arXiv subjects

Shuzhou Sun

Publications and source records attributed to Shuzhou Sun.

12 recordsLinked to original sources

arXiv2025

Chem-R: Learning to Reason as a Chemist

Although large language models (LLMs) have significant potential to advance chemical discovery, current LLMs lack core chemical knowledge, produce unreliable reasoning trajectories, and exhibit suboptimal performance across diverse chemical tasks. To address these challenges, we propose Chem-R, a generalizable Chemical Reasoning model designed to emulate the deliberative processes of chemists. Chem-R is trained through a three-phase framework that progressively builds advanced reasoning capabilities, including: 1) Chemical Foundation Training, which establishes core chemical knowledge. 2) Chemical Reasoning Protocol Distillation, incorporating structured, expert-like reasoning traces to guide systematic and reliable problem solving. 3) Multi-task Group Relative Policy Optimization that optimizes the model for balanced performance across diverse molecular- and reaction-level tasks. This structured pipeline enables Chem-R to achieve state-of-the-art performance on comprehensive benchmarks, surpassing leading large language models, including Gemini-2.5-Pro and DeepSeek-R1, by up to 32% on molecular tasks and 48% on reaction tasks. Meanwhile, Chem-R also consistently outperforms the existing chemical foundation models across both molecular and reaction level tasks. These results highlight Chem-R's robust generalization, interpretability, and potential as a foundation for next-generation AI-driven chemical discovery. The code and model are available at https://github.com/davidweidawang/Chem-R.

cs.CE↗

arXiv2025

SpecMol: A Spectroscopy-Grounded Foundation Model for Multi-Task Molecular Learning

Large language models have emerged as transformative tools in molecular science, demonstrating remarkable potential in molecular property prediction and de novo molecular design. However, their application to spectroscopy remains notably limited, despite its foundational role in experimental molecular characterization and structural validation. Progress in spectroscopy-grounded reasoning has been hindered by the lack of standardized spectral representations and comprehensive evaluation protocols, making cross-study comparisons difficult. To bridge this gap, we present a unified framework for spectroscopy-grounded molecular modeling and evaluation. At its core, the SpecMol foundation model integrates spectral interpretation, molecular representation learning, and three-dimensional structure generation within a single interface. Complementing this, we establish SpecMol-Bench as a systematic evaluation protocol encompassing cross-modal tasks: spectra-to-structure elucidation, structure-to-spectra simulation, and SMILES-to-3D conformation generation. Under this unified framework, SpecMol achieves accurate spectra-driven structure elucidation and reproduces experimental nuclear magnetic resonance characteristics with high fidelity. The model also generates chemically valid three-dimensional conformations directly from SMILES strings and consistently outperforms existing general-purpose molecular language models across standardized evaluation metrics. Code is available at https://github.com/Eurekashen/SpecMol

cs.LG↗

arXiv2025

ChemBOMAS: Accelerated BO in Chemistry with LLM-Enhanced Multi-Agent System

Bayesian optimization (BO) is a powerful tool for scientific discovery in chemistry, yet its efficiency is often hampered by the sparse experimental data and vast search space. Here, we introduce ChemBOMAS: a large language model (LLM)-enhanced multi-agent system that accelerates BO through synergistic data- and knowledge-driven strategies. Firstly, the data-driven strategy involves an 8B-scale LLM regressor fine-tuned on a mere 1% labeled samples for pseudo-data generation, robustly initializing the optimization process. Secondly, the knowledge-driven strategy employs a hybrid Retrieval-Augmented Generation approach to guide LLM in dividing the search space while mitigating LLM hallucinations. An Upper Confidence Bound algorithm then identifies high-potential subspaces within this established partition. Across the LLM-refined subspaces and supported by LLM-generated data, BO achieves the improvement of effectiveness and efficiency. Comprehensive evaluations across multiple scientific benchmarks demonstrate that ChemBOMAS set a new state-of-the-art, accelerating optimization efficiency by up to 5-fold compared to baseline methods.

cs.LG↗

arXiv2025

Object-level Correlation for Few-Shot Segmentation

Few-shot semantic segmentation (FSS) aims to segment objects of novel categories in the query images given only a few annotated support samples. Existing methods primarily build the image-level correlation between the support target object and the entire query image. However, this correlation contains the hard pixel noise, \textit{i.e.}, irrelevant background objects, that is intractable to trace and suppress, leading to the overfitting of the background. To address the limitation of this correlation, we imitate the biological vision process to identify novel objects in the object-level information. Target identification in the general objects is more valid than in the entire image, especially in the low-data regime. Inspired by this, we design an Object-level Correlation Network (OCNet) by establishing the object-level correlation between the support target object and query general objects, which is mainly composed of the General Object Mining Module (GOMM) and Correlation Construction Module (CCM). Specifically, GOMM constructs the query general object feature by learning saliency and high-level similarity cues, where the general objects include the irrelevant background objects and the target foreground object. Then, CCM establishes the object-level correlation by allocating the target prototypes to match the general object feature. The generated object-level correlation can mine the query target feature and suppress the hard pixel noise for the final prediction. Extensive experiments on PASCAL-${5}^{i}$ and COCO-${20}^{i}$ show that our model achieves the state-of-the-art performance.

cs.CV↗

arXiv2025

Chem3DLLM: 3D Multimodal Large Language Models for Chemistry

In the real world, a molecule is a 3D geometric structure. Compared to 1D SMILES sequences and 2D molecular graphs, 3D molecules represent the most informative molecular modality. Despite the rapid progress of autoregressive-based language models, they cannot handle the generation of 3D molecular conformation due to several challenges: 1) 3D molecular structures are incompatible with LLMs' discrete token space, 2) integrating heterogeneous inputs like proteins, ligands, and text remains difficult within a unified model, and 3) LLMs lack essential scientific priors, hindering the enforcement of physical and chemical constraints during generation. To tackle these issues, we present Chem3DLLM, a unified protein-conditioned multimodal large language model. Our approach designs a novel reversible text encoding for 3D molecular structures using run-length compression, achieving 3x size reduction while preserving complete structural information. This enables seamless integration of molecular geometry with protein pocket features in a single LLM architecture. We employ reinforcement learning with stability-based rewards to optimize chemical validity and incorporate a lightweight protein embedding projector for end-to-end training. Experimental results on structure-based drug design demonstrate state-of-the-art performance with a Vina score of -7.21, validating our unified multimodal approach for practical drug discovery applications.

cs.CE↗

arXiv2025

SpectrumWorld: Artificial Intelligence Foundation for Spectroscopy

Deep learning holds immense promise for spectroscopy, yet research and evaluation in this emerging field often lack standardized formulations. To address this issue, we introduce SpectrumLab, a pioneering unified platform designed to systematize and accelerate deep learning research in spectroscopy. SpectrumLab integrates three core components: a comprehensive Python library featuring essential data processing and evaluation tools, along with leaderboards; an innovative SpectrumAnnotator module that generates high-quality benchmarks from limited seed data; and SpectrumBench, a multi-layered benchmark suite covering 14 spectroscopic tasks and over 10 spectrum types, featuring spectra curated from over 1.2 million distinct chemical substances. Thorough empirical studies on SpectrumBench with 18 cutting-edge multimodal LLMs reveal critical limitations of current approaches. We hope SpectrumLab will serve as a crucial foundation for future advancements in deep learning-driven spectroscopy.

cs.LG↗

arXiv2025

A Reverse Causal Framework to Mitigate Spurious Correlations for Debiasing Scene Graph Generation

Existing two-stage Scene Graph Generation (SGG) frameworks typically incorporate a detector to extract relationship features and a classifier to categorize these relationships; therefore, the training paradigm follows a causal chain structure, where the detector's inputs determine the classifier's inputs, which in turn influence the final predictions. However, such a causal chain structure can yield spurious correlations between the detector's inputs and the final predictions, i.e., the prediction of a certain relationship may be influenced by other relationships. This influence can induce at least two observable biases: tail relationships are predicted as head ones, and foreground relationships are predicted as background ones; notably, the latter bias is seldom discussed in the literature. To address this issue, we propose reconstructing the causal chain structure into a reverse causal structure, wherein the classifier's inputs are treated as the confounder, and both the detector's inputs and the final predictions are viewed as causal variables. Specifically, we term the reconstructed causal paradigm as the Reverse causal Framework for SGG (RcSGG). RcSGG initially employs the proposed Active Reverse Estimation (ARE) to intervene on the confounder to estimate the reverse causality, \ie the causality from final predictions to the classifier's inputs. Then, the Maximum Information Sampling (MIS) is suggested to enhance the reverse causality estimation further by considering the relationship information. Theoretically, RcSGG can mitigate the spurious correlations inherent in the SGG framework, subsequently eliminating the induced biases. Comprehensive experiments on popular benchmarks and diverse SGG frameworks show the state-of-the-art mean recall rate.

cs.CV↗

arXiv2025

A Causal Adjustment Module for Debiasing Scene Graph Generation

While recent debiasing methods for Scene Graph Generation (SGG) have shown impressive performance, these efforts often attribute model bias solely to the long-tail distribution of relationships, overlooking the more profound causes stemming from skewed object and object pair distributions. In this paper, we employ causal inference techniques to model the causality among these observed skewed distributions. Our insight lies in the ability of causal inference to capture the unobservable causal effects between complex distributions, which is crucial for tracing the roots of model bias. Specifically, we introduce the Mediator-based Causal Chain Model (MCCM), which, in addition to modeling causality among objects, object pairs, and relationships, incorporates mediator variables, i.e., cooccurrence distribution, for complementing the causality. Following this, we propose the Causal Adjustment Module (CAModule) to estimate the modeled causal structure, using variables from MCCM as inputs to produce a set of adjustment factors aimed at correcting biased model predictions. Moreover, our method enables the composition of zero-shot relationships, thereby enhancing the model's ability to recognize such relationships. Experiments conducted across various SGG backbones and popular benchmarks demonstrate that CAModule achieves state-of-the-art mean recall rates, with significant improvements also observed on the challenging zero-shot recall rate metric.

cs.CV↗

arXiv2025

Uncovering Bias in Foundation Models: Impact, Testing, Harm, and Mitigation

Bias in Foundation Models (FMs) - trained on vast datasets spanning societal and historical knowledge - poses significant challenges for fairness and equity across fields such as healthcare, education, and finance. These biases, rooted in the overrepresentation of stereotypes and societal inequalities in training data, exacerbate real-world discrimination, reinforce harmful stereotypes, and erode trust in AI systems. To address this, we introduce Trident Probe Testing (TriProTesting), a systematic testing method that detects explicit and implicit biases using semantically designed probes. Here we show that FMs, including CLIP, ALIGN, BridgeTower, and OWLv2, demonstrate pervasive biases across single and mixed social attributes (gender, race, age, and occupation). Notably, we uncover mixed biases when social attributes are combined, such as gender x race, gender x age, and gender x occupation, revealing deeper layers of discrimination. We further propose Adaptive Logit Adjustment (AdaLogAdjustment), a post-processing technique that dynamically redistributes probability power to mitigate these biases effectively, achieving significant improvements in fairness without retraining models. These findings highlight the urgent need for ethical AI practices and interdisciplinary solutions to address biases not only at the model level but also in societal structures. Our work provides a scalable and interpretable solution that advances fairness in AI systems while offering practical insights for future research on fair AI technologies.

cs.LG↗

arXiv2024

Step-wise Distribution Alignment Guided Style Prompt Tuning for Source-free Cross-domain Few-shot Learning

Existing cross-domain few-shot learning (CDFSL) methods, which develop source-domain training strategies to enhance model transferability, face challenges with large-scale pre-trained models (LMs) due to inaccessible source data and training strategies. Moreover, fine-tuning LMs for CDFSL demands substantial computational resources, limiting practicality. This paper addresses the source-free CDFSL (SF-CDFSL) problem, tackling few-shot learning (FSL) in the target domain using only pre-trained models and a few target samples without source data or strategies. To overcome the challenge of inaccessible source data, this paper introduces Step-wise Distribution Alignment Guided Style Prompt Tuning (StepSPT), which implicitly narrows domain gaps through prediction distribution optimization. StepSPT proposes a style prompt to align target samples with the desired distribution and adopts a dual-phase optimization process. In the external process, a step-wise distribution alignment strategy factorizes prediction distribution optimization into a multi-step alignment problem to tune the style prompt. In the internal process, the classifier is updated using standard cross-entropy loss. Evaluations on five datasets demonstrate that StepSPT outperforms existing prompt tuning-based methods and SOTAs. Ablation studies further verify its effectiveness. Code will be made publicly available at https://github.com/xuhuali-mxj/StepSPT.

cs.CV↗

arXiv2023

Unbiased Scene Graph Generation via Two-stage Causal Modeling

Despite the impressive performance of recent unbiased Scene Graph Generation (SGG) methods, the current debiasing literature mainly focuses on the long-tailed distribution problem, whereas it overlooks another source of bias, i.e., semantic confusion, which makes the SGG model prone to yield false predictions for similar relationships. In this paper, we explore a debiasing procedure for the SGG task leveraging causal inference. Our central insight is that the Sparse Mechanism Shift (SMS) in causality allows independent intervention on multiple biases, thereby potentially preserving head category performance while pursuing the prediction of high-informative tail relationships. However, the noisy datasets lead to unobserved confounders for the SGG task, and thus the constructed causal models are always causal-insufficient to benefit from SMS. To remedy this, we propose Two-stage Causal Modeling (TsCM) for the SGG task, which takes the long-tailed distribution and semantic confusion as confounders to the Structural Causal Model (SCM) and then decouples the causal intervention into two stages. The first stage is causal representation learning, where we use a novel Population Loss (P-Loss) to intervene in the semantic confusion confounder. The second stage introduces the Adaptive Logit Adjustment (AL-Adjustment) to eliminate the long-tailed distribution confounder to complete causal calibration learning. These two stages are model agnostic and thus can be used in any SGG model that seeks unbiased predictions. Comprehensive experiments conducted on the popular SGG backbones and benchmarks show that our TsCM can achieve state-of-the-art performance in terms of mean recall rate. Furthermore, TsCM can maintain a higher recall rate than other debiasing methods, which indicates that our method can achieve a better tradeoff between head and tail relationships.

cs.CV↗

arXiv2023

Deep Learning for Cross-Domain Few-Shot Visual Recognition: A Survey

While deep learning excels in computer vision tasks with abundant labeled data, its performance diminishes significantly in scenarios with limited labeled samples. To address this, Few-shot learning (FSL) enables models to perform the target tasks with very few labeled examples by leveraging prior knowledge from related tasks. However, traditional FSL assumes that both the related and target tasks come from the same domain, which is a restrictive assumption in many real-world scenarios where domain differences are common. To overcome this limitation, Cross-domain few-shot learning (CDFSL) has gained attention, as it allows source and target data to come from different domains and label spaces. This paper presents the first comprehensive review of Cross-domain Few-shot Learning (CDFSL), a field that has received less attention compared to traditional FSL due to its unique challenges. We aim to provide both a position paper and a tutorial for researchers, covering key problems, existing methods, and future research directions. The review begins with a formal definition of CDFSL, outlining its core challenges, followed by a systematic analysis of current approaches, organized under a clear taxonomy. Finally, we discuss promising future directions in terms of problem setups, applications, and theoretical advancements.

cs.CV↗