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Yiheng Zhu

Publications and source records attributed to Yiheng Zhu.

At least 19 recordsLinked to original sources
arXiv2026

MultiCube: Compositional 3D Generation With Part-Level Semantic and Spatial Control

Digital 3D objects used in games and animation are often required to be compositional; that is, decomposed into semantically meaningful parts. Recent 3D generation methods can produce high-quality compositional objects conditioned on image or text prompts. Yet, such global conditioning lacks the precise part-level controllability required for professional creative workflows. To address this, we introduce MultiCube, a novel compositional 3D generation method that provides explicit, independent control over both the semantics and spatial arrangement of each part. MultiCube takes as input a global text prompt, a text schema specifying the desired parts, and a spatial layout indicating the bounding boxes of the parts in the given schema. It outputs a 3D object composed of distinct meshes, one per specified part, that adhere to the given semantic and spatial conditions. Our approach employs a two-stage diffusion process, first generating a schema- and layout-aligned monolithic mesh, then decomposing the mesh into individual parts simultaneously. A novel Part Layout Adapter is used to encode per-part conditions independently of the other parts. Experiments demonstrate that our method can generate high-quality compositional 3D objects with precise part-level control, including those with unique layouts difficult to achieve with text or image prompting alone. Project page: https://multi-cube.github.io

cs.GR↗
arXiv2026

Func-R1: Incentivizing Mathematical Function Reasoning in Multimodal Large Language Models

Performing deliberate mathematical reasoning in visual contexts is a hallmark of advanced Multimodal Large Language Models (MLLMs) and requires a sophisticated synthesis of perceptual grounding and symbolic logic. However, in the realm of mathematical functions, our investigation reveals a critical modality interference phenomenon: even advanced models, while performing textual computational reasoning, tend to disregard or misinterpret essential visual cues. To address this challenge, we propose Func-R1, which synergistically harmonizes precise visual perception and rigorous logical reasoning. Concretely, built upon an explicitly decoupled architecture, we employ a hierarchical post-training framework to progressively identify critical visual evidence and conduct in-depth theoretical reasoning. Furthermore, the Perception-Aligned Theoretic Optimization (PATO) strategy is proposed to steer policy updating towards internalizing fundamental theoretical properties while dynamically rectifying heterogeneous visual information throughout the reasoning process. Extensive experiments across diverse benchmarks demonstrate that Func-R1 delivers the optimal performance among open-source MLLMs, even surpassing GPT-5 with an 8.4% improvement on MathVerse's function-oriented tasks.

cs.CL↗
arXiv2026

UniVVT: A Unified End-to-End Framework for High-Fidelity Video Virtual Try-on

Video Virtual Try-On (VVT) synthesizes a video of a person wearing a target garment while preserving identity, motion, and scene dynamics. Dominant approaches cast VVT as mask-conditioned video inpainting and rely on separate modules for human parsing, pose estimation, and garment warping. This multi-stage design complicates deployment and, more critically, allows errors in explicit geometric priors to propagate irreversibly into the generated video. We present UniVVT, a unified end-to-end framework that reframes VVT as semantically conditioned video generation, eliminating mask, pose, and warping modules at inference. At its core, a scene-task perceiver built on a Multimodal Large Language Model jointly encodes the source video, target garment, and task instruction into compact, task-aware latent tokens, implicitly capturing what to transfer and where and how to transfer it. A lightweight semantic bridge then aligns these tokens with the conditioning space of a diffusion-based video generator, enabling coherent garment transfer. To robustly couple the heterogeneous components, we devise a three-stage progressive training strategy comprising semantic alignment, joint task adaptation, and flexible-resolution refinement. Extensive experiments demonstrate that UniVVT achieves state-of-the-art performance across multiple benchmarks, validating implicit semantic guidance as a simple and effective alternative to fragile geometric preprocessing for end-to-end virtual try-on.

cs.CV↗
arXiv2026

VTEdit-Bench: A Comprehensive Benchmark for Multi-Reference Image Editing Models in Virtual Try-On

As virtual try-on (VTON) continues to advance, a growing number of real-world scenarios have emerged, pushing beyond the ability of the existing specialized VTON models. Meanwhile, universal multi-reference image editing models have progressed rapidly and exhibit strong generalization in visual editing, suggesting a promising route toward more flexible VTON systems. However, despite their strong capabilities, the strengths and limitations of universal editors for VTON remain insufficiently explored due to the lack of systematic evaluation benchmarks. To address this gap, we introduce VTEdit-Bench, a comprehensive benchmark designed to evaluate universal multi-reference image editing models across various realistic VTON scenarios. VTEdit-Bench contains 24,220 test image pairs spanning five representative VTON tasks with progressively increasing complexity, enabling systematic analysis of robustness and generalization. We further propose VTEdit-QA, a reference-aware VLM-based evaluator that assesses VTON performance from three key aspects: model consistency, cloth consistency, and overall image quality. Through this framework, we systematically evaluate eight universal editing models and compare them with seven specialized VTON models. Results show that top universal editors are competitive on conventional tasks and generalize more stably to harder scenarios, but remain challenged by complex reference configurations, particularly multi-cloth conditioning.

cs.CV↗
arXiv2026

CubePart: An Open-Vocabulary Part-Controllable 3D Generator

Interactive 3D assets used in games and simulation are typically decomposed into specific semantic parts to support animation, physics, and scripted behaviors, yet most generative 3D models produce either monolithic meshes or arbitrary part decompositions that cannot be aligned with application-specific requirements. We present CubePart, a generative framework for open-vocabulary, part-controllable 3D mesh generation that exposes part structure as an explicit inference-time control signal. Given a global text prompt and a user-defined parts schema expressed as an open-ended list of part names, our method generates a set of meshes - one per schema element - that assemble into a coherent object while respecting the specified semantic structure. To enable this capability, we introduce a scalable data pipeline to construct a large open-vocabulary, part-labeled 3D dataset, along with a two-stage generative architecture that separates global shape synthesis from part-level decoding. We demonstrate that the resulting assets can be directly integrated into game engines and driven by animation and behavior scripts without manual post-processing. Project Page: https://cubepart.github.io/

cs.AI↗
arXiv2026

GENERator: A Long-Context Generative Genomic Foundation Model

The rapid advancement of DNA sequencing has produced vast genomic datasets, yet interpreting and engineering genomic function remain fundamental challenges. Recent large language models have opened new avenues for genomic analysis, but existing approaches are often limited by restricted training scope, constrained generative capability, or prohibitive computational cost. We introduce GENErator, a generative genomic foundation model for long-context DNA modeling, with a context length of 98k nucleotides, pre-trained on 386 billion nucleotides of eukaryotic DNA. Without task-specific fine-tuning, GENERator exhibits strong intrinsic capabilities: unsupervised embedding analyses reveal phylogenetically coherent structure, and sequence recovery benchmarks demonstrate generative accuracy comparable to or exceeding state-of-the-art models with substantially improved computational efficiency. In a zero-shot setting, GENERator achieves competitive variant effect prediction performance relative to alignment-based methods, while remaining fully alignment-free and broadly applicable across species. With task-specific fine-tuning, the model attains leading performance on established genomic benchmarks. We further demonstrate practical generative applications. GENERator can generate protein-coding DNA sequences that translate into structurally plausible proteins and, through a prompt-guided design framework, design cis-regulatory elements with targeted activity profiles, including synthetic super-enhancers validated by high-throughput UMI-STARR-seq assays. Together, these results establish GENERator as an efficient and biologically grounded framework for genomic interpretation and programmable sequence design. Code and supplementary resources are available at https://github.com/GenerTeam/GENERator.

cs.CL↗
arXiv2025

Efficient Autoregressive Shape Generation via Octree-Based Adaptive Tokenization

Many 3D generative models rely on variational autoencoders (VAEs) to learn compact shape representations. However, existing methods encode all shapes into a fixed-size token, disregarding the inherent variations in scale and complexity across 3D data. This leads to inefficient latent representations that can compromise downstream generation. We address this challenge by introducing Octree-based Adaptive Tokenization, a novel framework that adjusts the dimension of latent representations according to shape complexity. Our approach constructs an adaptive octree structure guided by a quadric-error-based subdivision criterion and allocates a shape latent vector to each octree cell using a query-based transformer. Building upon this tokenization, we develop an octree-based autoregressive generative model that effectively leverages these variable-sized representations in shape generation. Extensive experiments demonstrate that our approach reduces token counts by 50% compared to fixed-size methods while maintaining comparable visual quality. When using a similar token length, our method produces significantly higher-quality shapes. When incorporated with our downstream generative model, our method creates more detailed and diverse 3D content than existing approaches.

cs.CV↗
arXiv2025

Cube: A Roblox View of 3D Intelligence

Foundation models trained on vast amounts of data have demonstrated remarkable reasoning and generation capabilities in the domains of text, images, audio and video. Our goal at Roblox is to build such a foundation model for 3D intelligence, a model that can support developers in producing all aspects of a Roblox experience, from generating 3D objects and scenes to rigging characters for animation to producing programmatic scripts describing object behaviors. We discuss three key design requirements for such a 3D foundation model and then present our first step towards building such a model. We expect that 3D geometric shapes will be a core data type and describe our solution for 3D shape tokenizer. We show how our tokenization scheme can be used in applications for text-to-shape generation, shape-to-text generation and text-to-scene generation. We demonstrate how these applications can collaborate with existing large language models (LLMs) to perform scene analysis and reasoning. We conclude with a discussion outlining our path to building a fully unified foundation model for 3D intelligence.

cs.CV↗
arXiv2025

Structure-Enhanced Protein Instruction Tuning: Towards General-Purpose Protein Understanding with LLMs

Proteins, as essential biomolecules, play a central role in biological processes, including metabolic reactions and DNA replication. Accurate prediction of their properties and functions is crucial in biological applications. Recent development of protein language models (pLMs) with supervised fine tuning provides a promising solution to this problem. However, the fine-tuned model is tailored for particular downstream prediction task, and achieving general-purpose protein understanding remains a challenge. In this paper, we introduce Structure-Enhanced Protein Instruction Tuning (SEPIT) framework to bridge this gap. Our approach incorporates a novel structure-aware module into pLMs to enrich their structural knowledge, and subsequently integrates these enhanced pLMs with large language models (LLMs) to advance protein understanding. In this framework, we propose a novel instruction tuning pipeline. First, we warm up the enhanced pLMs using contrastive learning and structure denoising. Then, caption-based instructions are used to establish a basic understanding of proteins. Finally, we refine this understanding by employing a mixture of experts (MoEs) to capture more complex properties and functional information with the same number of activated parameters. Moreover, we construct the largest and most comprehensive protein instruction dataset to date, which allows us to train and evaluate the general-purpose protein understanding model. Extensive experiments on both open-ended generation and closed-set answer tasks demonstrate the superior performance of SEPIT over both closed-source general LLMs and open-source LLMs trained with protein knowledge.

cs.CL↗
arXiv2025

ProtFlow: Fast Protein Sequence Design via Flow Matching on Compressed Protein Language Model Embeddings

The design of protein sequences with desired functionalities is a fundamental task in protein engineering. Deep generative methods, such as autoregressive models and diffusion models, have greatly accelerated the discovery of novel protein sequences. However, these methods mainly focus on local or shallow residual semantics and suffer from low inference efficiency, large modeling space and high training cost. To address these challenges, we introduce ProtFlow, a fast flow matching-based protein sequence design framework that operates on embeddings derived from semantically meaningful latent space of protein language models. By compressing and smoothing the latent space, ProtFlow enhances performance while training on limited computational resources. Leveraging reflow techniques, ProtFlow enables high-quality single-step sequence generation. Additionally, we develop a joint design pipeline for the design scene of multichain proteins. We evaluate ProtFlow across diverse protein design tasks, including general peptides and long-chain proteins, antimicrobial peptides, and antibodies. Experimental results demonstrate that ProtFlow outperforms task-specific methods in these applications, underscoring its potential and broad applicability in computational protein sequence design and analysis.

cs.LG↗
arXiv2025

A Generalist Cross-Domain Molecular Learning Framework for Structure-Based Drug Discovery

Structure-based drug discovery (SBDD) is a systematic scientific process that develops new drugs by leveraging the detailed physical structure of the target protein. Recent advancements in pre-trained models for biomolecules have demonstrated remarkable success across various biochemical applications, including drug discovery and protein engineering. However, in most approaches, the pre-trained models primarily focus on the characteristics of either small molecules or proteins, without delving into their binding interactions which are essential cross-domain relationships pivotal to SBDD. To fill this gap, we propose a general-purpose foundation model named BIT (an abbreviation for Biomolecular Interaction Transformer), which is capable of encoding a range of biochemical entities, including small molecules, proteins, and protein-ligand complexes, as well as various data formats, encompassing both 2D and 3D structures. Specifically, we introduce Mixture-of-Domain-Experts (MoDE) to handle the biomolecules from diverse biochemical domains and Mixture-of-Structure-Experts (MoSE) to capture positional dependencies in the molecular structures. The proposed mixture-of-experts approach enables BIT to achieve both deep fusion and domain-specific encoding, effectively capturing fine-grained molecular interactions within protein-ligand complexes. Then, we perform cross-domain pre-training on the shared Transformer backbone via several unified self-supervised denoising tasks. Experimental results on various benchmarks demonstrate that BIT achieves exceptional performance in downstream tasks, including binding affinity prediction, structure-based virtual screening, and molecular property prediction.

cs.LG↗
arXiv2024

S$^2$ALM: Sequence-Structure Pre-trained Large Language Model for Comprehensive Antibody Representation Learning

Antibodies safeguard our health through their precise and potent binding to specific antigens, demonstrating promising therapeutic efficacy in the treatment of numerous diseases, including COVID-19. Recent advancements in biomedical language models have shown the great potential to interpret complex biological structures and functions. However, existing antibody specific models have a notable limitation that they lack explicit consideration for antibody structural information, despite the fact that both 1D sequence and 3D structure carry unique and complementary insights into antibody behavior and functionality. This paper proposes Sequence-Structure multi-level pre-trained Antibody Language Model (S$^2$ALM), combining holistic sequential and structural information in one unified, generic antibody foundation model. We construct a hierarchical pre-training paradigm incorporated with two customized multi-level training objectives to facilitate the modeling of comprehensive antibody representations. S$^2$ALM's representation space uncovers inherent functional binding mechanisms, biological evolution properties and structural interaction patterns. Pre-trained over 75 million sequences and 11.7 million structures, S$^2$ALM can be adopted for diverse downstream tasks: accurately predicting antigen-antibody binding affinities, precisely distinguishing B cell maturation stages, identifying antibody crucial binding positions, and specifically designing novel coronavirus-binding antibodies. Remarkably, S$^2$ALM outperforms well-established and renowned baselines and sets new state-of-the-art performance across extensive antibody specific understanding and generation tasks. S$^2$ALM's ability to model comprehensive and generalized representations further positions its potential to advance real-world therapeutic antibody development, potentially addressing unmet academic, industrial, and clinical needs.

cs.LG↗
arXiv2024

Bridge-IF: Learning Inverse Protein Folding with Markov Bridges

Inverse protein folding is a fundamental task in computational protein design, which aims to design protein sequences that fold into the desired backbone structures. While the development of machine learning algorithms for this task has seen significant success, the prevailing approaches, which predominantly employ a discriminative formulation, frequently encounter the error accumulation issue and often fail to capture the extensive variety of plausible sequences. To fill these gaps, we propose Bridge-IF, a generative diffusion bridge model for inverse folding, which is designed to learn the probabilistic dependency between the distributions of backbone structures and protein sequences. Specifically, we harness an expressive structure encoder to propose a discrete, informative prior derived from structures, and establish a Markov bridge to connect this prior with native sequences. During the inference stage, Bridge-IF progressively refines the prior sequence, culminating in a more plausible design. Moreover, we introduce a reparameterization perspective on Markov bridge models, from which we derive a simplified loss function that facilitates more effective training. We also modulate protein language models (PLMs) with structural conditions to precisely approximate the Markov bridge process, thereby significantly enhancing generation performance while maintaining parameter-efficient training. Extensive experiments on well-established benchmarks demonstrate that Bridge-IF predominantly surpasses existing baselines in sequence recovery and excels in the design of plausible proteins with high foldability. The code is available at https://github.com/violet-sto/Bridge-IF.

cs.LG↗
arXiv2024

Multi-Modal CLIP-Informed Protein Editing

Proteins govern most biological functions essential for life, but achieving controllable protein discovery and optimization remains challenging. Recently, machine learning-assisted protein editing (MLPE) has shown promise in accelerating optimization cycles and reducing experimental workloads. However, current methods struggle with the vast combinatorial space of potential protein edits and cannot explicitly conduct protein editing using biotext instructions, limiting their interactivity with human feedback. To fill these gaps, we propose a novel method called ProtET for efficient CLIP-informed protein editing through multi-modality learning. Our approach comprises two stages: in the pretraining stage, contrastive learning aligns protein-biotext representations encoded by two large language models (LLMs), respectively. Subsequently, during the protein editing stage, the fused features from editing instruction texts and original protein sequences serve as the final editing condition for generating target protein sequences. Comprehensive experiments demonstrated the superiority of ProtET in editing proteins to enhance human-expected functionality across multiple attribute domains, including enzyme catalytic activity, protein stability and antibody specific binding ability. And ProtET improves the state-of-the-art results by a large margin, leading to significant stability improvements of 16.67% and 16.90%. This capability positions ProtET to advance real-world artificial protein editing, potentially addressing unmet academic, industrial, and clinical needs.

cs.AI↗
arXiv2024

Dr3: Ask Large Language Models Not to Give Off-Topic Answers in Open Domain Multi-Hop Question Answering

Open Domain Multi-Hop Question Answering (ODMHQA) plays a crucial role in Natural Language Processing (NLP) by aiming to answer complex questions through multi-step reasoning over retrieved information from external knowledge sources. Recently, Large Language Models (LLMs) have demonstrated remarkable performance in solving ODMHQA owing to their capabilities including planning, reasoning, and utilizing tools. However, LLMs may generate off-topic answers when attempting to solve ODMHQA, namely the generated answers are irrelevant to the original questions. This issue of off-topic answers accounts for approximately one-third of incorrect answers, yet remains underexplored despite its significance. To alleviate this issue, we propose the Discriminate->Re-Compose->Re- Solve->Re-Decompose (Dr3) mechanism. Specifically, the Discriminator leverages the intrinsic capabilities of LLMs to judge whether the generated answers are off-topic. In cases where an off-topic answer is detected, the Corrector performs step-wise revisions along the reversed reasoning chain (Re-Compose->Re-Solve->Re-Decompose) until the final answer becomes on-topic. Experimental results on the HotpotQA and 2WikiMultiHopQA datasets demonstrate that our Dr3 mechanism considerably reduces the occurrence of off-topic answers in ODMHQA by nearly 13%, improving the performance in Exact Match (EM) by nearly 3% compared to the baseline method without the Dr3 mechanism.

cs.CL↗
arXiv2024

Making Pre-trained Language Models Great on Tabular Prediction

The transferability of deep neural networks (DNNs) has made significant progress in image and language processing. However, due to the heterogeneity among tables, such DNN bonus is still far from being well exploited on tabular data prediction (e.g., regression or classification tasks). Condensing knowledge from diverse domains, language models (LMs) possess the capability to comprehend feature names from various tables, potentially serving as versatile learners in transferring knowledge across distinct tables and diverse prediction tasks, but their discrete text representation space is inherently incompatible with numerical feature values in tables. In this paper, we present TP-BERTa, a specifically pre-trained LM for tabular data prediction. Concretely, a novel relative magnitude tokenization converts scalar numerical feature values to finely discrete, high-dimensional tokens, and an intra-feature attention approach integrates feature values with the corresponding feature names. Comprehensive experiments demonstrate that our pre-trained TP-BERTa leads the performance among tabular DNNs and is competitive with Gradient Boosted Decision Tree models in typical tabular data regime.

cs.CL↗
arXiv2024

Generative AI for Controllable Protein Sequence Design: A Survey

The design of novel protein sequences with targeted functionalities underpins a central theme in protein engineering, impacting diverse fields such as drug discovery and enzymatic engineering. However, navigating this vast combinatorial search space remains a severe challenge due to time and financial constraints. This scenario is rapidly evolving as the transformative advancements in AI, particularly in the realm of generative models and optimization algorithms, have been propelling the protein design field towards an unprecedented revolution. In this survey, we systematically review recent advances in generative AI for controllable protein sequence design. To set the stage, we first outline the foundational tasks in protein sequence design in terms of the constraints involved and present key generative models and optimization algorithms. We then offer in-depth reviews of each design task and discuss the pertinent applications. Finally, we identify the unresolved challenges and highlight research opportunities that merit deeper exploration.

q-bio.BM↗
arXiv2023

Sample-efficient Multi-objective Molecular Optimization with GFlowNets

Many crucial scientific problems involve designing novel molecules with desired properties, which can be formulated as a black-box optimization problem over the discrete chemical space. In practice, multiple conflicting objectives and costly evaluations (e.g., wet-lab experiments) make the diversity of candidates paramount. Computational methods have achieved initial success but still struggle with considering diversity in both objective and search space. To fill this gap, we propose a multi-objective Bayesian optimization (MOBO) algorithm leveraging the hypernetwork-based GFlowNets (HN-GFN) as an acquisition function optimizer, with the purpose of sampling a diverse batch of candidate molecular graphs from an approximate Pareto front. Using a single preference-conditioned hypernetwork, HN-GFN learns to explore various trade-offs between objectives. We further propose a hindsight-like off-policy strategy to share high-performing molecules among different preferences in order to speed up learning for HN-GFN. We empirically illustrate that HN-GFN has adequate capacity to generalize over preferences. Moreover, experiments in various real-world MOBO settings demonstrate that our framework predominantly outperforms existing methods in terms of candidate quality and sample efficiency. The code is available at https://github.com/violet-sto/HN-GFN.

cs.LG↗