arXiv subjects

Jiaying He

Publications and source records attributed to Jiaying He.

6 recordsLinked to original sources

arXiv2026

ABOPD: Antibody CDR Design via On-Policy Distillation

Antibodies are essential therapeutic molecules, and their complementarity-determining regions (CDRs) form the primary antigen-recognition interface. Recent protein generative models have demonstrated broad capabilities in biomolecular design, yet post-training strategies for downstream objectives remain limited. Standard denoising training operates on noisy states obtained by perturbing native structures, whereas recursive generation proceeds through model-generated intermediate states. For flexible antibody CDR loops such as CDR-H3, this mismatch can allow backbone deviations to accumulate along the denoising trajectory and compromise antigen-facing loop geometry. We introduce ABOPD, an antibody design framework based on on-policy distillation that leverages privileged native geometry during training to supervise states visited along the model's own denoising trajectories. With this fine-grained structural supervision, ABOPD substantially improves structural recovery on RAbD CDR-H3 generation, reducing RMSD by 0.42 {\AA} (from 2.37 {\AA} to 1.95 {\AA}) and outperforming supervised fine-tuning and offline distillation controls, offering a path to higher-fidelity protein design.

cs.LG↗

arXiv2026

Rethinking Scientific Discovery in the Agentic Era

Artificial intelligence has advanced scientific discovery, but most AI4Science systems remain fragmented tools that rely on humans to coordinate problem formulation, literature grounding, model use, simulation, validation, and knowledge reuse. This paper presents \textbf{SCION (Scientific Collaborative Innovation with Agentic Organizational Nexus)}, an agentic scientific operating system that acts as an \textbf{organizational nexus}. Through a Science Agent serving as a \textbf{Meta-Harness}, SCION connects scientific tasks, tools, agents, artifacts, and memory, transforming research into an executable, auditable, and reusable operational process. At its core is the \textbf{Research Execution Plan (REP)}, which compiles high-level scientific intent into staged objectives, dependencies, verification checkpoints, tool requirements, expected artifacts, and fallback conditions. SCION further integrates hierarchical multi-agent execution, profile-driven specialization, selective context construction, governed delegation, and layered epistemic memory to support long-horizon scientific work. We formulate discovery under SCION as \textbf{Target-conditioned Inverse Search} and extend it to hidden-target settings through batch active search under finite experimental budgets. Applications in materials analysis, molecule design, and protein or antibody screening, together with experiments on scientific reading, idea generation, molecule generation, and antibody screening, show that SCION outperforms existing autonomous research-agent baselines, especially in decomposition, verification, refinement, and memory reuse. Overall, SCION shifts AI from isolated tools toward a coordinated operational layer for traceable and reusable scientific innovation.

cs.CL↗

arXiv2026

Geometric Gradient Rectification for Safe Open-Set Semi-Supervised Learning

Open-set semi-supervised learning aims to leverage unlabeled data that may contain out-of-distribution outliers while maintaining performance on in-distribution classes. Existing methods mainly follow two paradigms: filtering suspicious samples or incorporating unlabeled objectives with soft weighting. We argue that both face a common trade-off: aggressive filtering can discard informative but hard ID samples, whereas utilization can introduce auxiliary gradients that conflict with supervised learning when pseudo labels are wrong. We therefore shift the focus from sample selection to gradient-level control. We propose \textit{Geometric Gradient Rectification} (GGR), a plug-in framework that uses the supervised gradient as an anchor and projects conflicting auxiliary gradients onto an admissible region in gradient space. This makes the applied auxiliary update first-order non-opposing within the rectified coordinate block while preserving orthogonal components that may still carry useful representation signals. We further extend GGR with subspace-aware rectification to stabilize the anchor under noisy mini-batch gradients. Experiments on CIFAR and ImageNet benchmarks show that GGR improves representative OSSL baselines in most settings and yields gains in both closed-set generalization and open-set robustness. Code will be available at https://github.com/JiaheChen2002/GGR.

cs.CV↗

arXiv2025

BioGraphFusion: Graph Knowledge Embedding for Biological Completion and Reasoning

Motivation: Biomedical knowledge graphs (KGs) are crucial for drug discovery and disease understanding, yet their completion and reasoning are challenging. Knowledge Embedding (KE) methods capture global semantics but struggle with dynamic structural integration, while Graph Neural Networks (GNNs) excel locally but often lack semantic understanding. Even ensemble approaches, including those leveraging language models, often fail to achieve a deep, adaptive, and synergistic co-evolution between semantic comprehension and structural learning. Addressing this critical gap in fostering continuous, reciprocal refinement between these two aspects in complex biomedical KGs is paramount. Results: We introduce BioGraphFusion, a novel framework for deeply synergistic semantic and structural learning. BioGraphFusion establishes a global semantic foundation via tensor decomposition, guiding an LSTM-driven mechanism to dynamically refine relation embeddings during graph propagation. This fosters adaptive interplay between semantic understanding and structural learning, further enhanced by query-guided subgraph construction and a hybrid scoring mechanism. Experiments across three key biomedical tasks demonstrate BioGraphFusion's superior performance over state-of-the-art KE, GNN, and ensemble models. A case study on Cutaneous Malignant Melanoma 1 (CMM1) highlights its ability to unveil biologically meaningful pathways. Availability and Implementation: Source code and all training data are freely available for download at https://github.com/Y-TARL/BioGraphFusion. Supplementary information: Supplementary data are available at Bioinformatics online.

cs.AI↗

arXiv2025

Curing Semantic Drift: A Dynamic Approach to Grounding Generation in Large Vision-Language Models

Large Vision-Language Models (LVLMs) face a tug-of-war between powerful linguistic priors and visual evidence, often leading to \emph{semantic drift}: a progressive detachment from the input image that can abruptly emerge at specific decoding steps. Through a token-level diagnosis, we show that hallucination is frequently triggered not by the absence of grounded candidates, but by a failure of selection -- the model chooses a linguistically convenient yet visually unfaithful token even when better grounded alternatives exist. Motivated by this insight, we propose \textbf{D}ynamic \textbf{L}ogits \textbf{C}alibration (DLC), a training-free decoding framework that introduces a lightweight visual referee to intervene exactly when drift happens. At each step, DLC performs a dual-aspect grounding check on top-$k$ candidates: (1) it assesses the intrinsic visual relevance of a candidate token and (2) its contextual visual coherence. These signals are evaluated against an adaptive historical baseline to compute a relative visual advantage, which is then used to dynamically calibrate logits and favor grounded tokens. Extensive experiments on CHAIR, POPE, SHR, GPT-4o evaluation, and MME demonstrate that DLC consistently reduces hallucinations across multiple LVLMs while preserving response quality. Further analyses validate robustness to different vision backbones and demonstrate a favorable trade-off between output quality and computational cost as the candidate pool size varies. Code will be released on https://github.com/JiaheChen2002/DLC.

cs.CV↗

arXiv2025

C3S3: Complementary Competition and Contrastive Selection for Semi-Supervised Medical Image Segmentation

For the immanent challenge of insufficiently annotated samples in the medical field, semi-supervised medical image segmentation (SSMIS) offers a promising solution. Despite achieving impressive results in delineating primary target areas, most current methodologies struggle to precisely capture the subtle details of boundaries. This deficiency often leads to significant diagnostic inaccuracies. To tackle this issue, we introduce C3S3, a novel semi-supervised segmentation model that synergistically integrates complementary competition and contrastive selection. This design significantly sharpens boundary delineation and enhances overall precision. Specifically, we develop an Outcome-Driven Contrastive Learning module dedicated to refining boundary localization. Additionally, we incorporate a Dynamic Complementary Competition module that leverages two high-performing sub-networks to generate pseudo-labels, thereby further improving segmentation quality. The proposed C3S3 undergoes rigorous validation on two publicly accessible datasets, encompassing the practices of both MRI and CT scans. The results demonstrate that our method achieves superior performance compared to previous cutting-edge competitors. Especially, on the 95HD and ASD metrics, our approach achieves a notable improvement of at least 6%, highlighting the significant advancements. The code is available at https://github.com/Y-TARL/C3S3.

cs.CV↗