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Haoran Li, Xingjian Li, Jiahua Shi, Huaming Chen, Bo Du, Daisuke Kihara, Johan Barthelemy, Jun Shen, Min Xu

Cryo-Electron Tomography (cryo-ET) is a 3D imaging technology that facilitates the study of macromolecular structures at near-atomic resolution. Recent volumetric segmentation approaches on cryo-ET images have drawn widespread interest in the biological sector. However, existing methods heavily rely on manually labeled data, which requires highly professional skills, thereby hindering the adoption of fully-supervised approaches for cryo-ET images. Some unsupervised domain adaptation (UDA) approaches have been designed to enhance the segmentation network performance using unlabeled data. However, applying these methods directly to cryo-ET image segmentation tasks remains challenging due to two main issues: 1) the source dataset, usually obtained through simulation, contains a fixed level of noise, while the target dataset, directly collected from raw-data from the real-world scenario, have unpredictable noise levels. 2) the source data used for training typically consists of known macromoleculars. In contrast, the target domain data are often unknown, causing the model to be biased towards those known macromolecules, leading to a domain shift problem. To address such challenges, in this work, we introduce a voxel-wise unsupervised domain adaptation approach, termed Vox-UDA, specifically for cryo-ET subtomogram segmentation. Vox-UDA incorporates a noise generation module to simulate target-like noises in the source dataset for cross-noise level adaptation. Additionally, we propose a denoised pseudo-labeling strategy based on the improved Bilateral Filter to alleviate the domain shift problem. More importantly, we construct the first UDA cryo-ET subtomogram segmentation benchmark on three experimental datasets. Extensive experimental results on multiple benchmarks and newly curated real-world datasets demonstrate the superiority of our proposed approach compared to state-of-the-art UDA methods.

Haoran Li, Yulin Chen, Zihao Zheng, Qi Hu, Chunkit Chan, Heshan Liu, Yangqiu Song

With rapid advances, generative large language models (LLMs) dominate various Natural Language Processing (NLP) tasks from understanding to reasoning. Yet, language models' inherent vulnerabilities may be exacerbated due to increased accessibility and unrestricted model training on massive data. A malicious adversary may publish poisoned data online and conduct backdoor attacks on the victim LLMs pre-trained on the poisoned data. Backdoored LLMs behave innocuously for normal queries and generate harmful responses when the backdoor trigger is activated. Despite significant efforts paid to LLMs' safety issues, LLMs are still struggling against backdoor attacks. As Anthropic recently revealed, existing safety training strategies, including supervised fine-tuning (SFT) and Reinforcement Learning from Human Feedback (RLHF), fail to revoke the backdoors once the LLM is backdoored during the pre-training stage. In this paper, we present Simulate and Eliminate (SANDE) to erase the undesired backdoored mappings for generative LLMs. We initially propose Overwrite Supervised Fine-tuning (OSFT) for effective backdoor removal when the trigger is known. Then, to handle scenarios where trigger patterns are unknown, we integrate OSFT into our two-stage framework, SANDE. Unlike other works that assume access to cleanly trained models, our safety-enhanced LLMs are able to revoke backdoors without any reference. Consequently, our safety-enhanced LLMs no longer produce targeted responses when the backdoor triggers are activated. We conduct comprehensive experiments to show that our proposed SANDE is effective against backdoor attacks while bringing minimal harm to LLMs' powerful capability.

Hao Li, Ruoyuan Gong, Hao Jiang

Predicting roll call votes through modeling political actors has emerged as a focus in quantitative political science and computer science. Widely used embedding-based methods generate vectors for legislators from diverse data sets to predict legislative behaviors. However, these methods often contend with challenges such as the need for manually predefined features, reliance on extensive training data, and a lack of interpretability. Achieving more interpretable predictions under flexible conditions remains an unresolved issue. This paper introduces the Political Actor Agent (PAA), a novel agent-based framework that utilizes Large Language Models to overcome these limitations. By employing role-playing architectures and simulating legislative system, PAA provides a scalable and interpretable paradigm for predicting roll-call votes. Our approach not only enhances the accuracy of predictions but also offers multi-view, human-understandable decision reasoning, providing new insights into political actor behaviors. We conducted comprehensive experiments using voting records from the 117-118th U.S. House of Representatives, validating the superior performance and interpretability of PAA. This study not only demonstrates PAA's effectiveness but also its potential in political science research.

Yao Lai, Sungyoung Lee, Guojin Chen, Souradip Poddar, Mengkang Hu, David Z. Pan, Ping Luo

Analog circuit design is a significant task in modern chip technology, focusing on the selection of component types, connectivity, and parameters to ensure proper circuit functionality. Despite advances made by Large Language Models (LLMs) in digital circuit design, the complexity and scarcity of data in analog circuitry pose significant challenges. To mitigate these issues, we introduce AnalogCoder, the first training-free LLM agent for designing analog circuits through Python code generation. Firstly, AnalogCoder incorporates a feedback-enhanced flow with tailored domain-specific prompts, enabling the automated and self-correcting design of analog circuits with a high success rate. Secondly, it proposes a circuit tool library to archive successful designs as reusable modular sub-circuits, simplifying composite circuit creation. Thirdly, extensive experiments on a benchmark designed to cover a wide range of analog circuit tasks show that AnalogCoder outperforms other LLM-based methods. It has successfully designed 20 circuits, 5 more than standard GPT-4o. We believe AnalogCoder can significantly improve the labor-intensive chip design process, enabling non-experts to design analog circuits efficiently.

Feifei Kou, Yuhan Yao, Siyuan Yao, Jiahao Wang, Lei Shi, Yawen Li, Xuejing Kang

Adding imperceptible watermarks to artwork images, such as paintings and photographs, can effectively safeguard the copyright of these images without compromising their usability. However, existing blind watermarking techniques encounter two major challenges in addressing this task: imperceptibility and robustness, particularly when subjected to various noise attacks. In this paper, we propose a blind watermarking method for artwork image copyright protection, IWRN, which can ensure both the Imperceptibility of the Watermark and Robustness against Noise attacks. For imperceptibility, we design a Learnable Wavelet Network (LWN) to adaptively embed the watermark into the high-frequency region where the watermark has better invisibility. For robustness, we establish a Deform-Attention based Invertible Neural Network (DA-INN) with a decoding optimization, which offers the advantage of computational reversion, and combines the deform-attention mechanism and decoding optimization to enhance the model's resistance against noises. Additionally, we design a Joint Contrast Learning (JCL) mechanism to improve imperceptibility and robustness simultaneously. Experiments show that our IWRN outperforms other state-of-the-art blind watermarking methods, achieves an average performance of 41.55 PSNR and 99.57% accuracy on the Coco2017, Wikiart, and Div2k datasets when facing 12 kinds of noise attacks.

Sizhuo Jin, Shuo Chen, Jianjun Qian, Ying Tai, Jun Li

Density Functional Theory (DFT) stands as a widely used and efficient approach for addressing the many-electron Schrödinger equation across various domains such as physics, chemistry, and biology. However, a core challenge that persists over the long term pertains to refining the exchange-correlation (XC) approximation. This approximation significantly influences the triumphs and shortcomings observed in DFT applications. Nonetheless, a prevalent issue among XC approximations is the presence of systematic errors, stemming from deviations from the mathematical properties of the exact XC functional. For example, although both B3LYP and DM21 (DeepMind 21) exhibit improvements over previous benchmarks, there is still potential for further refinement. In this paper, we propose a strategy for enhancing XC approximations by estimating the neural uncertainty of the XC functional, named Residual XC-Uncertain Functional. Specifically, our approach involves training a neural network to predict both the mean and variance of the XC functional, treating it as a Gaussian distribution. To ensure stability in each sampling point, we construct the mean by combining traditional XC approximations with our neural predictions, mitigating the risk of divergence or vanishing values. It is crucial to highlight that our methodology excels particularly in cases where systematic errors are pronounced. Empirical outcomes from three benchmark tests substantiate the superiority of our approach over existing state-of-the-art methods. Our approach not only surpasses related techniques but also significantly outperforms both the popular B3LYP and the recent DM21 methods, achieving average RMSE improvements of 62% and 37%, respectively, across the three benchmarks: W4-17, G21EA, and G21IP.

Pengcheng Jiang, Cao Xiao, Tianfan Fu, Parminder Bhatia, Taha Kass-Hout, Jimeng Sun, Jiawei Han

Molecular representation learning is vital for various downstream applications, including the analysis and prediction of molecular properties and side effects. While Graph Neural Networks (GNNs) have been a popular framework for modeling molecular data, they often struggle to capture the full complexity of molecular representations. In this paper, we introduce a novel method called Gode, which accounts for the dual-level structure inherent in molecules. Molecules possess an intrinsic graph structure and simultaneously function as nodes within a broader molecular knowledge graph. Gode integrates individual molecular graph representations with multi-domain biochemical data from knowledge graphs. By pre-training two GNNs on different graph structures and employing contrastive learning, Gode effectively fuses molecular structures with their corresponding knowledge graph substructures. This fusion yields a more robust and informative representation, enhancing molecular property predictions by leveraging both chemical and biological information. When fine-tuned across 11 chemical property tasks, our model significantly outperforms existing benchmarks, achieving an average ROC-AUC improvement of 12.7% for classification tasks and an average RMSE/MAE improvement of 34.4% for regression tasks. Notably, Gode surpasses the current leading model in property prediction, with advancements of 2.2% in classification and 7.2% in regression tasks.

Zhiheng Huang, Yannan Liu, Daojing He, Yu Li

Membership Inference Attack (MIA) aims to determine if a specific sample is present in the training dataset of a target machine learning model. Previous MIAs against fine-tuned Large Language Models (LLMs) either fail to address the unique challenges in the fine-tuned setting or rely on strong assumption of the training data distribution. This paper proposes a distribution-free MIA framework tailored for fine-tuned LLMs, named DF-MIA. We recognize that samples await to test can serve as a valuable reference dataset for fine-tuning reference models. By enhancing the signals of non-member samples within this reference dataset, we can achieve a more reliable and practical calibration of probabilities, improving the differentiation between members and non-members. Leveraging these insights, we have developed a two-stage framework that employs specially designed data augmentation and perturbation techniques to prioritize the significance of non-members and mitigate the influence of potential members within the reference dataset. We evaluate our method on three representative LLM models ranging from 1B to 8B on three datasets. The results demonstrate that the DF-MIA significantly enhances the performance of MIA.

Yinxuan Huang, Ke Liang, Yanyi Huang, Xiang Zeng, Kai Chen, Bin Zhou

Traditional recommendation system focus more on the correlations between users and items (user-item relationships), while research on user-user relationships has received significant attention these years, which is also known as social recommendation. Graph-based models have achieved a great success in this task by utilizing the complex topological information of the social networks. However, these models still face the insufficient expressive and overfitting problems. Counterfactual approaches are proven effective as information augmentation strategies towards above issues in various scenarios, but not fully utilized in social recommendations. To this end, we propose a novel social recommendation method, termed SR-GCA, via a plug-and-play Graph-Level Counterfactual Augmentation mechanism. Specifically, we first generate counterfactual social and item links by constructing a counterfactual matrix for data aug- mentation. Then, we employ a supervised learning strategy to refine data both factual and counterfactual links. Thirdly, we enhance representations learning between users via an alignment and self-supervised optimization techniques. Extensive experiments demonstrate the promising capacity of our model from five aspects, including superiority, effectively, transfer- ability, complexity, sensitively. In particular, the transferability is well-proven by extending our GCA module to three typical social recommendation models.

Xinlei Huang, Zhiqi Ma, Dian Meng, Yanran Liu, Shiwei Ruan, Qingqiang Sun, Xubin Zheng, Ziyue Qiao

Spatial multi-modal omics technology, highlighted by Nature Methods as an advanced biological technique in 2023, plays a critical role in resolving biological regulatory processes with spatial context. Recently, graph neural networks based on K-nearest neighbor (KNN) graphs have gained prominence in spatial multi-modal omics methods due to their ability to model semantic relations between sequencing spots. However, the fixed KNN graph fails to capture the latent semantic relations hidden by the inevitable data perturbations during the biological sequencing process, resulting in the loss of semantic information. In addition, the common lack of spot annotation and class number priors in practice further hinders the optimization of spatial multi-modal omics models. Here, we propose a novel spatial multi-modal omics resolved framework, termed Prototype-aware Graph Adaptative Aggregation for Spatial Multi-modal Omics Analysis (PRAGA). PRAGA constructs a dynamic graph to capture latent semantic relations and comprehensively integrate spatial information and feature semantics. The learnable graph structure can also denoise perturbations by learning cross-modal knowledge. Moreover, a dynamic prototype contrastive learning is proposed based on the dynamic adaptability of Bayesian Gaussian Mixture Models to optimize the multi-modal omics representations for unknown biological priors. Quantitative and qualitative experiments on simulated and real datasets with 7 competing methods demonstrate the superior performance of PRAGA.

Jingjing Hu, Dan Guo, Zhan Si, Deguang Liu, Yunfeng Diao, Jing Zhang, Jinxing Zhou, Meng Wang

Molecular representation learning plays a crucial role in various downstream tasks, such as molecular property prediction and drug design. To accurately represent molecules, Graph Neural Networks (GNNs) and Graph Transformers (GTs) have shown potential in the realm of self-supervised pretraining. However, existing approaches often overlook the relationship between molecular structure and electronic information, as well as the internal semantic reasoning within molecules. This omission of fundamental chemical knowledge in graph semantics leads to incomplete molecular representations, missing the integration of structural and electronic data. To address these issues, we introduce MOL-Mamba, a framework that enhances molecular representation by combining structural and electronic insights. MOL-Mamba consists of an Atom & Fragment Mamba-Graph (MG) for hierarchical structural reasoning and a Mamba-Transformer (MT) fuser for integrating molecular structure and electronic correlation learning. Additionally, we propose a Structural Distribution Collaborative Training and E-semantic Fusion Training framework to further enhance molecular representation learning. Extensive experiments demonstrate that MOL-Mamba outperforms state-of-the-art baselines across eleven chemical-biological molecular datasets.

Tran Thai Hoa, Tran Quang Duy, Khanh Quoc Tran, Kiet Van Nguyen

The rapid spread of information in the digital age highlights the critical need for effective fact-checking tools, particularly for languages with limited resources, such as Vietnamese. In response to this challenge, we introduce ViFactCheck, the first publicly available benchmark dataset designed specifically for Vietnamese fact-checking across multiple online news domains. This dataset contains 7,232 human-annotated pairs of claim-evidence combinations sourced from reputable Vietnamese online news, covering 12 diverse topics. It has been subjected to a meticulous annotation process to ensure high quality and reliability, achieving a Fleiss Kappa inter-annotator agreement score of 0.83. Our evaluation leverages state-of-the-art pre-trained and large language models, employing fine-tuning and prompting techniques to assess performance. Notably, the Gemma model demonstrated superior effectiveness, with an impressive macro F1 score of 89.90%, thereby establishing a new standard for fact-checking benchmarks. This result highlights the robust capabilities of Gemma in accurately identifying and verifying facts in Vietnamese. To further promote advances in fact-checking technology and improve the reliability of digital media, we have made the ViFactCheck dataset, model checkpoints, fact-checking pipelines, and source code freely available on GitHub. This initiative aims to inspire further research and enhance the accuracy of information in low-resource languages.

Chia-Tung Ho, Haoxing Ren, Brucek Khailany

Due to the growing complexity of modern Integrated Circuits (ICs), automating hardware design can prevent a significant amount of human error from the engineering process and result in less errors. Verilog is a popular hardware description language for designing and modeling digital systems; thus, Verilog generation is one of the emerging areas of research to facilitate the design process. In this work, we propose VerilogCoder, a system of multiple Artificial Intelligence (AI) agents for Verilog code generation, to autonomously write Verilog code and fix syntax and functional errors using collaborative Verilog tools (i.e., syntax checker, simulator, and waveform tracer). Firstly, we propose a task planner that utilizes a novel Task and Circuit Relation Graph retrieval method to construct a holistic plan based on module descriptions. To debug and fix functional errors, we develop a novel and efficient abstract syntax tree (AST)-based waveform tracing tool, which is integrated within the autonomous Verilog completion flow. The proposed methodology successfully generates 94.2% syntactically and functionally correct Verilog code, surpassing the state-of-the-art methods by 33.9% on the VerilogEval-Human v2 benchmark.

Qiang He, Yunting Bao, Hui Fang, Yuting Lin, Hao Sun

Infectious diseases have historically had profound effects on global health, economies, and social structures. Effective tracing of infectious diseases is essential not only for immediate public health responses but also for shaping future prevention strategies. Traditional tracing methods often emphasize homogeneous networks, overlooking the diverse transmission characteristics of heterogeneous populations. This research addresses two critical challenges: the heterogeneity of transmission across various media and modes, and the significant yet underexplored influence of community structures on epidemic spread and tracing.We propose a Heterogeneous Hypergraph Attention Network (HHAN) modelthat accounts for multiple transmission pathways and patterns within heterogeneous networks. HHAN integrates a heterogeneous graph neural network module to handle the complexity of communication among different populations, and an Agent-Based Modeling Module that combines agent-based ideas to model individual behaviors. This approach effectively captures complex interactions within community structures and addresses individual variability. Experimental results on three real-world datasets demonstrate that the HHAN model significantly outperforms other state-of-the-art methods in tackling the complex challenge of tracing infectious diseases in heterogeneous populations.

Meixia He, Peican Zhu, Keke Tang, Yangming Guo

Recent studies have shown that Hypergraph Neural Networks (HGNNs) are vulnerable to adversarial attacks. Existing approaches focus on hypergraph modification attacks guided by gradients, overlooking node spanning in the hypergraph and the group identity of hyperedges, thereby resulting in limited attack performance and detectable attacks. In this manuscript, we present a novel framework, i.e., Hypergraph Attacks via Injecting Homogeneous Nodes into Elite Hyperedges (IE-Attack), to tackle these challenges. Initially, utilizing the node spanning in the hypergraph, we propose the elite hyperedges sampler to identify hyperedges to be injected. Subsequently, a node generator utilizing Kernel Density Estimation (KDE) is proposed to generate the homogeneous node with the group identity of hyperedges. Finally, by injecting the homogeneous node into elite hyperedges, IE-Attack improves the attack performance and enhances the imperceptibility of attacks. Extensive experiments are conducted on five authentic datasets to validate the effectiveness of IE-Attack and the corresponding superiority to state-of-the-art methods.

Harish Haresamudram, Apoorva Beedu, Mashfiqui Rabbi, Sankalita Saha, Irfan Essa, Thomas Ploetz

Cross-modal contrastive pre-training between natural language and other modalities, e.g., vision and audio, has demonstrated astonishing performance and effectiveness across a diverse variety of tasks and domains. In this paper, we investigate whether such natural language supervision can be used for wearable sensor based Human Activity Recognition (HAR), and discover that--surprisingly--it performs substantially worse than standard end-to-end training and self-supervision. We identify the primary causes for this as: sensor heterogeneity and the lack of rich, diverse text descriptions of activities. To mitigate their impact, we also develop strategies and assess their effectiveness through an extensive experimental evaluation. These strategies lead to significant increases in activity recognition, bringing performance closer to supervised and self-supervised training, while also enabling the recognition of unseen activities and cross modal retrieval of videos. Overall, our work paves the way for better sensor-language learning, ultimately leading to the development of foundational models for HAR using wearables.

Zehua Han, Jing Xiao, Qirui Zhao, Zhexuan Cui, Yufeng Wang, Duona Zhang, Wenrui Ding

In complex electromagnetic environments, the identification and differentiation of diverse radio frequency (RF) emitters become particularly crucial. Existing RF fingerprinting methods demonstrate limitations when dealing with numerous unknown emitters, making it challenging for accurate classification and recognition. These limitations hinder the effective handling of specific unknown emitters.To address this issue, we introduce a novel RF fingerprinting method suitable for open-world conditions for the first time. We develop a novel RF fingerprinting model, Roinformer, to extract signal features with positional attention. We then leverage data augmentation strategies such as noise jitter and signal frame rearrangement to construct an effective pre-training model. Moreover, by incorporating instance-level similarity loss and a novel local entropy regularization approach, we significantly enhance the accuracy of known class identification and mitigate the catastrophic forgetting of known signal samples. Experimental results on three temporal signal datasets demonstrate that our method effectively recognizes both the known and unknown classes, outperforming several state-of-the-art methods by a large margin.

Xiao Han, Zijian Zhang, Xiangyu Zhao, Yuanshao Zhu, Guojiang Shen, Xiangjie Kong, Xuetao Wei, Liqiang Nie, Jieping Ye

As urban residents demand higher travel quality, vehicle dispatch has become a critical component of online ride-hailing services. However, current vehicle dispatch systems struggle to navigate the complexities of urban traffic dynamics, including unpredictable traffic conditions, diverse driver behaviors, and fluctuating supply and demand patterns. These challenges have resulted in travel difficulties for passengers in certain areas, while many drivers in other areas are unable to secure orders, leading to a decline in the overall quality of urban transportation services. To address these issues, this paper introduces GARLIC: a framework of GPT-Augmented Reinforcement Learning with Intelligent Control for vehicle dispatching. GARLIC utilizes multiview graphs to capture hierarchical traffic states, and learns a dynamic reward function that accounts for individual driving behaviors. The framework further integrates a GPT model trained with a custom loss function to enable high-precision predictions and optimize dispatching policies in real-world scenarios. Experiments conducted on two real-world datasets demonstrate that GARLIC effectively aligns with driver behaviors while reducing the empty load rate of vehicles.

Rong Han, Xiaohong Liu, Tong Pan, Jing Xu, Xiaoyu Wang, Wuyang Lan, Zhenyu Li, Zixuan Wang, Jiangning Song, Guangyu Wang 等

Accurately measuring protein-RNA binding affinity is crucial in many biological processes and drug design. Previous computational methods for protein-RNA binding affinity prediction rely on either sequence or structure features, unable to capture the binding mechanisms comprehensively. The recent emerging pre-trained language models trained on massive unsupervised sequences of protein and RNA have shown strong representation ability for various in-domain downstream tasks, including binding site prediction. However, applying different-domain language models collaboratively for complex-level tasks remains unexplored. In this paper, we propose CoPRA to bridge pre-trained language models from different biological domains via Complex structure for Protein-RNA binding Affinity prediction. We demonstrate for the first time that cross-biological modal language models can collaborate to improve binding affinity prediction. We propose a Co-Former to combine the cross-modal sequence and structure information and a bi-scope pre-training strategy for improving Co-Former's interaction understanding. Meanwhile, we build the largest protein-RNA binding affinity dataset PRA310 for performance evaluation. We also test our model on a public dataset for mutation effect prediction. CoPRA reaches state-of-the-art performance on all the datasets. We provide extensive analyses and verify that CoPRA can (1) accurately predict the protein-RNA binding affinity; (2) understand the binding affinity change caused by mutations; and (3) benefit from scaling data and model size.

Rong Han, Wenbing Huang, Lingxiao Luo, Xinyan Han, Jiaming Shen, Zhiqiang Zhang, Jun Zhou, Ting Chen

Understanding and leveraging the 3D structures of proteins is central to a variety of biological and drug discovery tasks. While deep learning has been applied successfully for structure-based protein function prediction tasks, current methods usually employ distinct training for each task. However, each of the tasks is of small size, and such a single-task strategy hinders the models' performance and generalization ability. As some labeled 3D protein datasets are biologically related, combining multi-source datasets for larger-scale multi-task learning is one way to overcome this problem. In this paper, we propose a neural network model to address multiple tasks jointly upon the input of 3D protein structures. In particular, we first construct a standard structure-based multi-task benchmark called Protein-MT, consisting of 6 biologically relevant tasks, including affinity prediction and property prediction, integrated from 4 public datasets. Then, we develop a novel graph neural network for multi-task learning, dubbed Heterogeneous Multichannel Equivariant Network (HeMeNet), which is E(3) equivariant and able to capture heterogeneous relationships between different atoms. Besides, HeMeNet can achieve task-specific learning via the task-aware readout mechanism. Extensive evaluations of our benchmark verify the effectiveness of multi-task learning, and our model generally surpasses state-of-the-art models.