MPRM: A Markov Path-based Rule Miner for Efficient and Interpretable Knowledge Graph Reasoning

Rule mining in knowledge graphs enables interpretable link prediction. However, deep learning-based rule mining methods face significant memory and time challenges for large-scale knowledge graphs, whereas traditional approaches, limited by rigid confidence metrics, incur high computational costs despite sampling techniques. To address these challenges, we propose MPRM, a novel rule mining method that models rule-based inference as a Markov chain and uses an efficient confidence metric derived from aggregated path probabilities, significantly lowering computational demands. Experiments on multiple datasets show that MPRM efficiently mines knowledge graphs with over a million facts, sampling less than 1% of facts on a single CPU in 22 seconds, while preserving interpretability and boosting inference accuracy by up to 11% over baselines.

One Shot Dominance: Knowledge Poisoning Attack on Retrieval-Augmented Generation Systems

Large Language Models (LLMs) enhanced with Retrieval-Augmented Generation (RAG) have shown improved performance in generating accurate responses. However, the dependence on external knowledge bases introduces potential security vulnerabilities, particularly when these knowledge bases are publicly accessible and modifiable. Poisoning attacks on knowledge bases for RAG systems face two fundamental challenges: the injected malicious content must compete with multiple authentic documents retrieved by the retriever, and LLMs tend to trust retrieved information that aligns with their internal memorized knowledge. Previous works attempt to address these challenges by injecting multiple malicious documents, but such saturation attacks are easily detectable and impractical in real-world scenarios. To enable the effective single document poisoning attack, we propose AuthChain, a novel knowledge poisoning attack method that leverages Chain-of-Evidence theory and authority effect to craft more convincing poisoned documents. AuthChain generates poisoned content that establishes strong evidence chains and incorporates authoritative statements, effectively overcoming the interference from both authentic documents and LLMs' internal knowledge. Extensive experiments across six popular LLMs demonstrate that AuthChain achieves significantly higher attack success rates while maintaining superior stealthiness against RAG defense mechanisms compared to state-of-the-art baselines.

Exploring Semantic Feature Discrimination for Perceptual Image Super-Resolution and Opinion-Unaware No-Reference Image Quality Assessment

Generative Adversarial Networks (GANs) have been widely applied to image super-resolution (SR) to enhance the perceptual quality. However, most existing GAN-based SR methods typically perform coarse-grained discrimination directly on images and ignore the semantic information of images, making it challenging for the super resolution networks (SRN) to learn fine-grained and semantic-related texture details. To alleviate this issue, we propose a semantic feature discrimination method, SFD, for perceptual SR. Specifically, we first design a feature discriminator (Feat-D), to discriminate the pixel-wise middle semantic features from CLIP, aligning the feature distributions of SR images with that of high-quality images. Additionally, we propose a text-guided discrimination method (TG-D) by introducing learnable prompt pairs (LPP) in an adversarial manner to perform discrimination on the more abstract output feature of CLIP, further enhancing the discriminative ability of our method. With both Feat-D and TG-D, our SFD can effectively distinguish between the semantic feature distributions of low-quality and high-quality images, encouraging SRN to generate more realistic and semantic-relevant textures. Furthermore, based on the trained Feat-D and LPP, we propose a novel opinion-unaware no-reference image quality assessment (OU NR-IQA) method, SFD-IQA, greatly improving OU NR-IQA performance without any additional targeted training. Extensive experiments on classical SISR, real-world SISR, and OU NR-IQA tasks demonstrate the effectiveness of our proposed methods.

A Generalist Cross-Domain Molecular Learning Framework for Structure-Based Drug Discovery

Structure-based drug discovery (SBDD) is a systematic scientific process that develops new drugs by leveraging the detailed physical structure of the target protein. Recent advancements in pre-trained models for biomolecules have demonstrated remarkable success across various biochemical applications, including drug discovery and protein engineering. However, in most approaches, the pre-trained models primarily focus on the characteristics of either small molecules or proteins, without delving into their binding interactions which are essential cross-domain relationships pivotal to SBDD. To fill this gap, we propose a general-purpose foundation model named BIT (an abbreviation for Biomolecular Interaction Transformer), which is capable of encoding a range of biochemical entities, including small molecules, proteins, and protein-ligand complexes, as well as various data formats, encompassing both 2D and 3D structures. Specifically, we introduce Mixture-of-Domain-Experts (MoDE) to handle the biomolecules from diverse biochemical domains and Mixture-of-Structure-Experts (MoSE) to capture positional dependencies in the molecular structures. The proposed mixture-of-experts approach enables BIT to achieve both deep fusion and domain-specific encoding, effectively capturing fine-grained molecular interactions within protein-ligand complexes. Then, we perform cross-domain pre-training on the shared Transformer backbone via several unified self-supervised denoising tasks. Experimental results on various benchmarks demonstrate that BIT achieves exceptional performance in downstream tasks, including binding affinity prediction, structure-based virtual screening, and molecular property prediction.

Mimicking the Familiar: Dynamic Command Generation for Information Theft Attacks in LLM Tool-Learning System

Information theft attacks pose a significant risk to Large Language Model (LLM) tool-learning systems. Adversaries can inject malicious commands through compromised tools, manipulating LLMs to send sensitive information to these tools, which leads to potential privacy breaches. However, existing attack approaches are black-box oriented and rely on static commands that cannot adapt flexibly to the changes in user queries and the invocation chain of tools. It makes malicious commands more likely to be detected by LLM and leads to attack failure. In this paper, we propose AutoCMD, a dynamic attack comment generation approach for information theft attacks in LLM tool-learning systems. Inspired by the concept of mimicking the familiar, AutoCMD is capable of inferring the information utilized by upstream tools in the toolchain through learning on open-source systems and reinforcement with target system examples, thereby generating more targeted commands for information theft. The evaluation results show that AutoCMD outperforms the baselines with +13.2% $ASR_{Theft}$, and can be generalized to new tool-learning systems to expose their information leakage risks. We also design four defense methods to effectively protect tool-learning systems from the attack.

GENERator: A Long-Context Generative Genomic Foundation Model

Advancements in DNA sequencing technologies have significantly improved our ability to decode genomic sequences. However, the prediction and interpretation of these sequences remain challenging due to the intricate nature of genetic material. Large language models (LLMs) have introduced new opportunities for biological sequence analysis. Recent developments in genomic language models have underscored the potential of LLMs in deciphering DNA sequences. Nonetheless, existing models often face limitations in robustness and application scope, primarily due to constraints in model structure and training data scale. To address these limitations, we present GENERator, a generative genomic foundation model featuring a context length of 98k base pairs (bp) and 1.2B parameters. Trained on an expansive dataset comprising 386B bp of eukaryotic DNA, the GENERator demonstrates state-of-the-art performance across both established and newly proposed benchmarks. The model adheres to the central dogma of molecular biology, accurately generating protein-coding sequences that translate into proteins structurally analogous to known families. It also shows significant promise in sequence optimization, particularly through the prompt-responsive generation of promoter sequences with specific activity profiles. These capabilities position the GENERator as a pivotal tool for genomic research and biotechnological advancement, enhancing our ability to interpret and predict complex biological systems and enabling precise genomic interventions.

Unpaired Translation of Point Clouds for Modeling Detector Response

Modeling detector response is a key challenge in time projection chambers. We cast this problem as an unpaired point cloud translation task, between data collected from simulations and from experimental runs. Effective translation can assist with both noise rejection and the construction of high-fidelity simulators. Building on recent work in diffusion probabilistic models, we present a novel framework for performing this mapping. We demonstrate the success of our approach in both synthetic domains and in data sourced from the Active-Target Time Projection Chamber.

SpikSSD: Better Extraction and Fusion for Object Detection with Spiking Neuron Networks

As the third generation of neural networks, Spiking Neural Networks (SNNs) have gained widespread attention due to their low energy consumption and biological interpretability. Recently, SNNs have made considerable advancements in computer vision. However, efficiently conducting feature extraction and fusion under the spiking characteristics of SNNs for object detection remains a pressing challenge. To address this problem, we propose the SpikSSD, a novel Spiking Single Shot Multibox Detector. Specifically, we design a full-spiking backbone network, MDS-ResNet, which effectively adjusts the membrane synaptic input distribution at each layer, achieving better spiking feature extraction. Additionally, for spiking feature fusion, we introduce the Spiking Bi-direction Fusion Module (SBFM), which for the first time realizes bi-direction fusion of spiking features, enhancing the multi-scale detection capability of the model. Experimental results show that SpikSSD achieves 40.8\% mAP on the GEN1 dataset, 76.3\% and 52.4\% mAP@0.5 on VOC 2007 and COCO 2017 datasets respectively with the lowest firing rate, outperforming existing SNN-based approaches at ultralow energy consumption. This work sets a new benchmark for future research in SNN-based object detection. Our code is publicly available in https://github.com/yimeng-fan/SpikSSD.

ProtCLIP: Function-Informed Protein Multi-Modal Learning

Multi-modality pre-training paradigm that aligns protein sequences and biological descriptions has learned general protein representations and achieved promising performance in various downstream applications. However, these works were still unable to replicate the extraordinary success of language-supervised visual foundation models due to the ineffective usage of aligned protein-text paired data and the lack of an effective function-informed pre-training paradigm. To address these issues, this paper curates a large-scale protein-text paired dataset called ProtAnno with a property-driven sampling strategy, and introduces a novel function-informed protein pre-training paradigm. Specifically, the sampling strategy determines selecting probability based on the sample confidence and property coverage, balancing the data quality and data quantity in face of large-scale noisy data. Furthermore, motivated by significance of the protein specific functional mechanism, the proposed paradigm explicitly model protein static and dynamic functional segments by two segment-wise pre-training objectives, injecting fine-grained information in a function-informed manner. Leveraging all these innovations, we develop ProtCLIP, a multi-modality foundation model that comprehensively represents function-aware protein embeddings. On 22 different protein benchmarks within 5 types, including protein functionality classification, mutation effect prediction, cross-modal transformation, semantic similarity inference and protein-protein interaction prediction, our ProtCLIP consistently achieves SOTA performance, with remarkable improvements of 75% on average in five cross-modal transformation benchmarks, 59.9% in GO-CC and 39.7% in GO-BP protein function prediction. The experimental results verify the extraordinary potential of ProtCLIP serving as the protein multi-modality foundation model.

What External Knowledge is Preferred by LLMs? Characterizing and Exploring Chain of Evidence in Imperfect Context

Incorporating external knowledge into large language models (LLMs) has emerged as a promising approach to mitigate outdated knowledge and hallucination in LLMs. However, external knowledge is often imperfect. In addition to useful knowledge, external knowledge is rich in irrelevant or misinformation in the context that can impair the reliability of LLM responses. This paper focuses on LLMs' preferred external knowledge in imperfect contexts when handling multi-hop QA. Inspired by criminal procedural law's Chain of Evidence (CoE), we characterize that knowledge preferred by LLMs should maintain both relevance to the question and mutual support among knowledge pieces. Accordingly, we propose an automated CoE discrimination approach and explore LLMs' preferences from their effectiveness, faithfulness and robustness, as well as CoE's usability in a naive Retrieval-Augmented Generation (RAG) case. The evaluation on five LLMs reveals that CoE enhances LLMs through more accurate generation, stronger answer faithfulness, better robustness against knowledge conflict, and improved performance in a popular RAG case.