Yadong Wang

Yuhan Li, Wei Shen, Jianbo Gao et al.

Community Question Answering (CQA) platforms contain plenty of CQA texts (i.e., questions and answers corresponding to the question) where named entities appear ubiquitously. In this paper, we define a new task of CQA entity linking (CQAEL) as linking the textual entity mentions detected from CQA texts with their corresponding entities in a knowledge base. This task can facilitate many downstream applications including expert finding and knowledge base enrichment. Traditional entity linking methods mainly focus on linking entities in news documents, and are suboptimal over this new task of CQAEL since they cannot effectively leverage various informative auxiliary data involved in the CQA platform to aid entity linking, such as parallel answers and two types of meta-data (i.e., topic tags and users). To remedy this crucial issue, we propose a novel transformer-based framework to effectively harness the knowledge delivered by different kinds of auxiliary data to promote the linking performance. We validate the superiority of our framework through extensive experiments over a newly released CQAEL data set against state-of-the-art entity linking methods.

Xianya Fang, Xianying Luo, Yadong Wang et al.

Despite the intrinsic risk-awareness of Large Language Models (LLMs), current defenses often result in shallow safety alignment, rendering models vulnerable to disguised attacks (e.g., prefilling) while degrading utility. To bridge this gap, we propose SafeThinker, an adaptive framework that dynamically allocates defensive resources via a lightweight gateway classifier. Based on the gateway's risk assessment, inputs are routed through three distinct mechanisms: (i) a Standardized Refusal Mechanism for explicit threats to maximize efficiency; (ii) a Safety-Aware Twin Expert (SATE) module to intercept deceptive attacks masquerading as benign queries; and (iii) a Distribution-Guided Think (DDGT) component that adaptively intervenes during uncertain generation. Experiments show that SafeThinker significantly lowers attack success rates across diverse jailbreak strategies without compromising utility, demonstrating that coordinating intrinsic judgment throughout the generation process effectively balances robustness and practicality.

Zheming Xing, Siyuan Zhou, Ruinan Wang et al.

Accurate prediction of synthetic lethality (SL) is important for guiding the development of cancer drugs and therapies. SL prediction faces significant challenges in the effective fusion of heterogeneous multi-source data. Existing multimodal methods often suffer from "modality laziness" due to disparate convergence speeds, which hinders the exploitation of complementary information. This is also one reason why most existing SL prediction models cannot perform well on both pan-cancer and single-cancer SL pair prediction. In this study, we propose SynLeaF, a dual-stage multimodal fusion framework for SL prediction across pan- and single-cancer contexts. The framework employs a VAE-based cross-encoder with a product of experts mechanism to fuse four omics data types (gene expression, mutation, methylation, and CNV), while simultaneously utilizing a relational graph convolutional network to capture structured gene representations from biomedical knowledge graphs. To mitigate modality laziness, SynLeaF introduces a dual-stage training mechanism employing featurelevel knowledge distillation with adaptive uni-modal teacher and ensemble strategies. In extensive experiments across eight specific cancer types and a pancancer dataset, SynLeaF achieves superior performance in 17 out of 19 scenarios. Ablation studies and gradient analyses further validate the critical contributions of the proposed fusion and distillation mechanisms to model robustness and generalization. To facilitate community use, a web server is available at https://synleaf.bioinformatics-lilab.cn.

Beibei Wang, Boyue Cui, Shiqu Chen et al.

Motivation: In recent years, protein function prediction has broken through the bottleneck of sequence features, significantly improving prediction accuracy using high-precision protein structures predicted by AlphaFold2. While single-species protein function prediction methods have achieved remarkable success, multi-species protein function prediction methods are still in the stage of using PPI networks and sequence features. Providing effective cross-species label propagation for species with sparse protein annotations remains a challenging issue. To address this problem, we propose the MSNGO model, which integrates structural features and network propagation methods. Our validation shows that using structural features can significantly improve the accuracy of multi-species protein function prediction. Results: We employ graph representation learning techniques to extract amino acid representations from protein structure contact maps and train a structural model using a graph convolution pooling module to derive protein-level structural features. After incorporating the sequence features from ESM-2, we apply a network propagation algorithm to aggregate information and update node representations within a heterogeneous network. The results demonstrate that MSNGO outperforms previous multi-species protein function prediction methods that rely on sequence features and PPI networks. Availability: https://github.com/blingbell/MSNGO.

Yadong Wang, Haodong Chen, Yu Tian et al.

Latent reasoning compresses the chain-of-thought (CoT) into continuous hidden states, yet existing methods rely on dense latent transitions that remain difficult to interpret and control. Meanwhile, sparse representation models uncover human-interpretable semantic features but remain largely confined to post-hoc analysis. We reconcile this tension by proposing LSTR (Latent Sparse Transcoder Reasoning), a latent reasoning framework that elevates functional sparse transcoders into active reasoning operators to perform multi-step computation through sparse semantic transitions. At its core, LSTR employs a Latent Transition Transcoder (LTT) with a residual skip architecture that decouples linear manifold transport from sparse semantic updates, enabling controllable semantic resolution via explicit sparsity constraints. Extensive experiments show that LSTR preserves reasoning accuracy and compression efficiency while substantially improving interpretability over dense latent baselines. Causal interventions and trajectory analyses further demonstrate that these sparse features act as both interpretable and causally effective operators in the reasoning process.

Dong Zhao, Yadong Wang, Xiang Chen et al.

Large Language Models (LLMs) show remarkable potential for few-shot information extraction (IE), yet their performance is highly sensitive to the choice of in-context examples. Conventional selection strategies often fail to provide informative guidance, as they overlook a key source of model fallibility: confusion stemming not just from semantic content, but also from the generation of well-structured formats required by IE tasks. To address this, we introduce Active Prompting for Information Extraction (APIE), a novel active prompting framework guided by a principle we term introspective confusion. Our method empowers an LLM to assess its own confusion through a dual-component uncertainty metric that uniquely quantifies both Format Uncertainty (difficulty in generating correct syntax) and Content Uncertainty (inconsistency in extracted semantics). By ranking unlabeled data with this comprehensive score, our framework actively selects the most challenging and informative samples to serve as few-shot exemplars. Extensive experiments on four benchmarks show that our approach consistently outperforms strong baselines, yielding significant improvements in both extraction accuracy and robustness. Our work highlights the critical importance of a fine-grained, dual-level view of model uncertainty when it comes to building effective and reliable structured generation systems.

Shengtao Wen, Haodong Chen, Yadong Wang et al.

Knowledge editing (KE) provides a scalable approach for updating factual knowledge in large language models without full retraining. While previous studies have demonstrated effectiveness in general domains and medical QA tasks, little attention has been paid to KE in multimodal medical scenarios. Unlike text-only settings, medical KE demands integrating updated knowledge with visual reasoning to support safe and interpretable clinical decisions. To address this gap, we propose MultiMedEdit, the first benchmark tailored to evaluating KE in clinical multimodal tasks. Our framework spans both understanding and reasoning task types, defines a three-dimensional metric suite (reliability, generality, and locality), and supports cross-paradigm comparisons across general and domain-specific models. We conduct extensive experiments under single-editing and lifelong-editing settings. Results suggest that current methods struggle with generalization and long-tail reasoning, particularly in complex clinical workflows. We further present an efficiency analysis (e.g., edit latency, memory footprint), revealing practical trade-offs in real-world deployment across KE paradigms. Overall, MultiMedEdit not only reveals the limitations of current approaches but also provides a solid foundation for developing clinically robust knowledge editing techniques in the future.

Yi Lu, Yadong Wang, Xingbo Jiang et al.

Infrared images captured under turbulent conditions are degraded by complex geometric distortions and blur. We address infrared deturbulence as an image restoration task, proposing DparNet, a parameter-assisted multi-frame network with a wide & deep architecture. DparNet learns a degradation prior (key parameter matrix) directly from degraded images without external knowledge. Its wide & deep architecture uses these learned parameters to directly modulate restoration, achieving spatially and intensity adaptive results. Evaluated on dedicated infrared deturbulence (49,744 images) and visible image denoising (109,536 images) datasets, DparNet significantly outperforms State-of-the-Art (SOTA) methods in restoration performance and efficiency. Notably, leveraging these parameters improves PSNR by 0.6-1.1 dB with less than 2% increase in model parameters and computational complexity. Our work demonstrates that degraded images hide key degradation information that can be learned and utilized to boost adaptive image restoration.

Lei Ma, Fuyuan Zhang, Minhui Xue et al.

Deep learning (DL) has achieved remarkable progress over the past decade and been widely applied to many safety-critical applications. However, the robustness of DL systems recently receives great concerns, such as adversarial examples against computer vision systems, which could potentially result in severe consequences. Adopting testing techniques could help to evaluate the robustness of a DL system and therefore detect vulnerabilities at an early stage. The main challenge of testing such systems is that its runtime state space is too large: if we view each neuron as a runtime state for DL, then a DL system often contains massive states, rendering testing each state almost impossible. For traditional software, combinatorial testing (CT) is an effective testing technique to reduce the testing space while obtaining relatively high defect detection abilities. In this paper, we perform an exploratory study of CT on DL systems. We adapt the concept in CT and propose a set of coverage criteria for DL systems, as well as a CT coverage guided test generation technique. Our evaluation demonstrates that CT provides a promising avenue for testing DL systems. We further pose several open questions and interesting directions for combinatorial testing of DL systems.

Lei Ma, Fuyuan Zhang, Jiyuan Sun et al.

Deep learning (DL) defines a new data-driven programming paradigm where the internal system logic is largely shaped by the training data. The standard way of evaluating DL models is to examine their performance on a test dataset. The quality of the test dataset is of great importance to gain confidence of the trained models. Using an inadequate test dataset, DL models that have achieved high test accuracy may still lack generality and robustness. In traditional software testing, mutation testing is a well-established technique for quality evaluation of test suites, which analyzes to what extent a test suite detects the injected faults. However, due to the fundamental difference between traditional software and deep learning-based software, traditional mutation testing techniques cannot be directly applied to DL systems. In this paper, we propose a mutation testing framework specialized for DL systems to measure the quality of test data. To do this, by sharing the same spirit of mutation testing in traditional software, we first define a set of source-level mutation operators to inject faults to the source of DL (i.e., training data and training programs). Then we design a set of model-level mutation operators that directly inject faults into DL models without a training process. Eventually, the quality of test data could be evaluated from the analysis on to what extent the injected faults could be detected. The usefulness of the proposed mutation testing techniques is demonstrated on two public datasets, namely MNIST and CIFAR-10, with three DL models.

Lei Ma, Felix Juefei-Xu, Fuyuan Zhang et al.

Deep learning (DL) defines a new data-driven programming paradigm that constructs the internal system logic of a crafted neuron network through a set of training data. We have seen wide adoption of DL in many safety-critical scenarios. However, a plethora of studies have shown that the state-of-the-art DL systems suffer from various vulnerabilities which can lead to severe consequences when applied to real-world applications. Currently, the testing adequacy of a DL system is usually measured by the accuracy of test data. Considering the limitation of accessible high quality test data, good accuracy performance on test data can hardly provide confidence to the testing adequacy and generality of DL systems. Unlike traditional software systems that have clear and controllable logic and functionality, the lack of interpretability in a DL system makes system analysis and defect detection difficult, which could potentially hinder its real-world deployment. In this paper, we propose DeepGauge, a set of multi-granularity testing criteria for DL systems, which aims at rendering a multi-faceted portrayal of the testbed. The in-depth evaluation of our proposed testing criteria is demonstrated on two well-known datasets, five DL systems, and with four state-of-the-art adversarial attack techniques against DL. The potential usefulness of DeepGauge sheds light on the construction of more generic and robust DL systems.

Haozhe Xie, Jie Li, Qiaosheng Zhang et al.

Random Projection (RP) technique has been widely applied in many scenarios because it can reduce high-dimensional features into low-dimensional space within short time and meet the need of real-time analysis of massive data. There is an urgent need of dimensionality reduction with fast increase of big genomics data. However, the performance of RP is usually lower. We attempt to improve classification accuracy of RP through combining other reduction dimension methods such as Principle Component Analysis (PCA), Linear Discriminant Analysis (LDA), and Feature Selection (FS). We compared classification accuracy and running time of different combination methods on three microarray datasets and a simulation dataset. Experimental results show a remarkable improvement of 14.77% in classification accuracy of FS followed by RP compared to RP on BC-TCGA dataset. LDA followed by RP also helps RP to yield a more discriminative subspace with an increase of 13.65% on classification accuracy on the same dataset. FS followed by RP outperforms other combination methods in classification accuracy on most of the datasets.