An official website of the United States government
Biomedical knowledge graphs (KGs) encode rich, structured information critical for drug discovery tasks, but extracting meaningful insights from large-scale KGs remains challenging due to their complex structure. Existing biomedical subgraph retrieval methods are tailored for graph neural networks (GNNs), limiting compatibility with other paradigms, including large language models (LLMs). We introduce K-Paths, a model-agnostic retrieval framework that extracts structured, diverse, and biologically meaningful multi-hop paths from dense biomedical KGs. These paths enable prediction of unobserved drug-drug and drug-disease interactions, including those involving entities not seen during training, thus supporting inductive reasoning. K-Paths is training-free and employs a diversity-aware adaptation of Yen's algorithm to extract the K shortest loopless paths between entities in a query, prioritizing biologically relevant and relationally diverse connections. These paths serve as concise, interpretable reasoning chains that can be directly integrated with LLMs or GNNs to improve generalization, accuracy, and enable explainable inference. Experiments on benchmark datasets show that K-Paths improves zero-shot reasoning across state-of-the-art LLMs. For instance, Tx-Gemma 27B improves by 19.8 and 4.0 F1 points on interaction severity prediction and drug repurposing tasks, respectively. Llama 70B achieves gains of 8.5 and 6.2 points on the same tasks. K-Paths also boosts the training efficiency of EmerGNN, a state-of-the-art GNN, by reducing the KG size by 90% while maintaining predictive performance. Beyond efficiency, K-Paths bridges the gap between KGs and LLMs, enabling scalable and explainable LLM-augmented scientific discovery. We release our code and the retrieved paths as a benchmark for inductive reasoning.
more »
« less
This content will become publicly available on May 1, 2026
SPEX: Scaling Feature Interaction Explanations for LLMs
Large language models (LLMs) have revolution- ized machine learning due to their ability to cap- ture complex interactions between input features. Popular post-hoc explanation methods like SHAP provide marginal feature attributions, while their extensions to interaction importances only scale to small input lengths (≈20). We propose Spectral Ex- plainer (SPEX), a model-agnostic interaction attri- bution algorithm that efficiently scales to large input lengths (≈1000). SPEX exploits underlying nat- ural sparsity among interactions—common in real- world data—and applies a sparse Fourier transform using a channel decoding algorithm to efficiently identify important interactions. We perform exper- iments across three difficult long-context datasets that require LLMs to utilize interactions between inputs to complete the task. For large inputs, SPEX outperforms marginal attribution methods by up to 20% in terms of faithfully reconstructing LLM out- puts. Further, SPEX successfully identifies key fea- tures and interactions that strongly influence model output. For one of our datasets, HotpotQA, SPEX provides interactions that align with human annota- tions. Finally, we use our model-agnostic approach to generate explanations to demonstrate abstract rea- soning in closed-source LLMs (GPT-4o mini) and compositional reasoning in vision-language models.
more »
« less
- PAR ID:
- 10635709
- Publisher / Repository:
- ICML 2025
- Date Published:
- ISBN:
- 978-3031948916
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
Automatic coding patient behaviors is essential to support decision making for psychotherapists during the motivational interviewing (MI), a collaborative communication intervention approach to address psychiatric issues, such as alcohol and drug addiction. While the behavior coding task has rapidly adapted language models to predict patient states during the MI sessions, lacking of domain-specific knowledge and overlooking patient-therapist interactions are major challenges in developing and deploying those models in real practice. To encounter those challenges, we introduce the Chain-of- Interaction (CoI) prompting method aiming to contextualize large language models (LLMs) for psychiatric decision support by the dyadic interactions. The CoI prompting approach systematically breaks down the coding task into three key reasoning steps, extract patient engagement, learn therapist question strategies, and integrates dyadic interactions between patients and therapists. This approach enables large language models to leverage the coding scheme, patient state, and domain knowledge for patient behavioral coding. Experiments on real-world datasets can prove the effectiveness and flexibility of our prompting method with multiple state-of-the-art LLMs over existing prompting baselines. We have conducted extensive ablation analysis and demonstrate the critical role of dyadic interactions in applying LLMs for psychotherapy behavior understanding.more » « less
-
In an era dominated by web-based intelligent customer services, the applications of Sentence Pair Matching are profoundly broad. Web agents, for example, automatically respond to customer queries by finding similar past questions, significantly reducing customer service expenses. While current large language models (LLMs) offer powerful text generation capabilities, they often struggle with opacity, potential text toxicity, and difficulty managing domain-specific and confidential business inquiries. Consequently, the widespread adoption of web-based intelligent customer services in real-world business still greatly relies on query-based interactions. In this paper, we introduce a series of model-agnostic techniques aimed at enhancing both the accuracy and interpretability of Chinese pairwise sentence-matching models. Our contributions include (1) An Edit-distance-weighted fine-tuning method, (2) A Bayesian Iterative Prediction algorithm, (3) A Lexical-based Dual Ranking Interpreter, and (4) A Bi-criteria Denoising strategy. Experimental results on the Large-scale Chinese Question Matching Corpus (LCQMC) with a disturbed test demonstrate that our fine-tuning and prediction methods can steadily improve matching accuracy, building on the current state-of-the-art models. Besides, our interpreter with denoising strategy markedly enhances token-level interpretation in rationality and loyalty. In both matching accuracy and interpretation, our approaches outperform classic methods and even LLMs.more » « less
-
Recent advancements in Large Language Models (LLMs) have showcased remarkable capabilities across various tasks in different domains. However, the emergence of biases and the potential for generating harmful content in LLMs, particularly under malicious inputs, pose significant challenges. Current mitigation strategies, while effective, are not resilient under adversarial attacks. This paper introduces Resilient Guardrails for Large Language Models (RigorLLM), a novel framework designed to efficiently and effectively moderate harmful and unsafe inputs and outputs for LLMs. By employing a multi-faceted approach that includes energy-based training data augmentation through Langevin dynamics, optimizing a safe suffix for inputs via minimax optimization, and integrating a fusion-based model combining robust KNN with LLMs based on our data augmentation, RigorLLM offers a robust solution to harmful content moderation. Our experimental evaluations demonstrate that RigorLLM not only outperforms existing baselines like OpenAI API and Perspective API in detecting harmful content but also exhibits unparalleled resilience to jailbreaking attacks. The innovative use of constrained optimization and a fusion-based guardrail approach represents a significant step forward in developing more secure and reliable LLMs, setting a new standard for content moderation frameworks in the face of evolving digital threats.more » « less
-
null (Ed.)Text classification is a fundamental problem, and recently, deep neural networks (DNN) have shown promising results in many natural language tasks. However, their human-level performance relies on high-quality annotations, which are time-consuming and expensive to collect. As we move towards large inexpensive datasets, the inherent label noise degrades the generalization of DNN. While most machine learning literature focuses on building complex networks to handle noise, in this work, we evaluate model-agnostic methods to handle inherent noise in large scale text classification that can be easily incorporated into existing machine learning workflows with minimal interruption. Specifically, we conduct a point-by-point comparative study between several noise-robust methods on three datasets encompassing three popular classification models. To our knowledge, this is the first time such a comprehensive study in text classification encircling popular models and model-agnostic loss methods has been conducted. In this study, we describe our learning and demonstrate the application of our approach, which outperformed baselines by up to 10% in classification accuracy while requiring no network modifications.more » « less
