arXiv subjects

Dingyi Rong

Publications and source records attributed to Dingyi Rong.

7 recordsLinked to original sources

arXiv2026

SafeAtlas-VL: Beyond Binary Multimodal Safety with Large-Scale Data and Guard Models

Multimodal safety moderation requires distinguishing risks arising from visual content, user intent, and assistant behavior. Existing safeguards, however, are typically trained for a single judgment target and reduce safety assessment to a binary decision. Consequently, risk becomes difficult to compare across a multimodal interaction, and ambiguous cases are obscured. We introduce SafeAtlas-VL, a dataset of 1.5M training instances that places image-, request-, and response-level judgments on a five-level ordered scale. We curate a broad collection of safety-relevant data from both real-world and synthetic sources and apply a disagreement-aware annotation procedure. The resulting dataset spans 15 harm categories and 55 fine-grained subcategories, covering a broad range of multimodal safety scenarios. We also construct SafeAtlas-Bench, a held-out set of 5,000 instances for evaluating five-level predictions and continuous risk scores. Upon this dataset, we train the SafeAtlas Guard series of models via target-conditioned tuning for multimodal safety detection. Our models not only perform five-way classification of safety levels but also map safety to continuous scores through a soft cumulative ordinal head. Experimental results demonstrate that guard models trained on our dataset exhibit strong generalization: even without using the training sets of other benchmarks, they achieve competitive performance on the corresponding test sets. Notably, our 8B model attains the overall best performance, outperforming the previous SOTA by approximately 4% in F1 score. Code, data, and models are released to support further research. Warning: this paper contains example data that may be offensive, harmful, graphic, or disturbing.

cs.AI↗

arXiv2026

H2R-Bench: Benchmarking Human-to-Robot Manipulation Video Generation in World Models

Large-scale manipulation data is essential for robot learning, yet collecting robot demonstrations remains expensive and difficult to scale. Meanwhile, abundant egocentric human manipulation videos provide rich behavioral experiences, but transferring them across embodiments remains challenging due to differences between human hands and robotic end-effectors. Recent advances in video world models offer a promising pathway to synthesize robot-centric manipulation videos from human observations, while their cross-embodiment transfer capability remains largely unexplored. Therefore, we introduce H2R-Bench, a benchmark for evaluating cross-embodiment human-to-robot manipulation video generation, where models transform egocentric human demonstrations into robot manipulation videos under specified embodiments. Each benchmark instance contains a human demonstration video, target embodiment constraints, and source-grounded annotations covering task goals, action events, functional contacts, and object responses. H2R-Bench evaluates generated videos through five dimensions, including goal-state completion, action-event completion, functional contact transfer, embodiment correctness, and general video quality. We benchmark eleven state-of-the-art video generation models across six manipulation families and two robot embodiments. Our evaluation reveals that current video world models remain limited in human-to-robot manipulation transfer: even leading models often fail in embodiment consistency, functional interaction, and task execution. H2R-Bench provides a systematic diagnostic framework for evaluating whether video world models can bridge the human-to-robot embodiment gap and convert human manipulation observations into robot-centric training resources.

cs.RO↗

arXiv2025

LiveProteinBench: A Contamination-Free Benchmark for Assessing Models' Specialized Capabilities in Protein Science

In contrast to their remarkable performance on general knowledge QA, the true abilities of Large Language Models (LLMs) in tasks demanding deep, specialized reasoning, such as in protein biology, have yet to be thoroughly investigated. Current benchmarks suffer from critical deficiencies, such as data contamination due to outdated test sets, insufficient focus on essential protein-specific tasks, and a neglect of multimodal assessments. To resolve these issues, we introduce LiveProteinBench, a contamination-free, multimodal benchmark of 12 tasks for evaluating LLM performance on protein property and function prediction. Its central innovation lies in a test set composed exclusively of proteins validated after the start of 2025, guaranteeing that the data is novel to all tested models. We benchmarked a suite of prominent general-purpose LLMs and specialized biological LLMs using both unimodal and multimodal input schemes. Our results show that: 1) General-purpose proprietary large models demonstrate superior zero-shot performance when encountering new protein data, outperforming their open-source and domain-specific counterparts by over 20\% accuracy. 2) The effective use of multi-view structural information remains a significant challenge, as the inclusion of structural images often fails to provide a consistent benefit and can even degrade performance. This highlights the limitations of current models in effectively fusing information across different modalities. 3) Models' performance scales more directly with the computational cost during inference than with its parameter count, underscoring the critical role of Chain-of-Thought reasoning capabilities for protein-specific tasks. LiveProteinBench delineates the current performance frontiers for LLMs in bioinformatics and presents new challenges for the development of future multimodal foundation models for biology

q-bio.QM↗

arXiv2025

EnerBridge-DPO: Energy-Guided Protein Inverse Folding with Markov Bridges and Direct Preference Optimization

Designing protein sequences with optimal energetic stability is a key challenge in protein inverse folding, as current deep learning methods are primarily trained by maximizing sequence recovery rates, often neglecting the energy of the generated sequences. This work aims to overcome this limitation by developing a model that directly generates low-energy, stable protein sequences. We propose EnerBridge-DPO, a novel inverse folding framework focused on generating low-energy, high-stability protein sequences. Our core innovation lies in: First, integrating Markov Bridges with Direct Preference Optimization (DPO), where energy-based preferences are used to fine-tune the Markov Bridge model. The Markov Bridge initiates optimization from an information-rich prior sequence, providing DPO with a pool of structurally plausible sequence candidates. Second, an explicit energy constraint loss is introduced, which enhances the energy-driven nature of DPO based on prior sequences, enabling the model to effectively learn energy representations from a wealth of prior knowledge and directly predict sequence energy values, thereby capturing quantitative features of the energy landscape. Our evaluations demonstrate that EnerBridge-DPO can design protein complex sequences with lower energy while maintaining sequence recovery rates comparable to state-of-the-art models, and accurately predicts $\Delta \Delta G$ values between various sequences.

cs.LG↗

arXiv2024

Autoregressive Enzyme Function Prediction with Multi-scale Multi-modality Fusion

Accurate prediction of enzyme function is crucial for elucidating biological mechanisms and driving innovation across various sectors. Existing deep learning methods tend to rely solely on either sequence data or structural data and predict the EC number as a whole, neglecting the intrinsic hierarchical structure of EC numbers. To address these limitations, we introduce MAPred, a novel multi-modality and multi-scale model designed to autoregressively predict the EC number of proteins. MAPred integrates both the primary amino acid sequence and the 3D tokens of proteins, employing a dual-pathway approach to capture comprehensive protein characteristics and essential local functional sites. Additionally, MAPred utilizes an autoregressive prediction network to sequentially predict the digits of the EC number, leveraging the hierarchical organization of EC classifications. Evaluations on benchmark datasets, including New-392, Price, and New-815, demonstrate that our method outperforms existing models, marking a significant advance in the reliability and granularity of protein function prediction within bioinformatics.

q-bio.QM↗

arXiv2022

DARF: Depth-Aware Generalizable Neural Radiance Field

Neural Radiance Field (NeRF) has revolutionized novel-view rendering tasks and achieved impressive results. However, the inefficient sampling and per-scene optimization hinder its wide applications. Though some generalizable NeRFs have been proposed, the rendering quality is unsatisfactory due to the lack of geometry and scene uniqueness. To address these issues, we propose the Depth-Aware Generalizable Neural Radiance Field (DARF) with a Depth-Aware Dynamic Sampling (DADS) strategy to perform efficient novel view rendering and unsupervised depth estimation on unseen scenes without per-scene optimization. Distinct from most existing generalizable NeRFs, our framework infers the unseen scenes on both pixel level and geometry level with only a few input images. By introducing a pre-trained depth estimation module to derive the depth prior, narrowing down the ray sampling interval to the proximity space of the estimated surface, and sampling in expectation maximum position, we preserve scene characteristics while learning common attributes for novel-view synthesis. Moreover, we introduce a Multi-level Semantic Consistency loss (MSC) to assist with more informative representation learning. Extensive experiments on indoor and outdoor datasets show that compared with state-of-the-art generalizable NeRF methods, DARF reduces samples by 50%, while improving rendering quality and depth estimation. Our code is available on https://github.com/shiyue001/GARF.git.

cs.CV↗

arXiv2022

Differentiable Projection from Optical Coherence Tomography B-Scan without Retinal Layer Segmentation Supervision

Projection map (PM) from optical coherence tomography (OCT) B-scan is an important tool to diagnose retinal diseases, which typically requires retinal layer segmentation. In this study, we present a novel end-to-end framework to predict PMs from B-scans. Instead of segmenting retinal layers explicitly, we represent them implicitly as predicted coordinates. By pixel interpolation on uniformly sampled coordinates between retinal layers, the corresponding PMs could be easily obtained with pooling. Notably, all the operators are differentiable; therefore, this Differentiable Projection Module (DPM) enables end-to-end training with the ground truth of PMs rather than retinal layer segmentation. Our framework produces high-quality PMs, significantly outperforming baselines, including a vanilla CNN without DPM and an optimization-based DPM without a deep prior. Furthermore, the proposed DPM, as a novel neural representation of areas/volumes between curves/surfaces, could be of independent interest for geometric deep learning.

eess.IV↗