Knowledge graph completion (KGC) aims to alleviate the inherent incompleteness of knowledge graphs (KGs), a crucial task for numerous applications such as recommendation systems and drug repurposing. The success of knowledge graph embedding (KGE) models provokes the question about the explainability: ``\textit{Which the patterns of the input KG are most determinant to the prediction}?'' Particularly, path-based explainers prevail in existing methods because of their strong capability for human understanding. In this paper, based on the observation that a fact is usually determined by the synergy of multiple reasoning chains, we propose a novel explainable framework, dubbed KGExplainer, to explore synergistic pathways. KGExplainer is a model-agnostic approach that employs a perturbation-based greedy search algorithm to identify the most crucial synergistic paths as explanations within the local structure of target predictions. To evaluate the quality of these explanations, KGExplainer distills an evaluator from the target KGE model, allowing for the examination of their fidelity. We experimentally demonstrate that the distilled evaluator has comparable predictive performance to the target KGE. Experimental results on benchmark datasets demonstrate the effectiveness of KGExplainer, achieving a human evaluation accuracy of 83.3\% and showing promising improvements in explainability. Code is available at \url{https://github.com/xiaomingaaa/KGExplainer}

Large Language Models (LLMs) demonstrate strong reasoning abilities but face limitations such as hallucinations and outdated knowledge. Knowledge Graph (KG)-based Retrieval-Augmented Generation (RAG) addresses these issues by grounding LLM outputs in structured external knowledge from KGs. However, current KG-based RAG frameworks still struggle to optimize the trade-off between retrieval effectiveness and efficiency in identifying a suitable amount of relevant graph information for the LLM to digest. We introduce SubgraphRAG, extending the KG-based RAG framework that retrieves subgraphs and leverages LLMs for reasoning and answer prediction. Our approach innovatively integrates a lightweight multilayer perceptron (MLP) with a parallel triple-scoring mechanism for efficient and flexible subgraph retrieval while encoding directional structural distances to enhance retrieval effectiveness. The size of retrieved subgraphs can be flexibly adjusted to match the query's needs and the downstream LLM's capabilities. This design strikes a balance between model complexity and reasoning power, enabling scalable and generalizable retrieval processes. Notably, based on our retrieved subgraphs, smaller LLMs like Llama3.1-8B-Instruct deliver competitive results with explainable reasoning, while larger models like GPT-4o achieve state-of-the-art accuracy compared with previous baselines—all without fine-tuning. Extensive evaluations on the WebQSP and CWQ benchmarks highlight SubgraphRAG's strengths in efficiency, accuracy, and reliability by reducing hallucinations and improving response grounding.

Directed acyclic graphs (DAGs) serve as crucial data representations in domains such as hardware synthesis and compiler/program optimization for computing systems. DAG generative models facilitate the creation of synthetic DAGs, which can be used for benchmarking computing systems while preserving intellectual property. However, generating realistic DAGs is challenging due to their inherent directional and logical dependencies. This paper introduces LayerDAG, an autoregressive diffusion model, to address these challenges. LayerDAG decouples the strong node dependencies into manageable units that can be processed sequentially. By interpreting the partial order of nodes as a sequence of bipartite graphs, LayerDAG leverages autoregressive generation to model directional dependencies and employs diffusion models to capture logical dependencies within each bipartite graph. Comparative analyses demonstrate that LayerDAG outperforms existing DAG generative models in both expressiveness and generalization, particularly for generating large-scale DAGs with up to 400 nodes—a critical scenario for system benchmarking. Extensive experiments on both synthetic and real-world flow graphs from various computing platforms show that LayerDAG generates valid DAGs with superior statistical properties and benchmarking performance. The synthetic DAGs generated by LayerDAG enhance the training of ML-based surrogate models, resulting in improved accuracy in predicting performance metrics of real-world DAGs across diverse computing platforms.

Large Language Models (LLMs) embed sensitive, human-generated data, prompting the need for unlearning methods. Although certified unlearning offers strong privacy guarantees, its restrictive assumptions make it unsuitable for LLMs, giving rise to various heuristic approaches typically assessed through empirical evaluations. These standard evaluations randomly select data for removal, apply unlearning techniques, and use membership inference attacks (MIAs) to compare unlearned models against models retrained without the removed data. However, to ensure robust privacy protections for every data point, it is essential to account for scenarios in which certain data subsets face elevated risks. Prior research suggests that outliers, particularly including data tied to minority groups, often exhibit higher memorization propensity which indicates they may be more difficult to unlearn. Building on these insights, we introduce a complementary, minority-aware evaluation framework to highlight blind spots in existing frameworks. We substantiate our findings with carefully designed experiments, using canaries with personally identifiable information (PII) to represent these minority subsets and demonstrate that they suffer at least 20\% higher privacy leakage across various unlearning methods, MIAs, datasets, and LLM scales. Our proposed minority-aware evaluation framework marks an essential step toward more equitable and comprehensive assessments of LLM unlearning efficacy.

Modern large language models (LLMs) are inherently auto-regressive, requiring input to be serialized into flat sequences regardless of their structural dependencies. This serialization hinders the model’s ability to leverage structural inductive biases, especially in tasks such as retrieval-augmented generation (RAG) and reasoning on data with native graph structures, where inter-segment dependencies are crucial. We introduce Graph-KV with the potential to overcome this limitation. Graph-KV leverages the KV-cache of text segments as condensed representations and governs their interaction through structural inductive biases. In this framework, ''target'' segments selectively attend only to the KV-caches of their designated ''source'' segments, rather than all preceding segments in a serialized sequence. This approach induces a graph-structured block mask, sparsifying attention and enabling a message-passing-like step within the LLM. Furthermore, strategically allocated positional encodings for source and target segments reduce positional bias and context window consumption. We evaluate Graph-KV across three scenarios: (1) seven RAG benchmarks spanning direct inference, multi-hop reasoning, and long-document understanding; (2) Arxiv-QA, a novel academic paper QA task with full-text scientific papers structured as citation ego-graphs; and (3) paper topic classification within a citation network. By effectively reducing positional bias and harnessing structural inductive biases, Graph-KV substantially outperforms baselines, including standard costly sequential encoding, across various settings.

Graphs (or networks) are ubiquitous representation in life sciences and medicine, from molecular interactions maps, signaling transduction pathways, to graphs of scientific knowledge and patient- disease-intervention relationships derived from population studies and/or real-world data, such as electronic health records and insurance claims. Recent advance in graph machine learning (ML) approaches such as graph neural networks (GNNs) has transformed a diverse set of problems relying on biomedical networks that traditionally depend on descriptive topological data analyses. Small- and macro- molecules that were not modeled as graphs also saw a bloom in GNN-based algorithms improving the state-of-the-art performance for learning their properties. Comparing to graph ML applications from other domains, life sciences offer many unique problems and nuances ranging from graph construction to graph- level, and bi-graph-level supervision tasks.

Artificial intelligence, such as deep generative methods, represents a promising solution to de novo design of molecules with the desired properties. However, generating new molecules with biological activities toward two specific targets remains an extremely difficult challenge. In this work, we conceive a novel computational framework, herein called dual-target ligand generative network (DLGN), for the de novo generation of bioactive molecules toward two given objectives. Via adversarial training and reinforcement learning, DLGN treats a sequence-based simplified molecular input line entry system (SMILES) generator as a stochastic policy for exploring chemical spaces. Two discriminators are then used to encourage the generation of molecules that belong to the intersection of two bioactive-compound distributions. In a case study, we employ our methods to design a library of dual-target ligands targeting dopamine receptor D2 and 5-hydroxytryptamine receptor 1A as new antipsychotics. Experimental results demonstrate that the proposed model can generate novel compounds with high similarity to both bioactive datasets in several structure-based metrics. Our model exhibits a performance comparable to that of various state-of-the-art multi-objective molecule generation models. We envision that this framework will become a generally applicable approach for designing dual-target drugs in silico.