Jiahe Chen

Viet Duong, Qiong Wu, Zhengyi Zhou et al.

Out-of-distribution (OOD) detection identifies test samples that differ from the training data, which is critical to ensuring the safety and reliability of machine learning (ML) systems. While a plethora of methods have been developed to detect uni-modal OOD samples, only a few have focused on multi-modal OOD detection. Current contrastive learning-based methods primarily study multi-modal OOD detection in a scenario where both a given image and its corresponding textual description come from a new domain. However, real-world deployments of ML systems may face more anomaly scenarios caused by multiple factors like sensor faults, bad weather, and environmental changes. Hence, the goal of this work is to simultaneously detect from multiple different OOD scenarios in a fine-grained manner. To reach this goal, we propose a general-purpose weakly-supervised OOD detection framework, called WOOD, that combines a binary classifier and a contrastive learning component to reap the benefits of both. In order to better distinguish the latent representations of in-distribution (ID) and OOD samples, we adopt the Hinge loss to constrain their similarity. Furthermore, we develop a new scoring metric to integrate the prediction results from both the binary classifier and contrastive learning for identifying OOD samples. We evaluate the proposed WOOD model on multiple real-world datasets, and the experimental results demonstrate that the WOOD model outperforms the state-of-the-art methods for multi-modal OOD detection. Importantly, our approach is able to achieve high accuracy in OOD detection in three different OOD scenarios simultaneously. The source code will be made publicly available upon publication.

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.

Jiahe Chen, Jiahe Ying, Shen Wang et al.

Confronting the critical challenge of insufficiently annotated samples in medical domain, semi-supervised medical image segmentation (SSMIS) emerges as a promising solution. Specifically, most methodologies following the Mean Teacher (MT) or Dual Students (DS) architecture have achieved commendable results. However, to date, these approaches face a performance bottleneck due to two inherent limitations, \textit{e.g.}, the over-coupling problem within MT structure owing to the employment of exponential moving average (EMA) mechanism, as well as the severe cognitive bias between two students of DS structure, both of which potentially lead to reduced efficacy, or even model collapse eventually. To mitigate these issues, a Decoupled Competitive Framework (DCF) is elaborated in this work, which utilizes a straightforward competition mechanism for the update of EMA, effectively decoupling students and teachers in a dynamical manner. In addition, the seamless exchange of invaluable and precise insights is facilitated among students, guaranteeing a better learning paradigm. The DCF introduced undergoes rigorous validation on three publicly accessible datasets, which encompass both 2D and 3D datasets. The results demonstrate the superiority of our method over previous cutting-edge competitors. Code will be available at https://github.com/JiaheChen2002/DCF.

Qiyuan Chen, Jiahe Chen, Hongsen Huang et al.

The paradigm shift from traditional ranked-based search to Generative Search Engines has rendered conventional SEO metrics obsolete, creating an urgent need to understand, measure, and optimize for content influence on synthesized answers. This paper introduces a comprehensive, end-to-end framework for Generative Search Engine Optimization (GSEO) to address this challenge. We make two primary contributions. First, we construct CC-GSEO-Bench, a large-scale, content-centric benchmark, and propose a multi-dimensional evaluation framework that systematically quantifies influence, moving beyond surface-level attribution to assess substantive semantic impact. Second, we design a novel multi-agent system that operationalizes this framework, automating the strategic refinement of content through a collaborative analyze-revise-evaluate workflow. Our empirical analysis using this framework reveals novel insights into the dynamics of content influence, offering actionable strategies for creators and establishing a principled foundation for future GSEO research.

Qiyuan Chen, Hongsen Huang, Qian Shao et al.

Large Language Models (LLMs) require high quality preference datasets to align with human preferences. However, conventional methods for constructing such datasets face significant challenges: reliance on pre-collected instructions often leads to distribution mismatches with target models, while the need for sampling multiple stochastic responses introduces substantial computational overhead. In this work, we explore a paradigm shift by leveraging inherent regulation of LLMs' representation space for efficient and tailored preference dataset construction, named Icon$^{2}$. Specifically, it first extracts layer-wise direction vectors to encode sophisticated human preferences and then uses these vectors to filter self-synthesized instructions based on their inherent consistency. During decoding, bidirectional inherent control is applied to steer token representations, enabling the precise generation of response pairs with clear alignment distinctions. Experimental results demonstrate significant improvements in both alignment and efficiency. Llama3-8B and Qwen2-7B achieve an average win rate improvement of 13.89% on AlpacaEval 2.0 and 13.45% on Arena-Hard, while reducing computational costs by up to 48.1%.

Jiahe Chen, Naoki Tomii, Ichiro Sakuma et al.

Tissue deformation recovery based on stereo endoscopic images is crucial for tool-tissue interaction analysis and benefits surgical navigation and autonomous soft tissue manipulation. Previous research suffers from the problems raised from camera motion, occlusion, large tissue deformation, lack of tissue-specific biomechanical priors, and reliance on offline processing. Unlike previous studies where the tissue geometry and deformation are represented by 3D points and displacements, the proposed method models tissue geometry as the 3D point and derivative map and tissue deformation as the 3D displacement and local deformation map. For a single surface point, 6 parameters are used to describe its rigid motion and 3 parameters for its local deformation. The method is formulated under the camera-centric setting, where all motions are regarded as the scene motion with respect to the camera. Inter-frame alignment is realized by optimizing the inter-frame deformation, making it unnecessary to estimate camera pose. The concept of the canonical map is introduced to optimize tissue geometry and deformation in an online approach. Quantitative and qualitative experiments were conducted using in vivo and ex vivo laparoscopic datasets. With the inputs of depth and optical flow, the method stably models tissue geometry and deformation even when the tissue is partially occluded or moving outside the field of view. Results show that the 3D reconstruction accuracy in the non-occluded and occluded areas reaches 0.37$\pm$0.27 mm and 0.39$\pm$0.21 mm in terms of surface distance, respectively. The method can also estimate surface strain distribution during various manipulations as an extra modality for mechanical-based analysis.