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.

From Allies to Adversaries: Manipulating LLM Tool-Calling through Adversarial Injection

Tool-calling has changed Large Language Model (LLM) applications by integrating external tools, significantly enhancing their functionality across diverse tasks. However, this integration also introduces new security vulnerabilities, particularly in the tool scheduling mechanisms of LLM, which have not been extensively studied. To fill this gap, we present ToolCommander, a novel framework designed to exploit vulnerabilities in LLM tool-calling systems through adversarial tool injection. Our framework employs a well-designed two-stage attack strategy. Firstly, it injects malicious tools to collect user queries, then dynamically updates the injected tools based on the stolen information to enhance subsequent attacks. These stages enable ToolCommander to execute privacy theft, launch denial-of-service attacks, and even manipulate business competition by triggering unscheduled tool-calling. Notably, the ASR reaches 91.67% for privacy theft and hits 100% for denial-of-service and unscheduled tool calling in certain cases. Our work demonstrates that these vulnerabilities can lead to severe consequences beyond simple misuse of tool-calling systems, underscoring the urgent need for robust defensive strategies to secure LLM Tool-calling systems.

Through the Curved Cover: Synthesizing Cover Aberrated Scenes with Refractive Field

Recent extended reality headsets and field robots have adopted covers to protect the front-facing cameras from environmental hazards and falls. The surface irregularities on the cover can lead to optical aberrations like blurring and non-parametric distortions. Novel view synthesis methods like NeRF and 3D Gaussian Splatting are ill-equipped to synthesize from sequences with optical aberrations. To address this challenge, we introduce SynthCover to enable novel view synthesis through protective covers for downstream extended reality applications. SynthCover employs a Refractive Field that estimates the cover's geometry, enabling precise analytical calculation of refracted rays. Experiments on synthetic and real-world scenes demonstrate our method's ability to accurately model scenes viewed through protective covers, achieving a significant improvement in rendering quality compared to prior methods. We also show that the model can adjust well to various cover geometries with synthetic sequences captured with covers of different surface curvatures. To motivate further studies on this problem, we provide the benchmarked dataset containing real and synthetic walkable scenes captured with protective cover optical aberrations.