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Property-Aware Relation Networks for Few-Shot Molecular Property Prediction

Neural Information Processing Systems

Molecular property prediction plays a fundamental role in drug discovery to identify candidate molecules with target properties. However, molecular property prediction is essentially a few-shot problem, which makes it hard to use regular machine learning models. In this paper, we propose Property-Aware Relation networks (PAR) to handle this problem. In comparison to existing works, we leverage the fact that both relevant substructures and relationships among molecules change across different molecular properties. We first introduce a property-aware embedding function to transform the generic molecular embeddings to substructure-aware space relevant to the target property. Further, we design an adaptive relation graph learning module to jointly estimate molecular relation graph and refine molecular embeddings w.r.t. the target property, such that the limited labels can be effectively propagated among similar molecules. We adopt a meta-learning strategy where the parameters are selectively updated within tasks in order to model generic and property-aware knowledge separately. Extensive experiments on benchmark molecular property prediction datasets show that PAR consistently outperforms existing methods and can obtain property-aware molecular embeddings and model molecular relation graph properly.


CORGI: Efficient Pattern Matching With Quadratic Guarantees

Weitekamp, Daniel

arXiv.org Artificial Intelligence

Rule-based systems must solve complex matching problems within tight time constraints to be effective in real-time applications, such as planning and reactive control for AI agents, as well as low-latency relational database querying. Pattern-matching systems can encounter issues where exponential time and space are required to find matches for rules with many underconstrained variables, or which produce combinatorial intermediate partial matches (but are otherwise well-constrained). When online AI systems automatically generate rules from example-driven induction or code synthesis, they can easily produce worst-case matching patterns that slow or halt program execution by exceeding available memory. In our own work with cognitive systems that learn from example, we've found that aggressive forms of anti-unification-based generalization can easily produce these circumstances. To make these systems practical without hand-engineering constraints or succumbing to unpredictable failure modes, we introduce a new matching algorithm called CORGI (Collection-Oriented Relational Graph Iteration). Unlike RETE-based approaches, CORGI offers quadratic time and space guarantees for finding single satisficing matches, and the ability to iteratively stream subsequent matches without committing entire conflict sets to memory. CORGI differs from RETE in that it does not have a traditional $β$-memory for collecting partial matches. Instead, CORGI takes a two-step approach: a graph of grounded relations is built/maintained in a forward pass, and an iterator generates matches as needed by working backward through the graph. This approach eliminates the high-latency delays and memory overflows that can result from populating full conflict sets. In a performance evaluation, we demonstrate that CORGI significantly outperforms RETE implementations from SOAR and OPS5 on a simple combinatorial matching task.




SymbolicThought: Integrating Language Models and Symbolic Reasoning for Consistent and Interpretable Human Relationship Understanding

Zhao, Runcong, Zhu, Qinglin, Xu, Hainiu, Liang, Bin, Gui, Lin, He, Yulan

arXiv.org Artificial Intelligence

Understanding character relationships is essential for interpreting complex narratives and conducting socially grounded AI research. However, manual annotation is time-consuming and low in coverage, while large language models (LLMs) often produce hallucinated or logically inconsistent outputs. We present SymbolicThought, a human-in-the-loop framework that combines LLM-based extraction with symbolic reasoning. The system constructs editable character relationship graphs, refines them using seven types of logical constraints, and enables real-time validation and conflict resolution through an interactive interface. To support logical supervision and explainable social analysis, we release a dataset of 160 interpersonal relationships with corresponding logical structures. Experiments show that SymbolicThought improves annotation accuracy and consistency while significantly reducing time cost, offering a practical tool for narrative understanding, explainable AI, and LLM evaluation.


TRIX: A More Expressive Model for Zero-shot Domain Transfer in Knowledge Graphs

Zhang, Yucheng, Bevilacqua, Beatrice, Galkin, Mikhail, Ribeiro, Bruno

arXiv.org Artificial Intelligence

Fully inductive knowledge graph models can be trained on multiple domains and subsequently perform zero-shot knowledge graph completion (KGC) in new unseen domains. This is an important capability towards the goal of having foundation models for knowledge graphs. In this work, we introduce a more expressive and capable fully inductive model, dubbed TRIX, which not only yields strictly more expressive triplet embeddings (head entity, relation, tail entity) compared to state-of-the-art methods, but also introduces a new capability: directly handling both entity and relation prediction tasks in inductive settings. Empirically, we show that TRIX outperforms the state-of-the-art fully inductive models in zero-shot entity and relation predictions in new domains, and outperforms large-context LLMs in out-of-domain predictions. The source code is available at https://github.com/yuchengz99/TRIX.


Property-Aware Relation Networks for Few-Shot Molecular Property Prediction

Neural Information Processing Systems

Molecular property prediction plays a fundamental role in drug discovery to identify candidate molecules with target properties. However, molecular property prediction is essentially a few-shot problem, which makes it hard to use regular machine learning models. In this paper, we propose Property-Aware Relation networks (PAR) to handle this problem. In comparison to existing works, we leverage the fact that both relevant substructures and relationships among molecules change across different molecular properties. We first introduce a property-aware embedding function to transform the generic molecular embeddings to substructure-aware space relevant to the target property.


CYCLE: Cross-Year Contrastive Learning in Entity-Linking

Zhang, Pengyu, Cao, Congfeng, Zaporojets, Klim, Groth, Paul

arXiv.org Artificial Intelligence

Knowledge graphs constantly evolve with new entities emerging, existing definitions being revised, and entity relationships changing. These changes lead to temporal degradation in entity linking models, characterized as a decline in model performance over time. To address this issue, we propose leveraging graph relationships to aggregate information from neighboring entities across different time periods. This approach enhances the ability to distinguish similar entities over time, thereby minimizing the impact of temporal degradation. We introduce \textbf{CYCLE}: \textbf{C}ross-\textbf{Y}ear \textbf{C}ontrastive \textbf{L}earning for \textbf{E}ntity-Linking. This model employs a novel graph contrastive learning method to tackle temporal performance degradation in entity linking tasks. Our contrastive learning method treats newly added graph relationships as \textit{positive} samples and newly removed ones as \textit{negative} samples. This approach helps our model effectively prevent temporal degradation, achieving a 13.90\% performance improvement over the state-of-the-art from 2023 when the time gap is one year, and a 17.79\% improvement as the gap expands to three years. Further analysis shows that CYCLE is particularly robust for low-degree entities, which are less resistant to temporal degradation due to their sparse connectivity, making them particularly suitable for our method. The code and data are made available at \url{https://github.com/pengyu-zhang/CYCLE-Cross-Year-Contrastive-Learning-in-Entity-Linking}.