Jiaying He

Yitong Lin, Jiaying He, Jiahe Chen et al.

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.

Jiahe Chen, Jiaying He, Qiyuan Chen et al.

Large Vision-Language Models (LVLMs) face a tug-of-war between powerful linguistic priors and visual evidence, often leading to ``semantic drift'' -- the progressive detachment from visual input that we identify as the root cause of hallucination. While several existing training-free decoding strategies have achieved considerable success, they still suffer from inherent limitations. Many are computationally prohibitive, requiring multiple forward passes through the entire LVLM, while others rely on indirect, heuristic-based proxies that are unreliable correlates for a direct semantic conflict. We propose \textbf{D}ynamic \textbf{L}ogits \textbf{C}alibration (DLC), a novel training-free framework that is the first to cure semantic drift in a direct, dynamic, and efficient manner. At each decoding step, DLC introduces a real-time visual referee that performs a dual-aspect visual alignment check: (1) it assesses the intrinsic visual relevance of a candidate token and (2) its contextual visual coherence. By dynamically balancing these two checks and evaluating them against an adaptive baseline, DLC surgically modulates the output logits to favor grounded tokens. Extensive experiments show DLC significantly outperforms existing methods in mitigating hallucinations while, crucially, maintaining high inference efficiency by avoiding costly multiple LVLM forward passes. Our work presents a powerful and practical solution for building more reliable and visually-grounded LVLMs. Code will be released on https://github.com/JiaheChen2002/DLC.

Jiaying He, Yitong Lin, Jiahe Chen et al.

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.