arXiv subjects

Zichen Wang

Publications and source records attributed to Zichen Wang.

At least 37 records · Page 2Linked to original sources

arXiv2026

MoE3D: A Mixture-of-Experts Module for 3D Reconstruction

We propose a simple yet effective approach to enhance the performance of feed-forward 3D reconstruction models. Existing methods often struggle near depth discontinuities, where standard regression losses encourage spatial averaging and thus blur sharp boundaries. To address this issue, we introduce a mixture-of-experts formulation that handles uncertainty at depth boundaries by combining multiple smooth depth predictions. A softmax weighting head dynamically selects among these hypotheses on a per-pixel basis. By integrating our mixture model into a pre-trained state-of-the-art 3D model, we achieve a substantial reduction of boundary artifacts and gains in overall reconstruction accuracy. Notably, our approach is highly compute efficient, delivering generalizable improvements even when fine-tuned on a small subset of training data while incurring only negligible additional inference computation, suggesting a promising direction for lightweight and accurate 3D reconstruction.

cs.CV↗

arXiv2026

PKI: Prior Knowledge-Infused Neural Network for Few-Shot Class-Incremental Learning

Few-shot class-incremental learning (FSCIL) aims to continually adapt a model on a limited number of new-class examples, facing two well-known challenges: catastrophic forgetting and overfitting to new classes. Existing methods tend to freeze more parts of network components and finetune others with an extra memory during incremental sessions. These methods emphasize preserving prior knowledge to ensure proficiency in recognizing old classes, thereby mitigating catastrophic forgetting. Meanwhile, constraining fewer parameters can help in overcoming overfitting with the assistance of prior knowledge. Following previous methods, we retain more prior knowledge and propose a prior knowledge-infused neural network (PKI) to facilitate FSCIL. PKI consists of a backbone, an ensemble of projectors, a classifier, and an extra memory. In each incremental session, we build a new projector and add it to the ensemble. Subsequently, we finetune the new projector and the classifier jointly with other frozen network components, ensuring the rich prior knowledge is utilized effectively. By cascading projectors, PKI integrates prior knowledge accumulated from previous sessions and learns new knowledge flexibly, which helps to recognize old classes and efficiently learn new classes. Further, to reduce the resource consumption associated with keeping many projectors, we design two variants of the prior knowledge-infused neural network (PKIV-1 and PKIV-2) to trade off a balance between resource consumption and performance by reducing the number of projectors. Extensive experiments on three popular benchmarks demonstrate that our approach outperforms state-of-the-art methods.

cs.CV↗

arXiv2026

Computational Mapping of Reactive Stroma in Prostate Cancer Yields Interpretable, Prognostic Biomarkers

Current histopathological grading of prostate cancer relies primarily on glandular architecture, largely overlooking the tumor microenvironment. Here, we present PROTAS, a deep learning framework that quantifies reactive stroma (RS) in routine hematoxylin and eosin (H&E) slides and links stromal morphology to underlying biology. PROTAS-defined RS is characterized by nuclear enlargement, collagen disorganization, and transcriptomic enrichment of contractile pathways. PROTAS detects RS robustly in the external Prostate, Lung, Colorectal, and Ovarian (PLCO) dataset and, using domain-adversarial training, generalizes to diagnostic biopsies. In head-to-head comparisons, PROTAS outperforms pathologists for RS detection, and spatial RS features predict biochemical recurrence independently of established prognostic variables (c-index 0.80). By capturing subtle stromal phenotypes associated with tumor progression, PROTAS provides an interpretable, scalable biomarker to refine risk stratification.

q-bio.QM↗

arXiv2025

RTR-GS: 3D Gaussian Splatting for Inverse Rendering with Radiance Transfer and Reflection

3D Gaussian Splatting (3DGS) has demonstrated impressive capabilities in novel view synthesis. However, rendering reflective objects remains a significant challenge, particularly in inverse rendering and relighting. We introduce RTR-GS, a novel inverse rendering framework capable of robustly rendering objects with arbitrary reflectance properties, decomposing BRDF and lighting, and delivering credible relighting results. Given a collection of multi-view images, our method effectively recovers geometric structure through a hybrid rendering model that combines forward rendering for radiance transfer with deferred rendering for reflections. This approach successfully separates high-frequency and low-frequency appearances, mitigating floating artifacts caused by spherical harmonic overfitting when handling high-frequency details. We further refine BRDF and lighting decomposition using an additional physically-based deferred rendering branch. Experimental results show that our method enhances novel view synthesis, normal estimation, decomposition, and relighting while maintaining efficient training inference process.

cs.GR↗

arXiv2025

SUPERChem: A Multimodal Reasoning Benchmark in Chemistry

Current benchmarks for evaluating the chemical reasoning capabilities of Large Language Models (LLMs) are limited by oversimplified tasks, lack of process-level evaluation, and misalignment with expert-level chemistry skills. To address these issues, we introduce SUPERChem, a benchmark of 500 expert-curated reasoning-intensive chemistry problems, covering diverse subfields and provided in both multimodal and text-only formats. Original content and an iterative curation pipeline eliminate flawed items and mitigate data contamination. Each problem is paired with an expert-authored solution path, enabling Reasoning Path Fidelity (RPF) scoring to evaluate reasoning quality beyond final-answer accuracy. Evaluations against a human baseline of 40.3% accuracy show that even the best-performing model, GPT-5 (High), reaches only 38.5%, followed closely by Gemini 2.5 Pro (37.9%) and DeepSeek-V3.1-Think (37.3%). SUPERChem elicits multi-step, multimodal reasoning, reveals model-dependent effects of visual information, and distinguishes high-fidelity reasoners from heuristic ones. By providing a challenging benchmark and a reliable evaluation framework, SUPERChem aims to facilitate the advancement of LLMs toward expert-level chemical intelligence. The dataset of the benchmark is available at https://huggingface.co/datasets/ZehuaZhao/SUPERChem.

cs.CL↗

arXiv2025

SITA: A Framework for Structure-to-Instance Theorem Autoformalization

While large language models (LLMs) have shown progress in mathematical reasoning, they still face challenges in formalizing theorems that arise from instantiating abstract structures in concrete settings. With the goal of auto-formalizing mathematical results at the research level, we develop a framework for structure-to-instance theorem autoformalization (SITA), which systematically bridges the gap between abstract mathematical theories and their concrete applications in Lean proof assistant. Formalized abstract structures are treated as modular templates that contain definitions, assumptions, operations, and theorems. These templates serve as reusable guides for the formalization of concrete instances. Given a specific instantiation, we generate corresponding Lean definitions and instance declarations, integrate them using Lean's typeclass mechanism, and construct verified theorems by checking structural assumptions. We incorporate LLM-based generation with feedback-guided refinement to ensure both automation and formal correctness. Experiments on a dataset of optimization problems demonstrate that SITA effectively formalizes diverse instances grounded in abstract structures.

cs.AI↗

arXiv2025

Retrieval Augmented Diffusion Model for Structure-informed Antibody Design and Optimization

Antibodies are essential proteins responsible for immune responses in organisms, capable of specifically recognizing antigen molecules of pathogens. Recent advances in generative models have significantly enhanced rational antibody design. However, existing methods mainly create antibodies from scratch without template constraints, leading to model optimization challenges and unnatural sequences. To address these issues, we propose a retrieval-augmented diffusion framework, termed RADAb, for efficient antibody design. Our method leverages a set of structural homologous motifs that align with query structural constraints to guide the generative model in inversely optimizing antibodies according to desired design criteria. Specifically, we introduce a structure-informed retrieval mechanism that integrates these exemplar motifs with the input backbone through a novel dual-branch denoising module, utilizing both structural and evolutionary information. Additionally, we develop a conditional diffusion model that iteratively refines the optimization process by incorporating both global context and local evolutionary conditions. Our approach is agnostic to the choice of generative models. Empirical experiments demonstrate that our method achieves state-of-the-art performance in multiple antibody inverse folding and optimization tasks, offering a new perspective on biomolecular generative models.

cs.AI↗

arXiv2025

Toward Engineering AGI: Benchmarking the Engineering Design Capabilities of LLMs

Modern engineering, spanning electrical, mechanical, aerospace, civil, and computer disciplines, stands as a cornerstone of human civilization and the foundation of our society. However, engineering design poses a fundamentally different challenge for large language models (LLMs) compared with traditional textbook-style problem solving or factual question answering. Although existing benchmarks have driven progress in areas such as language understanding, code synthesis, and scientific problem solving, real-world engineering design demands the synthesis of domain knowledge, navigation of complex trade-offs, and management of the tedious processes that consume much of practicing engineers' time. Despite these shared challenges across engineering disciplines, no benchmark currently captures the unique demands of engineering design work. In this work, we introduce EngDesign, an Engineering Design benchmark that evaluates LLMs' abilities to perform practical design tasks across nine engineering domains. Unlike existing benchmarks that focus on factual recall or question answering, EngDesign uniquely emphasizes LLMs' ability to synthesize domain knowledge, reason under constraints, and generate functional, objective-oriented engineering designs. Each task in EngDesign represents a real-world engineering design problem, accompanied by a detailed task description specifying design goals, constraints, and performance requirements. EngDesign pioneers a simulation-based evaluation paradigm that moves beyond textbook knowledge to assess genuine engineering design capabilities and shifts evaluation from static answer checking to dynamic, simulation-driven functional verification, marking a crucial step toward realizing the vision of engineering Artificial General Intelligence (AGI).

cs.CE↗

arXiv2025

RiboFlow: Conditional De Novo RNA Co-Design via Synergistic Flow Matching

Ribonucleic acid (RNA) binds to molecules to achieve specific biological functions. While generative models are advancing biomolecule design, existing methods for designing RNA that target specific ligands face limitations in capturing RNA's conformational flexibility, ensuring structural validity, and overcoming data scarcity. To address these challenges, we introduce RiboFlow, a synergistic flow matching model to co-design RNA structures and sequences based on target molecules. By integrating RNA backbone frames, torsion angles, and sequence features in an unified architecture, RiboFlow explicitly models RNA's dynamic conformations while enforcing sequence-structure consistency to improve validity. Additionally, we curate RiboBind, a large-scale dataset of RNA-molecule interactions, to resolve the scarcity of high-quality structural data. Extensive experiments reveal that RiboFlow not only outperforms state-of-the-art RNA design methods by a large margin but also showcases controllable capabilities for achieving high binding affinity to target ligands. Our work bridges critical gaps in controllable RNA design, offering a framework for structure-aware, data-efficient generation.

q-bio.BM↗

arXiv2025

SPADE: Spatial Transcriptomics and Pathology Alignment Using a Mixture of Data Experts for an Expressive Latent Space

The rapid growth of digital pathology and advances in self-supervised deep learning have enabled the development of foundational models for various pathology tasks across diverse diseases. While multimodal approaches integrating diverse data sources have emerged, a critical gap remains in the comprehensive integration of whole-slide images (WSIs) with spatial transcriptomics (ST), which is crucial for capturing critical molecular heterogeneity beyond standard hematoxylin & eosin (H&E) staining. We introduce SPADE, a foundation model that integrates histopathology with ST data to guide image representation learning within a unified framework, in effect creating an ST-informed latent space. SPADE leverages a mixture-of-data experts technique, where experts are created via two-stage imaging feature-space clustering using contrastive learning to learn representations of co-registered WSI patches and gene expression profiles. Pre-trained on the comprehensive HEST-1k dataset, SPADE is evaluated on 20 downstream tasks, demonstrating significantly superior few-shot performance compared to baseline models, highlighting the benefits of integrating morphological and molecular information into one latent space. Code and pretrained weights are available at https://github.com/uclabair/SPADE.

cs.CV↗

arXiv2025

Design-Based Bandits Under Network Interference: Trade-Off Between Regret and Statistical Inference

In multi-armed bandits with network interference (MABNI), the action taken by one node can influence the rewards of others, creating complex interdependence. While existing research on MABNI largely concentrates on minimizing regret, it often overlooks the crucial concern that an excessive emphasis on the optimal arm can undermine the inference accuracy for sub-optimal arms. Although initial efforts have been made to address this trade-off in single-unit scenarios, these challenges have become more pronounced in the context of MABNI. In this paper, we establish, for the first time, a theoretical Pareto frontier characterizing the trade-off between regret minimization and inference accuracy in adversarial (design-based) MABNI. We further introduce an anytime-valid asymptotic confidence sequence along with a corresponding algorithm, $\texttt{EXP3-N-CS}$, specifically designed to balance the trade-off between regret minimization and inference accuracy in this setting.

cs.LG↗

arXiv2025

Embedding Domain Knowledge for Large Language Models via Reinforcement Learning from Augmented Generation

Large language models (LLMs) often exhibit limited performance on domain-specific tasks due to the natural disproportionate representation of specialized information in their training data and the static nature of these datasets. Knowledge scarcity and temporal lag create knowledge gaps for domain applications. While post-training on domain datasets can embed knowledge into models, existing approaches have some limitations. Continual Pre-Training (CPT) treats all tokens in domain documents with equal importance, failing to prioritize critical knowledge points, while supervised fine-tuning (SFT) with question-answer pairs struggles to develop the coherent knowledge structures necessary for complex reasoning tasks. To address these challenges, we propose Reinforcement Learning from Augmented Generation (RLAG). Our approach iteratively cycles between sampling generations and optimizing the model through calculated rewards, effectively embedding critical and contextually coherent domain knowledge. We select generated outputs with the highest log probabilities as the sampling result, then compute three tailored reward metrics to guide the optimization process. To comprehensively evaluate domain expertise, we assess answer accuracy and the rationality of explanations generated for correctly answered questions. Experimental results across medical, legal, astronomy, and current events datasets demonstrate that our proposed method significantly outperforms baseline approaches. Our code and data are open sourced at https://github.com/ChaojunNie/RLAG.

cs.CL↗

arXiv2025

DreamSwapV: Mask-guided Subject Swapping for Any Customized Video Editing

With the rapid progress of video generation, demand for customized video editing is surging, where subject swapping constitutes a key component yet remains under-explored. Prevailing swapping approaches either specialize in narrow domains--such as human-body animation or hand-object interaction--or rely on some indirect editing paradigm or ambiguous text prompts that compromise final fidelity. In this paper, we propose DreamSwapV, a mask-guided, subject-agnostic, end-to-end framework that swaps any subject in any video for customization with a user-specified mask and reference image. To inject fine-grained guidance, we introduce multiple conditions and a dedicated condition fusion module that integrates them efficiently. In addition, an adaptive mask strategy is designed to accommodate subjects of varying scales and attributes, further improving interactions between the swapped subject and its surrounding context. Through our elaborate two-phase dataset construction and training scheme, our DreamSwapV outperforms existing methods, as validated by comprehensive experiments on VBench indicators and our first introduced DreamSwapV-Benchmark.

cs.CV↗

arXiv2025

A particle view of many-body electronic structure with neural network wavefunction

In the study of electronic structure, the wavefunction view dominates the current research landscape and forms the theoretical foundation of modern quantum mechanics. In contrast, Valence Bond (VB) theory represents chemical bonds as shared electron-pairs and can provide an intuitive, particle-based insight into chemical bonding. In this work, using a newly developed Periodic Dynamic Voronoi Metropolis Sampling (PDVMS) method, we project classical many-body electronic configurations from the neural network wavefunction, and apply VB theory to construct a complementary particle-view paradigm. The powerful neural network wavefunction can achieve near-exact ab initio solutions for the ground state of both molecular and solid systems. It allows us to definitively characterize the ground state of benzene by reassessing the competition between its two VB structures. Extending PDVMS to solids for the first time, we also predict a spin-staggered VB structure in graphene, which explains emergent magnetic properties in graphene-based nanostructures. Furthermore, this particle view provides insight into the optimization process of the neural network wavefunction itself. Our work thus introduces a novel framework for analyzing many-body electronic structure in molecules and solids, opening new avenues for investigating this complex problem and its associated exotic phenomena.

physics.chem-ph↗

arXiv2025

Zero-shot Medical Event Prediction Using a Generative Pre-trained Transformer on Electronic Health Records

Longitudinal data in electronic health records (EHRs) represent an individual`s clinical history through a sequence of codified concepts, including diagnoses, procedures, medications, and laboratory tests. Generative pre-trained transformers (GPT) can leverage this data to predict future events. While fine-tuning of these models can enhance task-specific performance, it becomes costly when applied to many clinical prediction tasks. In contrast, a pretrained foundation model can be used in zero-shot forecasting setting, offering a scalable alternative to fine-tuning separate models for each outcome. This study presents the first comprehensive analysis of zero-shot forecasting with GPT-based foundational models in EHRs, introducing a novel pipeline that formulates medical concept prediction as a generative modeling task. Unlike supervised approaches requiring extensive labeled data, our method enables the model to forecast a next medical event purely from a pretraining knowledge. We evaluate performance across multiple time horizons and clinical categories, demonstrating model`s ability to capture latent temporal dependencies and complex patient trajectories without task supervision. Model performance for predicting the next medical concept was evaluated using precision and recall metrics, achieving an average top1 precision of 0.614 and recall of 0.524. For 12 major diagnostic conditions, the model demonstrated strong zero-shot performance, achieving high true positive rates while maintaining low false positives. We demonstrate the power of a foundational EHR GPT model in capturing diverse phenotypes and enabling robust, zero-shot forecasting of clinical outcomes. This capability enhances the versatility of predictive healthcare models and reduces the need for task-specific training, enabling more scalable applications in clinical settings.

cs.LG↗

arXiv2025

Protein Structure Tokenization: Benchmarking and New Recipe

Recent years have witnessed a surge in the development of protein structural tokenization methods, which chunk protein 3D structures into discrete or continuous representations. Structure tokenization enables the direct application of powerful techniques like language modeling for protein structures, and large multimodal models to integrate structures with protein sequences and functional texts. Despite the progress, the capabilities and limitations of these methods remain poorly understood due to the lack of a unified evaluation framework. We first introduce StructTokenBench, a framework that comprehensively evaluates the quality and efficiency of structure tokenizers, focusing on fine-grained local substructures rather than global structures, as typical in existing benchmarks. Our evaluations reveal that no single model dominates all benchmarking perspectives. Observations of codebook under-utilization led us to develop AminoAseed, a simple yet effective strategy that enhances codebook gradient updates and optimally balances codebook size and dimension for improved tokenizer utilization and quality. Compared to the leading model ESM3, our method achieves an average of 6.31% performance improvement across 24 supervised tasks, with sensitivity and utilization rates increased by 12.83% and 124.03%, respectively. Source code and model weights are available at https://github.com/KatarinaYuan/StructTokenBench

q-bio.QM↗

arXiv2025

VideoPDE: Unified Generative PDE Solving via Video Inpainting Diffusion Models

We present a unified framework for solving partial differential equations (PDEs) using video-inpainting diffusion transformer models. Unlike existing methods that devise specialized strategies for either forward or inverse problems under full or partial observation, our approach unifies these tasks under a single, flexible generative framework. Specifically, we recast PDE-solving as a generalized inpainting problem, e.g., treating forward prediction as inferring missing spatiotemporal information of future states from initial conditions. To this end, we design a transformer-based architecture that conditions on arbitrary patterns of known data to infer missing values across time and space. Our method proposes pixel-space video diffusion models for fine-grained, high-fidelity inpainting and conditioning, while enhancing computational efficiency through hierarchical modeling. Extensive experiments show that our video inpainting-based diffusion model offers an accurate and versatile solution across a wide range of PDEs and problem setups, outperforming state-of-the-art baselines.

cs.LG↗

arXiv2025

Toward Rich Video Human-Motion2D Generation

Generating realistic and controllable human motions, particularly those involving rich multi-character interactions, remains a significant challenge due to data scarcity and the complexities of modeling inter-personal dynamics. To address these limitations, we first introduce a new large-scale rich video human motion 2D dataset (Motion2D-Video-150K) comprising 150,000 video sequences. Motion2D-Video-150K features a balanced distribution of diverse single-character and, crucially, double-character interactive actions, each paired with detailed textual descriptions. Building upon this dataset, we propose a novel diffusion-based rich video human motion2D generation (RVHM2D) model. RVHM2D incorporates an enhanced textual conditioning mechanism utilizing either dual text encoders (CLIP-L/B) or T5-XXL with both global and local features. We devise a two-stage training strategy: the model is first trained with a standard diffusion objective, and then fine-tuned using reinforcement learning with an FID-based reward to further enhance motion realism and text alignment. Extensive experiments demonstrate that RVHM2D achieves leading performance on the Motion2D-Video-150K benchmark in generating both single and interactive double-character scenarios.

cs.CV↗