论文检索

Xuan Lin, Qingrui Liu, Hongxin Xiang, Daojian Zeng, Xiangxiang Zeng

Chemical reaction and retrosynthesis prediction are fundamental tasks in drug discovery. Recently, large language models (LLMs) have shown potential in many domains. However, directly applying LLMs to these tasks faces two major challenges: (i) lacking a large-scale chemical synthesis-related instruction dataset; (ii) ignoring the close correlation between reaction and retrosynthesis prediction for the existing fine-tuning strategies. To address these challenges, we propose ChemDual, a novel LLM framework for accurate chemical synthesis. Specifically, considering the high cost of data acquisition for reaction and retrosynthesis, ChemDual regards the reaction-and-retrosynthesis of molecules as a related recombination-and-fragmentation process and constructs a large-scale of 4.4 million instruction dataset. Furthermore, ChemDual introduces an enhanced LLaMA, equipped with a multi-scale tokenizer and dual-task learning strategy, to jointly optimize the process of recombination and fragmentation as well as the tasks between reaction and retrosynthesis prediction. Extensive experiments on Mol-Instruction and USPTO-50K datasets demonstrate that ChemDual achieves state-of-the-art performance in both predictions of reaction and retrosynthesis, outperforming the existing conventional single-task approaches and the general open-source LLMs. Through molecular docking analysis, ChemDual generates compounds with diverse and strong protein binding affinity, further highlighting its strong potential in drug design.

Xiaoli Lin, Xiongwei Liao, Jun Pang, Bo Li, Xiaolong Zhang

Efficient generation of targeted drug molecules is crucial in the field of drug discovery. Most existing methods neglect the high-order information in the structure of protein pockets, limiting the performance of generated drug molecules. This paper proposes a pocket-aware drug design framework, namely PAMol, constructing the hypergraph to represent the spatial structure of protein pockets, effectively capturing high-order relations and neighborhood information within the pocket structures. This framework also fuses different modal embeddings from proteins and molecules, to generate high-quality molecules. In addition, a conditional molecule generation module uses the high-order structural information in protein pockets as constraints to more accurately generate molecules for specific targets. The performance of PAMol has been assessed by analyzing generated molecules in terms of vina score, high affinity, QED, SA, LogP, Lipinski, diversity, and time. Experimental results demonstrate the potential of PAMol for targeted drug design. The source code is available at https://github.com/YICHUANSYQ/PAMol.git.

Anchen Lin, Weikun Wang, Haijun Han, Fanwei Zhu, Qi Ma, Zengwei Zheng, Binbin Zhou

Major Depressive Disorder (MDD) is a prevalent and severe mental disease. Functional Magnetic Resonance Imaging (fMRI)-based diagnostic methods, which analyze Functional Connectivity (FC) to identify abnormal functional connections, have shown promise as biomarker-based approaches for diagnosing depression. However, the high costs of fMRI data result in small sample sizes, hindering the effective identification of abnormal FC patterns. Moreover, existing methods often overlook the potential benefits of incorporating domain knowledge into their models. In this paper, we propose KnowMDD, a novel knowledge-guided cross contrastive learning framework for MDD diagnosis. By incorporating domain knowledge and employing data augmentation, KnowMDD addresses data sparsity while improving robustness and interpretability. Specifically, multiple atlases are used to construct complementary brain graph representations. The default mode network, closely associated with depression, is introduced into the contrastive learning paradigm for diverse subgraph augmentations, while an attention mechanism captures global semantic relationships between brain regions. Based on them, a cross contrastive learning is designed to learn robust representations for accurate diagnosis. Extensive experiments demonstrate the effectiveness, robustness, and interpretability of KnowMDD, which outperforms state-of-the-art methods. We also develop a demonstration system to show its practical application.

Zhengze Li, Zilin Song, Tingting Yuan, Xiaoming Fu

Forecasting stock prices is complex and challenging. Uncovering correlations among stocks has proven to enhance stock price forecasting. However, existing correlation discovery methods, such as concept-based methods, are slow, inaccurate, and limited by their reliance on predefined concepts and manual analysis. In this paper, we propose COGRASP, a novel approach for stock price forecasting that constructs stock co-occurrence graphs automatically by analyzing rapidly updated sources such as reports, newspapers, and social media. Besides, we aggregate forecasts across multiple timescales (i.e., long-, medium-, and short-term) to capture multi-timescale trends fluctuations, thereby enhancing price forecasting accuracy. In experiments with real-world open-source stock market data, COGRASP outperforms state-of-the-art methods.

Xuqiang Li, Wenjie Du, Jun Xia, Jianmin Wang, Xiaoqi Wang, Yang Yang, Yang Wang

Accurate prediction of ADMET (Absorption, Distribution, Metabolism, Excretion, and Toxicity) properties is crucial in drug development, as these properties directly impact a drug's efficacy and safety. However, existing multi-task learning models often face challenges related to noise interference and task conflicts when dealing with complex molecular structures. To address these issues, we propose a novel multi-task Graph Neural Network (GNN) model, \textbf{MTGIB-UNet}. The model begins by encoding molecular graphs to capture intricate molecular structure information. Subsequently, based on the Graph Information Bottleneck (GIB) principle, the model compresses the information flow by extracting subgraphs, retaining task-relevant features while removing noise for each task. These embeddings are then fused through a gated network that dynamically adjusts the contribution weights of auxiliary tasks to the primary task. Specifically, an uncertainty weighting (UW) strategy is applied, with additional emphasis placed on the primary task, allowing dynamic adjustment of task weights while strengthening the influence of the primary task on model training. Experiments on standard ADMET datasets demonstrate that our model outperforms existing methods. Additionally, the model shows good interpretability by identifying key molecular substructures related to specific ADMET endpoints.

Xinjie Li, Abhinav Verma

Single-step retrosynthesis is a crucial task in organic synthesis, where the objective is to identify the reactants needed to produce a given product. In recent years, a variety of machine learning methods have been developed to tackle retrosynthesis prediction. In our study, we introduce RetroMoE, a novel generative model designed for the single-step retrosynthesis task. We start with a non-symmetric variational autoencoder (VAE) that incorporates a graph encoder to map molecular graphs into a latent space, followed by a transformer decoder for precise prediction of molecular SMILES strings. Additionally, we implement a simple yet effective mixture-of-experts (MoE) network to translate the product latent embedding into the reactant latent embedding. To our knowledge, this is the first approach that frames single-step retrosynthesis as a latent translation problem. Extensive experiments on the USPTO-50K and USPTO-MIT datasets demonstrate the superiority of our method, which not only surpasses most semi-template-based and template-free methods but also delivers competitive results against template-based methods. Notably, under the class-known setting on the USPTO-50K, our method achieves top-1 exact match accuracy comparable to the state-of-the-art template method, RetroKNN.

Shicheng Li, Jinshan Zhang, Feng Wang

Portfolio selection is a critical task in finance, involving the allocation of resources across various assets. However, current methods often struggle to maintain robust performance due to the inherent low signal-to-noise ratio in raw financial data and shifts in data distribution. We propose AlphaGAT, a novel two-stage learning approach for portfolio selection, designed to adapt to different market scenarios. Inspired by the concept of alpha factors, which transform historical market data into actionable signals, the first stage introduces an advanced model named CATimeMixer for alpha factor generation with a novel loss function to improve the effectiveness and robustness. CATimeMixer integrates TimeMixer with Conv1D (C) and cross-asset Attention (A). Specifically, Conv1D enhances TimeMixer by capturing trend and seasonal features across different scales, while cross-asset attention enables TimeMixer to extract interrelationships between different assets. The second stage applies reinforcement learning to dynamically adjust weights, integrating alpha factors into trading signals. Recognizing the varying effectiveness of alpha factors across different periods, our RL agent innovatively transforms the alpha factors into graphs and employs graph attention networks (GAT) to discern the significance of different alpha factors, enhancing policy robustness. Extensive experiments on real-world market data show that our approach outperforms state-of-the-art methods.

Jiayi Li, Junhua Fang, Pingfu Chao, Jiajie Xu, Pengpeng Zhao

Trajectory similarity aims to identify pairs of similar trajectories, serving as a crucial operation in spatial-temporal data mining. Although several approaches have been proposed, they encounter the following two issues: 1) An overemphasis on spatial similarity in road networks while the rich semantic information embedded in trajectories is not fully exploited; 2) Dependence on Recurrent Neural Network (RNN) architectures would struggle to capture long-term dependencies. To address these limitations, we propose a Dual-branch Attention-based framework with Spatial and Semantic information (DASS) based on self-supervised learning. Specifically, DASS comprises two core components: 1) A trajectory representation module that models spatial-temporal adjacent relationships in the form of graph and converts semantics into numerical embeddings. 2) A backbone encoder with a co-attention module to independently process two features before they are integrated. Extensive experiments on real-world datasets demonstrate that DASS outperforms state-of-the-art methods, establishing itself as a novel paradigm.

Chaozhuo Li, Tianqi Yang, Litian Zhang, Xi Zhang

The prediction of information popularity propagation is critical for applications such as recommendation systems, targeted advertising, and social media trend analysis. Traditional approaches primarily rely on historical cascade data, often sacrificing timeliness for prediction accuracy. These methods capture aggregate diffusion patterns but fail to account for the complex temporal dynamics of early-stage propagation. In this paper, we introduce Diffusion Guided Propagation Augmentation(DGPA), a novel framework designed to improve early-stage popularity prediction. DGPA models cascade dynamics by leveraging a generative approach, where a temporal conditional interpolator serves as a noising process and forecasting as a denoising process. By iteratively generating cascade representations through a sampling procedure, DGPA effectively incorporates the evolving time steps of diffusion, significantly enhancing prediction timeliness and accuracy. Extensive experiments on benchmark datasets from Twitter, Weibo, and APS demonstrate that DGPA outperforms state-of-the-art methods in early-stage popularity prediction.

Liangqi Lei, Keke Gai, Jing Yu, Liehuang Zhu, Qi Wu

Latent diffusion models have exhibited considerable potential in generative tasks. Watermarking is considered to be an alternative to safeguard the copyright of generative models and prevent their misuse. However, in the context of model distribution scenarios, the accessibility of models to large scale of model users brings new challenges to the security, efficiency and robustness of existing watermark solutions. To address these issues, we propose a secure and efficient watermarking solution. A new security mechanism is designed to prevent watermark leakage and watermark escape, which considers watermark randomness and watermark-model association as two constraints for mandatory watermark injection. To reduce the time cost of training the security module, watermark injection and the security mechanism are decoupled, ensuring that fine-tuning VAE only accomplishes the security mechanism without the burden of learning watermark patterns. A watermark distribution-based verification strategy is proposed to enhance the robustness against diverse attacks in the model distribution scenarios. Experimental results prove that our watermarking consistently outperforms existing six baselines on effectiveness and robustness against ten image processing attacks and adversarial attacks, while enhancing security in the distribution scenarios. The code is available at https://anonymous.4open.science/r/DistriMark-F11F/.

Hong kyu Lee, Qiuchen Zhang, Carl Yang, Jian Lou, Li Xiong

Machine unlearning aims to eliminate the influence of a subset of training samples (i.e., unlearning samples) from a trained model. Effectively and efficiently removing the unlearning samples without negatively impacting the overall model performance is challenging. Existing works mainly exploit input and output space and classification loss, which can result in ineffective unlearning or performance loss. In addition, they utilize unlearning or remaining samples ineffectively, sacrificing either unlearning efficacy or efficiency. Our main insight is that the direct optimization on the representation space utilizing both unlearning and remaining samples can effectively remove influence of unlearning samples while maintaining representations learned from remaining samples. We propose a contrastive unlearning framework, leveraging the concept of representation learning for more effective unlearning. It removes the influence of unlearning samples by contrasting their embeddings against the remaining samples' embeddings so that their embeddings are closer to the embeddings of unseen samples. Experiments on a variety of datasets and models on both class unlearning and sample unlearning showed that contrastive unlearning achieves the best unlearning effects and efficiency with the lowest performance loss compared with the state-of-the-art algorithms. In addition, it is generalizable to different contrastive frameworks and other models such as vision-language models. Our main code is available on github.com/Emory-AIMS/Contrastive-Unlearning

Li Kuang, Qi Xie, HaiYang Yang, Yang Yang, Xiang Wei, HaoYue Kang, YingJie Xia

API migration is essential for software maintenance due to the rapid evolution of third-party libraries where API elements may change continuously through updates. There are two main challenges for API migration at the project level, especially across multiple versions: 1) lack of specific library evolution knowledge across multi-version; 2) difficulty in identifying the chain of changes at the project level. This paper proposes a project-level cross-multi-version API migration framework APIMig. We first construct an API evolution knowledge graph (KG) to capture changes between adjacent library versions and then derive coherent cross-version API evolution knowledge by KG reasoning. Second, we design a chain exploration algorithm to track the chain of changes and aggregate the affected code segments. Finally, a large language model is employed in completing API migration by providing the API evolution knowledge and the chain of changes. We construct an evolution KG for the Lucene library from version 4.0.0 to 10.1.0 and evaluate our approach through project migration pairs that depend on different major versions. Our framework shows improvements over the baseline in migrating projects across 7 major versions, achieving average increases of 16.52% in CodeBLEU scores and 28.49% in VCEU scores in GPT-4o.

Yan-Ru Ju, Tai-Lin Wu, Chung-Chin Shih, Ti-Rong Wu

Although AlphaZero has achieved superhuman performance in board games, recent studies reveal its limitations in handling scenarios requiring a comprehensive understanding of the entire board, such as recognizing long-sequence patterns in Go. To address this challenge, we propose ResTNet, a network that interleaves residual and Transformer blocks to bridge local and global knowledge. ResTNet improves playing strength across multiple board games, increasing win rate from 54.6% to 60.8% in 9x9 Go, 53.6% to 60.9% in 19x19 Go, and 50.4% to 58.0% in 19x19 Hex. In addition, ResTNet effectively processes global information and tackles two long-sequence patterns in 19x19 Go, including circular pattern and ladder pattern. It reduces the mean square error for circular pattern recognition from 2.58 to 1.07 and lowers the attack probability against an adversary program from 70.44% to 23.91%. ResTNet also improves ladder pattern recognition accuracy from 59.15% to 80.01%. By visualizing attention maps, we demonstrate that ResTNet captures critical game concepts in both Go and Hex, offering insights into AlphaZero's decision-making process. Overall, ResTNet shows a promising approach to integrating local and global knowledge, paving the way for more effective AlphaZero-based algorithms in board games. Our code is available at https://rlg.iis.sinica.edu.tw/papers/restnet.

Jiaxin Ju, Yizhen Zheng, Huan Yee Koh, Can Wang, Shirui Pan

Accurate molecular property prediction is a critical challenge with wide-ranging applications in chemistry, materials science, and drug discovery. Molecular representation methods, including fingerprints and graph neural networks (GNNs), achieve state-of-the-art results by effectively deriving features from molecular structures. However, these methods often overlook decades of accumulated semantic and contextual knowledge. Recent advancements in large language models (LLMs) demonstrate remarkable reasoning abilities and prior knowledge across scientific domains, leading us to hypothesize that LLMs can generate rich molecular representations when guided to reason in multiple perspectives. To address these gaps, we propose M^2LLM, a multi-view framework that integrates three perspectives: the molecular structure view, the molecular task view, and the molecular rules view. These views are fused dynamically to adapt to task requirements, and experiments demonstrate that M^2LLM achieves state-of-the-art performance on multiple benchmarks across classification and regression tasks. Moreover, we demonstrate that representation derived from LLM achieves exceptional performance by leveraging two core functionalities: the generation of molecular embeddings through their encoding capabilities and the curation of molecular features through advanced reasoning processes.

Anastasia Isychev, Valentin Wüstholz, Maria Christakis

Checking the reliability of machine-learning models is a crucial, but challenging task. Nomos is an existing, automated framework for testing general, user-provided functional properties of models, including so-called hyperproperties expressed over more than one model execution. Nomos aims to find model inputs that expose ``bugs'', that is, property violations. However, performing thousands of model invocations during testing is costly both in terms of time and money (for metered APIs, such as OpenAI's). We present LaZ (pronounced ``lazy''), an extension of Nomos that automatically minimizes the number of model invocations to boost the test throughput and thereby find bugs more efficiently. During test execution, LaZ automatically identifies redundant invocations---invocations where the model output does not affect the final test outcome---and skips them, much like lazy evaluation in certain programming languages. This optimization enables a second one that dynamically reorders model invocations to skip the more expensive ones. As a result, LaZ finds the same number of bugs as Nomos, but does so median 33% and up to 60% faster.

Zhejing Hu, Yan Liu, Gong Chen, Bruce X. B. Yu

Generative artificial intelligence in music has made significant strides, yet it still falls short of the substantial achievements seen in natural language processing, primarily due to the limited availability of music data. Knowledge-informed approaches have been shown to enhance the performance of music generation models, even when only a few pieces of musical knowledge are integrated. This paper seeks to leverage comprehensive music theory in AI-driven music generation tasks, such as algorithmic composition and style transfer, which traditionally require significant manual effort with existing techniques. We introduce a novel automatic music lexicon construction model that generates a lexicon, named CompLex, comprising 37,432 items derived from just 9 manually input category keywords and 5 sentence prompt templates. A new multi-agent algorithm is proposed to automatically detect and mitigate hallucinations. CompLex demonstrates impressive performance improvements across three state-of-the-art text-to-music generation models, encompassing both symbolic and audio-based methods. Furthermore, we evaluate CompLex in terms of completeness, accuracy, non-redundancy, and executability, confirming that it possesses the key characteristics of an effective lexicon.

Xiaodi Hou, Xiaobo Li, Mingyu Lu, Simiao Wang, Yijia Zhang

Recent advancements in radiology report generation have utilized deep neural networks such as CNNs and Transformers, achieving notable improvements in generating accurate and detailed reports. However, their practical adoption is hindered by the challenge of balancing global dependency modeling with computational efficiency. The state space model, particularly its enhanced variant Mamba, offers promising linear-complexity solutions for long-range dependency modeling. Despite its strengths, Mamba’s fixed positional encoding limits its ability to effectively capture complex spatial dependencies. To address this gap, we propose RRG-Mamba, an advanced framework for efficient radiology report generation. Within the RRGMamba, we enhance the vanilla Mamba by integrating rotary position encoding (RoPE), enabling dynamic modeling of relative positional information in visual feature sequences. Furthermore, we design a global dependency learning module to optimize long-range visual feature sequence modeling. Extensive experiments on publicly available datasets, including IU X-Ray and MIMIC-CXR, demonstrate that RRG-Mamba achieves a 3.7% improvement in BLEU-4 score over existing models, along with significant gains in computational and memory efficiency. Our code is available at https://github.com/Eleanorhxd/RRG-Mamba.

Wenkang Han, Wang Lin, Liya Hu, Zhenlong Dai, Yiyun Zhou, Mengze Li, Zemin Liu, Chang Yao, Jingyuan Chen

Knowledge tracing (KT) aims to predict learners' future performance based on historical learning interactions. However, existing KT models predominantly focus on data from a single course, limiting their ability to capture a comprehensive understanding of learners' knowledge states. In this paper, we propose TransKT, a contrastive cross-course knowledge tracing method that leverages concept graph guided knowledge transfer to model the relationships between learning behaviors across different courses, thereby enhancing knowledge state estimation. Specifically, TransKT constructs a cross-course concept graph by leveraging zero-shot Large Language Model (LLM) prompts to establish implicit links between related concepts across different courses. This graph serves as the foundation for knowledge transfer, enabling the model to integrate and enhance the semantic features of learners' interactions across courses. Furthermore, TransKT includes an LLM-to-LM pipeline for incorporating summarized semantic features, which significantly improves the performance of Graph Convolutional Networks (GCNs) used for knowledge transfer. Additionally, TransKT employs a contrastive objective that aligns single-course and cross-course knowledge states, thereby refining the model's ability to provide a more robust and accurate representation of learners' overall knowledge states. Our code and datasets are available at https://github.com/DQYZHWK/TransKT/.

Jiayi Dong, Jiahao Li, Fei Wang

Single-cell sequencing technology provides deep insights into gene activity at the individual cell level, facilitating the study of gene regulatory mechanisms. However, observed gene expression are often influenced by confounding factors such as batch effects, perturbations, and spatial position, which obscure the true gene regulatory network that governs the cell’s intrinsic state. To address these challenges, we propose scConCRL, a novel conditionally causal representation learning framework designed to extract the true gene regulatory relationships independent of confounding information. By considering both fine-grained molecular gene variables and coarse-grained latent domain variables, scConCRL not only uncovers the intrinsic biological signals but also models the complex relationships between these variables. This dual function enables the separation of genuine cellular states from domain information, providing valuable insights for downstream analyses and biological discovery. We demonstrate the effectiveness of our model on multi-domain datasets from different platforms and perturbation conditions, showing its ability to accurately disentangle confounding influences and discover novel gene relationships. Extensive comparisons across various scenarios illustrate the superior performance of scConCRL in several tasks compared to existing methods.

Anjali de Silva, Gang Chen, Hui Ma, Seyed Mohammad Nekooei, Xingquan Zuo

Community detection, a vital technology for real-world applications, uncovers cohesive node groups (communities) by leveraging both topological and attribute similarities in social networks. However, existing Graph Convolutional Networks (GCNs) trained to maximize modularity often converge to suboptimal solutions. Additionally, directly using human-labeled communities for training can undermine topological cohesiveness by grouping disconnected nodes based solely on node attributes. We address these issues by proposing a novel Topological and Attributive Similarity-based Community detection (TAS-Com) method. TAS-Com introduces a novel loss function that exploits the highly effective and scalable Leiden algorithm to detect community structures with global optimal modularity. Leiden is further utilized to refine human-labeled communities to ensure connectivity within each community, enabling TAS-Com to detect community structures with desirable trade-offs between modularity and compliance with human labels. Experimental results on multiple benchmark networks confirm that TAS-Com can significantly outperform several state-of-the-art algorithms.