, with its advantage most pronounced under structural-size and chemical-family shifts. Infrequently generated rules contributed complementary predictive information, showing that generation frequency does not determine utility. The same workflow yielded competitive representations for formation energy and ionic conductivity while revealing task-dependent limits for shear modulus, establishing a dataset-blind, auditable route from broad chemical knowledge to transferable computational representations.

cond-mat.mtrl-sci↗

arXiv2026

MolBioKG: Grounding Out-of-Graph Molecules in Biomedical Knowledge Graphs via Multi-Resolution Structural Anchoring

Biomedical knowledge graphs (KGs) accelerate drug discovery, but standard pipelines assume query molecules already exist as graph entities, leaving unregistered molecules disconnected. We address this cold-start challenge, termed the out-of-graph molecule problem, by introducing MolBioKG. This two-layer system grounds unseen molecules in biomedical evidence via multi-resolution structural anchoring. It connects an index of 2.74 million molecules (represented by scaffolds, fragments, functional groups, and fingerprints) to a 9.6-million-edge KG. Given only a SMILES string, MolBioKG retrieves structurally related graph entities and traverses their biomedical neighborhoods without task-specific training. It features two inference mechanisms: static multi-anchor retrieval using Reciprocal Rank Fusion, and Adapt-KG, a tool-using LLM policy for adaptive traversal. Evaluated across in-graph link recovery, complex multi-hop reasoning, and out-of-graph generalization, MolBioKG outperforms strong baselines. Notably, it raises Hits@10 from 0.585 to 0.876 in multi-hop reasoning and out-of-graph target recall from 0.145 to 0.269, all while ensuring predictions retain traceable structural anchors and source-attributed KG evidence.

cs.AI↗

arXiv2025

SynTwins: A Retrosynthesis-Guided Framework for Synthesizable Molecular Analog Generation

The disconnect between AI-generated molecules with desirable properties and their synthetic feasibility remains a critical bottleneck in computational discovery of drugs and materials. While generative AI has accelerated the proposal of candidate molecules, many of these structures prove challenging or impossible to synthesize using established chemical reactions. Here, we introduce SynTwins, a novel retrosynthesis-guided molecule design framework that finds synthetically accessible molecular analogs by emulating expert chemists' strategies in three steps: retrosynthesis, searching similar building blocks, and virtual synthesis. Using a search algorithm instead of a stochastic data-driven generator, SynTwins outperforms state-of-the-art machine learning models at exploring synthetically accessible analogs while maintaining high structural similarity to original target molecules. Furthermore, when integrated into existing molecular property-optimization frameworks, our hybrid approach produces synthetically feasible analogs with minimal loss in property scores. Our comprehensive benchmarking across diverse molecular datasets demonstrates that SynTwins effectively bridges the gap between computational design and experimental synthesis, providing a practical solution for accelerating the discovery of synthesizable molecules with desired properties for a wide range of applications.

physics.chem-ph↗

arXiv2025

Predicting Chemical Reaction Outcomes Based on Electron Movements Using Machine Learning

Accurately predicting chemical reaction outcomes and potential byproducts is a fundamental task of modern chemistry, enabling the efficient design of synthetic pathways and driving progress in chemical science. Reaction mechanism, which tracks electron movements during chemical reactions, is critical for understanding reaction kinetics and identifying unexpected products. Here, we present Reactron, the first electron-based machine learning model for general reaction prediction. Reactron integrates electron movement into its predictions, generating detailed arrow-pushing diagrams that elucidate each mechanistic step leading to product formation. We demonstrate the high predictive performance of Reactron over existing product-only models by a large-scale reaction outcome prediction benchmark, and the adaptability of the model to learn new reactivity upon providing a few examples. Furthermore, it explores combinatorial reaction spaces, uncovering novel reactivities beyond its training data. With robust performance in both in- and out-of-distribution predictions, Reactron embodies human-like reasoning in chemistry and opens new frontiers in reaction discovery and synthesis design.

physics.chem-ph↗

arXiv2024

MIPI 2024 Challenge on Nighttime Flare Removal: Methods and Results

The increasing demand for computational photography and imaging on mobile platforms has led to the widespread development and integration of advanced image sensors with novel algorithms in camera systems. However, the scarcity of high-quality data for research and the rare opportunity for in-depth exchange of views from industry and academia constrain the development of mobile intelligent photography and imaging (MIPI). Building on the achievements of the previous MIPI Workshops held at ECCV 2022 and CVPR 2023, we introduce our third MIPI challenge including three tracks focusing on novel image sensors and imaging algorithms. In this paper, we summarize and review the Nighttime Flare Removal track on MIPI 2024. In total, 170 participants were successfully registered, and 14 teams submitted results in the final testing phase. The developed solutions in this challenge achieved state-of-the-art performance on Nighttime Flare Removal. More details of this challenge and the link to the dataset can be found at https://mipi-challenge.org/MIPI2024/.

cs.CV↗

arXiv2024

Assessing the Extrapolation Capability of Template-Free Retrosynthesis Models

Despite the acknowledged capability of template-free models in exploring unseen reaction spaces compared to template-based models for retrosynthesis prediction, their ability to venture beyond established boundaries remains relatively uncharted. In this study, we empirically assess the extrapolation capability of state-of-the-art template-free models by meticulously assembling an extensive set of out-of-distribution (OOD) reactions. Our findings demonstrate that while template-free models exhibit potential in predicting precursors with novel synthesis rules, their top-10 exact-match accuracy in OOD reactions is strikingly modest (< 1%). Furthermore, despite the capability of generating novel reactions, our investigation highlights a recurring issue where more than half of the novel reactions predicted by template-free models are chemically implausible. Consequently, we advocate for the future development of template-free models that integrate considerations of chemical feasibility when navigating unexplored regions of reaction space.

physics.chem-ph↗

arXiv2020

Explaining How Deep Neural Networks Forget by Deep Visualization

Explaining the behaviors of deep neural networks, usually considered as black boxes, is critical especially when they are now being adopted over diverse aspects of human life. Taking the advantages of interpretable machine learning (interpretable ML), this paper proposes a novel tool called Catastrophic Forgetting Dissector (or CFD) to explain catastrophic forgetting in continual learning settings. We also introduce a new method called Critical Freezing based on the observations of our tool. Experiments on ResNet articulate how catastrophic forgetting happens, particularly showing which components of this famous network are forgetting. Our new continual learning algorithm defeats various recent techniques by a significant margin, proving the capability of the investigation. Critical freezing not only attacks catastrophic forgetting but also exposes explainability.

cs.LG↗

arXiv2020

Dissecting Catastrophic Forgetting in Continual Learning by Deep Visualization

Interpreting the behaviors of Deep Neural Networks (usually considered as a black box) is critical especially when they are now being widely adopted over diverse aspects of human life. Taking the advancements from Explainable Artificial Intelligent, this paper proposes a novel technique called Auto DeepVis to dissect catastrophic forgetting in continual learning. A new method to deal with catastrophic forgetting named critical freezing is also introduced upon investigating the dilemma by Auto DeepVis. Experiments on a captioning model meticulously present how catastrophic forgetting happens, particularly showing which components are forgetting or changing. The effectiveness of our technique is then assessed; and more precisely, critical freezing claims the best performance on both previous and coming tasks over baselines, proving the capability of the investigation. Our techniques could not only be supplementary to existing solutions for completely eradicating catastrophic forgetting for life-long learning but also explainable.

cs.LG↗