arXiv subjects

Pheng-Ann Heng

Publications and source records attributed to Pheng-Ann Heng.

At least 73 records · Page 4Linked to original sources

arXiv2025

ManualVLA: A Unified VLA Model for Chain-of-Thought Manual Generation and Robotic Manipulation

Vision-Language-Action (VLA) models have recently emerged, demonstrating strong generalization in robotic scene understanding and manipulation. However, when confronted with long-horizon tasks that require defined goal states, such as LEGO assembly or object rearrangement, existing VLA models still face challenges in coordinating high-level planning with precise manipulation. Therefore, we aim to endow a VLA model with the capability to infer the "how" process from the "what" outcomes, transforming goal states into executable procedures. In this paper, we introduce ManualVLA, a unified VLA framework built upon a Mixture-of-Transformers (MoT) architecture, enabling coherent collaboration between multimodal manual generation and action execution. Unlike prior VLA models that directly map sensory inputs to actions, we first equip ManualVLA with a planning expert that generates intermediate manuals consisting of images, position prompts, and textual instructions. Building upon these multimodal manuals, we design a Manual Chain-of-Thought (ManualCoT) reasoning process that feeds them into the action expert, where each manual step provides explicit control conditions, while its latent representation offers implicit guidance for accurate manipulation. To alleviate the burden of data collection, we develop a high-fidelity digital-twin toolkit based on 3D Gaussian Splatting, which automatically generates manual data for planning expert training. ManualVLA demonstrates strong real-world performance, achieving an average success rate 32% higher than the previous hierarchical SOTA baseline on LEGO assembly and object rearrangement tasks.

cs.RO↗

arXiv2025

Rethinking Intermediate Representation for VLM-based Robot Manipulation

Vision-Language Model (VLM) is an important component to enable robust robot manipulation. Yet, using it to translate human instructions into an action-resolvable intermediate representation often needs a tradeoff between VLM-comprehensibility and generalizability. Inspired by context-free grammar, we design the Semantic Assembly representation named SEAM, by decomposing the intermediate representation into vocabulary and grammar. Doing so leads us to a concise vocabulary of semantically-rich operations and a VLM-friendly grammar for handling diverse unseen tasks. In addition, we design a new open-vocabulary segmentation paradigm with a retrieval-augmented few-shot learning strategy to localize fine-grained object parts for manipulation, effectively with the shortest inference time over all state-of-the-art parallel works. Also, we formulate new metrics for action-generalizability and VLM-comprehensibility, demonstrating the compelling performance of SEAM over mainstream representations on both aspects. Extensive real-world experiments further manifest its SOTA performance under varying settings and tasks.

cs.RO↗

arXiv2025

Thinking-while-Generating: Interleaving Textual Reasoning throughout Visual Generation

Recent advances in visual generation have increasingly explored the integration of reasoning capabilities. They incorporate textual reasoning, i.e., think, either before (as pre-planning) or after (as post-refinement) the generation process, yet they lack on-the-fly multimodal interaction during the generation itself. In this preliminary study, we introduce Thinking-while-Generating (TwiG), the first interleaved framework that enables co-evolving textual reasoning throughout the visual generation process. As visual content is progressively generating, textual reasoning is interleaved to both guide upcoming local regions and reflect on previously synthesized ones. This dynamic interplay produces more context-aware and semantically rich visual outputs. To unveil the potential of this framework, we investigate three candidate strategies, zero-shot prompting, supervised fine-tuning (SFT) on our curated TwiG-50K dataset, and reinforcement learning (RL) via a customized TwiG-GRPO strategy, each offering unique insights into the dynamics of interleaved reasoning. We hope this work inspires further research into interleaving textual reasoning for enhanced visual generation. Code will be released at: https://github.com/ZiyuGuo99/Thinking-while-Generating.

cs.CV↗

arXiv2025

Rethinking Facial Expression Recognition in the Era of Multimodal Large Language Models: Benchmark, Datasets, and Beyond

Multimodal Large Language Models (MLLMs) have revolutionized numerous research fields, including computer vision and affective computing. As a pivotal challenge in this interdisciplinary domain, facial expression recognition (FER) has evolved from separate, domain-specific models to more unified approaches. One promising avenue to unify FER tasks is converting conventional FER datasets into visual question-answering (VQA) formats, enabling the direct application of powerful generalist MLLMs for inference. However, despite the success of cutting-edge MLLMs in various tasks, their performance on FER tasks remains largely unexplored. To address this gap, we provide FERBench, a systematic benchmark that incorporates 20 state-of-the-art MLLMs across four widely used FER datasets. Our results reveal that, while MLLMs exhibit good classification performance, they still face significant limitations in reasoning and interpretability. To this end, we introduce post-training strategies aimed at enhancing the facial expression reasoning capabilities of MLLMs. Specifically, we curate two high-quality and large-scale datasets: UniFER-CoT-230K for cold-start initialization and UniFER-RLVR-360K for reinforcement learning with verifiable rewards (RLVR), respectively. Building upon them, we develop a unified and interpretable FER foundation model termed UniFER-7B, which outperforms many open-sourced and closed-source generalist MLLMs (e.g., Gemini-2.5-Pro and Qwen2.5-VL-72B).

cs.CV↗

arXiv2025

Lost in Tokenization: Context as the Key to Unlocking Biomolecular Understanding in Scientific LLMs

Scientific Large Language Models (Sci-LLMs) have emerged as a promising frontier for accelerating biological discovery. However, these models face a fundamental challenge when processing raw biomolecular sequences: the tokenization dilemma. Whether treating sequences as a specialized language, risking the loss of functional motif information, or as a separate modality, introducing formidable alignment challenges, current strategies fundamentally limit their reasoning capacity. We challenge this sequence-centric paradigm by positing that a more effective strategy is to provide Sci-LLMs with high-level structured context derived from established bioinformatics tools, thereby bypassing the need to interpret low-level noisy sequence data directly. Through a systematic comparison of leading Sci-LLMs on biological reasoning tasks, we tested three input modes: sequence-only, context-only, and a combination of both. Our findings are striking: the context-only approach consistently and substantially outperforms all other modes. Even more revealing, the inclusion of the raw sequence alongside its high-level context consistently degrades performance, indicating that raw sequences act as informational noise, even for models with specialized tokenization schemes. These results suggest that the primary strength of existing Sci-LLMs lies not in their nascent ability to interpret biomolecular syntax from scratch, but in their profound capacity for reasoning over structured, human-readable knowledge. Therefore, we argue for reframing Sci-LLMs not as sequence decoders, but as powerful reasoning engines over expert knowledge. This work lays the foundation for a new class of hybrid scientific AI agents, repositioning the developmental focus from direct sequence interpretation towards high-level knowledge synthesis. The code is available at https://github.com/opendatalab-raiser/CoKE.

cs.AI↗

arXiv2025

Are Video Models Ready as Zero-Shot Reasoners? An Empirical Study with the MME-CoF Benchmark

Recent video generation models can produce high-fidelity, temporally coherent videos, indicating that they may encode substantial world knowledge. Beyond realistic synthesis, they also exhibit emerging behaviors indicative of visual perception, modeling, and manipulation. Yet, an important question still remains: Are video models ready to serve as zero-shot reasoners in challenging visual reasoning scenarios? In this work, we conduct an empirical study to comprehensively investigate this question, focusing on the leading and popular Veo-3. We evaluate its reasoning behavior across 12 dimensions, including spatial, geometric, physical, temporal, and embodied logic, systematically characterizing both its strengths and failure modes. To standardize this study, we curate the evaluation data into MME-CoF, a compact benchmark that enables in-depth and thorough assessment of Chain-of-Frame (CoF) reasoning. Our findings reveal that while current video models demonstrate promising reasoning patterns on short-horizon spatial coherence, fine-grained grounding, and locally consistent dynamics, they remain limited in long-horizon causal reasoning, strict geometric constraints, and abstract logic. Overall, they are not yet reliable as standalone zero-shot reasoners, but exhibit encouraging signs as complementary visual engines alongside dedicated reasoning models. Project page: https://video-cof.github.io

cs.CV↗

arXiv2025

RiboPO: Preference Optimization for Structure- and Stability-Aware RNA Design

Designing RNA sequences that reliably adopt specified three-dimensional structures while maintaining thermodynamic stability remains challenging for synthetic biology and therapeutics. Current inverse folding approaches optimize for sequence recovery or single structural metrics, failing to simultaneously ensure global geometry, local accuracy, and ensemble stability-three interdependent requirements for functional RNA design. This gap becomes critical when designed sequences encounter dynamic biological environments. We introduce RiboPO, a Ribonucleic acid Preference Optimization framework that addresses this multi-objective challenge through reinforcement learning from physical feedback (RLPF). RiboPO fine-tunes gRNAde by constructing preference pairs from composite physical criteria that couple global 3D fidelity and thermodynamic stability. Preferences are formed using structural gates, PLDDT geometry assessments, and thermostability proxies with variability-aware margins, and the policy is updated with Direct Preference Optimization (DPO). On RNA inverse folding benchmarks, RiboPO demonstrates a superior balance of structural accuracy and stability. Compared to the best non-overlap baselines, our multi-round model improves Minimum Free Energy (MFE) by 12.3% and increases secondary-structure self-consistency (EternaFold scMCC) by 20%, while maintaining competitive 3D quality and high sequence diversity. In sampling efficiency, RiboPO achieves 11% higher pass@64 than the gRNAde base under the conjunction of multiple requirements. A multi-round variant with preference-pair reconstruction delivers additional gains on unseen RNA structures. These results establish RLPF as an effective paradigm for structure-accurate and ensemble-robust RNA design, providing a foundation for extending to complex biological objectives.

q-bio.BM↗

arXiv2025

SceneDecorator: Towards Scene-Oriented Story Generation with Scene Planning and Scene Consistency

Recent text-to-image models have revolutionized image generation, but they still struggle with maintaining concept consistency across generated images. While existing works focus on character consistency, they often overlook the crucial role of scenes in storytelling, which restricts their creativity in practice. This paper introduces scene-oriented story generation, addressing two key challenges: (i) scene planning, where current methods fail to ensure scene-level narrative coherence by relying solely on text descriptions, and (ii) scene consistency, which remains largely unexplored in terms of maintaining scene consistency across multiple stories. We propose SceneDecorator, a training-free framework that employs VLM-Guided Scene Planning to ensure narrative coherence across different scenes in a ``global-to-local'' manner, and Long-Term Scene-Sharing Attention to maintain long-term scene consistency and subject diversity across generated stories. Extensive experiments demonstrate the superior performance of SceneDecorator, highlighting its potential to unleash creativity in the fields of arts, films, and games.

cs.CV↗

arXiv2025

COS3D: Collaborative Open-Vocabulary 3D Segmentation

Open-vocabulary 3D segmentation is a fundamental yet challenging task, requiring a mutual understanding of both segmentation and language. However, existing Gaussian-splatting-based methods rely either on a single 3D language field, leading to inferior segmentation, or on pre-computed class-agnostic segmentations, suffering from error accumulation. To address these limitations, we present COS3D, a new collaborative prompt-segmentation framework that contributes to effectively integrating complementary language and segmentation cues throughout its entire pipeline. We first introduce the new concept of collaborative field, comprising an instance field and a language field, as the cornerstone for collaboration. During training, to effectively construct the collaborative field, our key idea is to capture the intrinsic relationship between the instance field and language field, through a novel instance-to-language feature mapping and designing an efficient two-stage training strategy. During inference, to bridge distinct characteristics of the two fields, we further design an adaptive language-to-instance prompt refinement, promoting high-quality prompt-segmentation inference. Extensive experiments not only demonstrate COS3D's leading performance over existing methods on two widely-used benchmarks but also show its high potential to various applications,~\ie, novel image-based 3D segmentation, hierarchical segmentation, and robotics. The code is publicly available at \href{https://github.com/Runsong123/COS3D}{https://github.com/Runsong123/COS3D}.

cs.CV↗

arXiv2025

ProteinAE: Protein Diffusion Autoencoders for Structure Encoding

Developing effective representations of protein structures is essential for advancing protein science, particularly for protein generative modeling. Current approaches often grapple with the complexities of the SE(3) manifold, rely on discrete tokenization, or the need for multiple training objectives, all of which can hinder the model optimization and generalization. We introduce ProteinAE, a novel and streamlined protein diffusion autoencoder designed to overcome these challenges by directly mapping protein backbone coordinates from E(3) into a continuous, compact latent space. ProteinAE employs a non-equivariant Diffusion Transformer with a bottleneck design for efficient compression and is trained end-to-end with a single flow matching objective, substantially simplifying the optimization pipeline. We demonstrate that ProteinAE achieves state-of-the-art reconstruction quality, outperforming existing autoencoders. The resulting latent space serves as a powerful foundation for a latent diffusion model that bypasses the need for explicit equivariance. This enables efficient, high-quality structure generation that is competitive with leading structure-based approaches and significantly outperforms prior latent-based methods. Code is available at https://github.com/OnlyLoveKFC/ProteinAE_v1.

cs.LG↗

arXiv2025

REAR: Rethinking Visual Autoregressive Models via Generator-Tokenizer Consistency Regularization

Visual autoregressive (AR) generation offers a promising path toward unifying vision and language models, yet its performance remains suboptimal against diffusion models. Prior work often attributes this gap to tokenizer limitations and rasterization ordering. In this work, we identify a core bottleneck from the perspective of generator-tokenizer inconsistency, i.e., the AR-generated tokens may not be well-decoded by the tokenizer. To address this, we propose reAR, a simple training strategy introducing a token-wise regularization objective: when predicting the next token, the causal transformer is also trained to recover the visual embedding of the current token and predict the embedding of the target token under a noisy context. It requires no changes to the tokenizer, generation order, inference pipeline, or external models. Despite its simplicity, reAR substantially improves performance. On ImageNet, it reduces gFID from 3.02 to 1.86 and improves IS to 316.9 using a standard rasterization-based tokenizer. When applied to advanced tokenizers, it achieves a gFID of 1.42 with only 177M parameters, matching the performance with larger state-of-the-art diffusion models (675M).

cs.CV↗

arXiv2025

From Supervision to Exploration: What Does Protein Language Model Learn During Reinforcement Learning?

Protein language models (PLMs) have advanced computational protein science through large-scale pretraining and scalable architectures. In parallel, reinforcement learning (RL) has broadened exploration and enabled precise multi-objective optimization in protein design. Yet whether RL can push PLMs beyond their pretraining priors to uncover latent sequence-structure-function rules remains unclear. We address this by pairing RL with PLMs across four domains: antimicrobial peptide design, kinase variant optimization, antibody engineering, and inverse folding. Using diverse RL algorithms and model classes, we ask if RL improves sampling efficiency and, more importantly, if it reveals capabilities not captured by supervised learning. Across benchmarks, RL consistently boosts success rates and sample efficiency. Performance follows a three-factor interaction: task headroom, reward fidelity, and policy capacity jointly determine gains. When rewards are accurate and informative, policies have sufficient capacity, and tasks leave room beyond supervised baselines, improvements scale; when rewards are noisy or capacity is constrained, gains saturate despite exploration. This view yields practical guidance for RL in protein design: prioritize reward modeling and calibration before scaling policy size, match algorithm and regularization strength to task difficulty, and allocate capacity where marginal gains are largest. Implementation is available at https://github.com/chq1155/RL-PLM.

cs.LG↗

arXiv2025

DisCo-Layout: Disentangling and Coordinating Semantic and Physical Refinement in a Multi-Agent Framework for 3D Indoor Layout Synthesis

3D indoor layout synthesis is crucial for creating virtual environments. Traditional methods struggle with generalization due to fixed datasets. While recent LLM and VLM-based approaches offer improved semantic richness, they often lack robust and flexible refinement, resulting in suboptimal layouts. We develop DisCo-Layout, a novel framework that disentangles and coordinates physical and semantic refinement. For independent refinement, our Semantic Refinement Tool (SRT) corrects abstract object relationships, while the Physical Refinement Tool (PRT) resolves concrete spatial issues via a grid-matching algorithm. For collaborative refinement, a multi-agent framework intelligently orchestrates these tools, featuring a planner for placement rules, a designer for initial layouts, and an evaluator for assessment. Experiments demonstrate DisCo-Layout's state-of-the-art performance, generating realistic, coherent, and generalizable 3D indoor layouts. Our code will be publicly available.

cs.RO↗

arXiv2025

Lightweight MSA Design Advances Protein Folding From Evolutionary Embeddings

Protein structure prediction often hinges on multiple sequence alignments (MSAs), which underperform on low-homology and orphan proteins. We introduce PLAME, a lightweight MSA design framework that leverages evolutionary embeddings from pretrained protein language models to generate MSAs that better support downstream folding. PLAME couples these embeddings with a conservation--diversity loss that balances agreement on conserved positions with coverage of plausible sequence variation. Beyond generation, we develop (i) an MSA selection strategy to filter high-quality candidates and (ii) a sequence-quality metric that is complementary to depth-based measures and predictive of folding gains. On AlphaFold2 low-homology/orphan benchmarks, PLAME delivers state-of-the-art improvements in structure accuracy (e.g., lDDT/TM-score), with consistent gains when paired with AlphaFold3. Ablations isolate the benefits of the selection strategy, and case studies elucidate how MSA characteristics shape AlphaFold confidence and error modes. Finally, we show PLAME functions as a lightweight adapter, enabling ESMFold to approach AlphaFold2-level accuracy while retaining ESMFold-like inference speed. PLAME thus provides a practical path to high-quality folding for proteins lacking strong evolutionary neighbors.

cs.LG↗

arXiv2025

MEJO: MLLM-Engaged Surgical Triplet Recognition via Inter- and Intra-Task Joint Optimization

Surgical triplet recognition, which involves identifying instrument, verb, target, and their combinations, is a complex surgical scene understanding challenge plagued by long-tailed data distribution. The mainstream multi-task learning paradigm benefiting from cross-task collaborative promotion has shown promising performance in identifying triples, but two key challenges remain: 1) inter-task optimization conflicts caused by entangling task-generic and task-specific representations; 2) intra-task optimization conflicts due to class-imbalanced training data. To overcome these difficulties, we propose the MLLM-Engaged Joint Optimization (MEJO) framework that empowers both inter- and intra-task optimization for surgical triplet recognition. For inter-task optimization, we introduce the Shared-Specific-Disentangled (S$^2$D) learning scheme that decomposes representations into task-shared and task-specific components. To enhance task-shared representations, we construct a Multimodal Large Language Model (MLLM) powered probabilistic prompt pool to dynamically augment visual features with expert-level semantic cues. Additionally, comprehensive task-specific cues are modeled via distinct task prompts covering the temporal-spatial dimensions, effectively mitigating inter-task ambiguities. To tackle intra-task optimization conflicts, we develop a Coordinated Gradient Learning (CGL) strategy, which dissects and rebalances the positive-negative gradients originating from head and tail classes for more coordinated learning behaviors. Extensive experiments on the CholecT45 and CholecT50 datasets demonstrate the superiority of our proposed framework, validating its effectiveness in handling optimization conflicts.

cs.CV↗

arXiv2025

A deep reinforcement learning platform for antibiotic discovery

Antimicrobial resistance (AMR) is projected to cause up to 10 million deaths annually by 2050, underscoring the urgent need for new antibiotics. Here we present ApexAmphion, a deep-learning framework for de novo design of antibiotics that couples a 6.4-billion-parameter protein language model with reinforcement learning. The model is first fine-tuned on curated peptide data to capture antimicrobial sequence regularities, then optimised with proximal policy optimization against a composite reward that combines predictions from a learned minimum inhibitory concentration (MIC) classifier with differentiable physicochemical objectives. In vitro evaluation of 100 designed peptides showed low MIC values (nanomolar range in some cases) for all candidates (100% hit rate). Moreover, 99 our of 100 compounds exhibited broad-spectrum antimicrobial activity against at least two clinically relevant bacteria. The lead molecules killed bacteria primarily by potently targeting the cytoplasmic membrane. By unifying generation, scoring and multi-objective optimization with deep reinforcement learning in a single pipeline, our approach rapidly produces diverse, potent candidates, offering a scalable route to peptide antibiotics and a platform for iterative steering toward potency and developability within hours.

cs.LG↗

arXiv2025

SurgPub-Video: A Comprehensive Surgical Video Dataset for Enhanced Surgical Intelligence in Vision-Language Model

Vision-Language Models (VLMs) have shown significant potential in surgical scene analysis, yet existing models are limited by frame-level datasets and lack high-quality video data with procedural surgical knowledge. To address these challenges, we make the following contributions: (i) SurgPub-Video, a comprehensive dataset of over 3,000 surgical videos and 25 million annotated frames across 11 specialties, sourced from peer-reviewed clinical journals, (ii) SurgLLaVA-Video, a specialized VLM for surgical video understanding, built upon the TinyLLaVA-Video architecture that supports both video-level and frame-level inputs, and (iii) a video-level surgical Visual Question Answering (VQA) benchmark, covering diverse 11 surgical specialities, such as vascular, cardiology, and thoracic. Extensive experiments, conducted on the proposed benchmark and three additional surgical downstream tasks (action recognition, skill assessment, and triplet recognition), show that SurgLLaVA-Video significantly outperforms both general-purpose and surgical-specific VLMs with only three billion parameters. The dataset, model, and benchmark will be released to enable further advancements in surgical video understanding.

q-bio.OT↗

arXiv2025

From Learning to Unlearning: Biomedical Security Protection in Multimodal Large Language Models

The security of biomedical Multimodal Large Language Models (MLLMs) has attracted increasing attention. However, training samples easily contain private information and incorrect knowledge that are difficult to detect, potentially leading to privacy leakage or erroneous outputs after deployment. An intuitive idea is to reprocess the training set to remove unwanted content and retrain the model from scratch. Yet, this is impractical due to significant computational costs, especially for large language models. Machine unlearning has emerged as a solution to this problem, which avoids complete retraining by selectively removing undesired knowledge derived from harmful samples while preserving required capabilities on normal cases. However, there exist no available datasets to evaluate the unlearning quality for security protection in biomedical MLLMs. To bridge this gap, we propose the first benchmark Multimodal Large Language Model Unlearning for BioMedicine (MLLMU-Med) built upon our novel data generation pipeline that effectively integrates synthetic private data and factual errors into the training set. Our benchmark targets two key scenarios: 1) Privacy protection, where patient private information is mistakenly included in the training set, causing models to unintentionally respond with private data during inference; and 2) Incorrectness removal, where wrong knowledge derived from unreliable sources is embedded into the dataset, leading to unsafe model responses. Moreover, we propose a novel Unlearning Efficiency Score that directly reflects the overall unlearning performance across different subsets. We evaluate five unlearning approaches on MLLMU-Med and find that these methods show limited effectiveness in removing harmful knowledge from biomedical MLLMs, indicating significant room for improvement. This work establishes a new pathway for further research in this promising field.

cs.CV↗