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From Top-1 to Top-K: A Reproducibility Study and Benchmarking of Counterfactual Explanations for Recommender Systems Impact of large language models on peer review opinions from a fine-grained perspective: Evidence from top conference proceedings in AI Diagnosable ColBERT: Debugging Late-Interaction Retrieval Models Using a Learned Latent Space as Reference Enhancing Unsupervised Keyword Extraction in Academic Papers through Integrating Highlights with Abstract CAST: Modeling Semantic-Level Transitions for Complementary-Aware Sequential Recommendation IndiaFinBench: An Evaluation Benchmark for Large Language Model Performance on Indian Financial Regulatory Text Think Before Writing: Feature-Level Multi-Objective Optimization for Generative Citation Visibility RARE: Redundancy-Aware Retrieval Evaluation Framework for High-Similarity Corpora Personalized Benchmarking: Evaluating LLMs by Individual Preferences Modular Representation Compression: Adapting LLMs for Efficient and Effective Recommendations JFinTEB: Japanese Financial Text Embedding Benchmark UsefulBench: Towards Decision-Useful Information as a Target for Information Retrieval SIMMER: Cross-Modal Food Image--Recipe Retrieval via MLLM-Based Embedding Rethinking the Necessity of Adaptive Retrieval-Augmented Generation through the Lens of Adaptive Listwise Ranking BioHiCL: Hierarchical Multi-Label Contrastive Learning for Biomedical Retrieval with MeSH Labels Learning Behaviorally Grounded Item Embeddings via Personalized Temporal Contexts Collaborative Filtering Through Weighted Similarities of User and Item Embeddings IG-Search: Step-Level Information Gain Rewards for Search-Augmented Reasoning Metric-agnostic Learning-to-Rank via Boosting and Rank Approximation GenRec: A Preference-Oriented Generative Framework for Large-Scale Recommendation Uncertainty-aware Generative Learning Path Recommendation with Cognition-Adaptive Diffusion CPGRec+: A Balance-oriented Framework for Personalized Video Game Recommendations Don't Retrieve, Navigate: Distilling Enterprise Knowledge into Navigable Agent Skills for QA and RAG NewsTorch: A PyTorch-based Toolkit for Learner-oriented News Recommendation Controlling Authority Retrieval: A Missing Retrieval Objective for Authority-Governed Knowledge APEX-MEM: Agentic Semi-Structured Memory with Temporal Reasoning for Long-Term Conversational AI ID and Graph View Contrastive Learning with Multi-View Attention Fusion for Sequential Recommendation Large Language Models to Enhance Business Process Modeling: Past, Present, and Future Trends Dual-Enhancement Product Bundling: Bridging Interactive Graph and Large Language Model Evaluation of Agents under Simulated AI Marketplace Dynamics
Molecular Graph Representation Learning Integrating Large...
Tianyu Zhang, Yuxiang Ren, Chengbin Hou, Hairong Lv, Xuegong Zha · 2024-08-20 · via cs.IR updates on arXiv.org

Molecular property prediction is a crucial foundation for drug discovery. In recent years, pre-trained deep learning models have been widely applied to this task. Some approaches that incorporate prior biological domain knowledge into the pre-training framework have achieved impressive results. However, these methods heavily rely on biochemical experts, and retrieving and summarizing vast amounts of domain knowledge literature is both time-consuming and expensive. Large Language Models (LLMs) have demonstrated remarkable performance in understanding and efficiently providing general knowledge. Nevertheless, they occasionally exhibit hallucinations and lack precision in generating domain-specific knowledge. Conversely, Domain-specific Small Models (DSMs) possess rich domain knowledge and can accurately calculate molecular domain-related metrics. However, due to their limited model size and singular functionality, they lack the breadth of knowledge necessary for comprehensive representation learning. To leverage the advantages of both approaches in molecular property prediction, we propose a novel Molecular Graph representation learning framework that integrates Large language models and Domain-specific small models (MolGraph-LarDo). Technically, we design a two-stage prompt strategy where DSMs are introduced to calibrate the knowledge provided by LLMs, enhancing the accuracy of domain-specific information and thus enabling LLMs to generate more precise textual descriptions for molecular samples. Subsequently, we employ a multi-modal alignment method to coordinate various modalities, including molecular graphs and their corresponding descriptive texts, to guide the pre-training of molecular representations. Extensive experiments demonstrate the effectiveness of the proposed method.