Uncertainty estimation is essential for enhancing the reliability of Large Language Models (LLMs), particularly in high-stakes applications. Existing methods often overlook semantic dependencies, relying on token-level probability measures that fail to capture structural relationships within the generated text. We propose GENUINE: Graph ENhanced mUlti-level uncertaINty Estimation for Large Language Models, a structure-aware framework that leverages dependency parse trees and hierarchical graph pooling to refine uncertainty quantification. By incorporating supervised learning, GENUINE effectively models semantic and structural relationships, improving confidence assessments. Extensive experiments across NLP tasks show that GENUINE achieves up to 29% higher AUROC than semantic entropy-based approaches and reduces calibration errors by over 15%, demonstrating the effectiveness of graph-based uncertainty modeling. The code is available at https://github.com/ODYSSEYWT/GUQ.

The exponential growth of scientific publications has overwhelmed reviewers and researchers, with top conferences receiving thousands of submissions annually. Reviewers must assess feasibility, novelty, and impact under tight deadlines, often lacking tools to identify relevant prior work. Early-career researchers face similar challenges, with limited support to navigate fast-evolving fields. Existing LLM-based systems struggle with static retrieval, surface-level features, and lack multi-hop reasoning, leading to shallow or hallucinated assessments. Scientific evaluation requires a deep, relational understanding, which current retrieval-augmented generation (RAG) methods fail to achieve. We introduce SciCompanion, a graph-grounded reasoning framework for structured scientific evaluation. Given a paper or abstract-like input, SciCompanion builds a dynamic knowledge graph from recent publications, domain-specific databases, and curated metadata. It employs multi-hop reasoning to iteratively construct contextual graphs and generate structured critiques, enabling deeper exploration of scientific literature. Unlike sentiment-biased LLM evaluations, SciCompanion directly optimizes retrieval and graph refinement using Group Relative Policy Optimization (GRPO), producing reviews aligned with expert judgments. Experiments on ICLR and ACL datasets show that SciCompanion reduces evaluation error by over 30% compared to prompting-only baselines and allows smaller models to outperform larger ones. Evaluations across three datasets, using metrics for retrieval accuracy, semantic overlap, and multi-hop sensitivity, along with a case study, demonstrate SciCompanion’s robustness and versatility.

The discovery of novel mechanical metamaterials, whose properties are dominated by their engineered structures rather than chemical composition, is a knowledge-intensive and resource-demanding process. To accelerate the design of novel metamaterials, we present MetaScientist, a human-in-the-loop system that integrates advanced AI capabilities with expert oversight with two primary phases: (1) hypothesis generation, where the system performs complex reasoning to generate novel and scientifically sound hypotheses, supported with domain-specific foundation models and inductive biases retrieved from existing literature; (2) 3D structure synthesis, where a 3D structure is synthesized with a novel 3D diffusion model based on the textual hypothesis and refined it with a LLM-based refinement model to achieve better structure properties. At each phase, domain experts iteratively validate the system outputs, and provide feedback and supplementary materials to ensure the alignment of the outputs with scientific principles and human preferences. Through extensive evaluation from human scientists, MetaScientist is able to deliver novel and valid mechanical metamaterial designs that have the potential to be highly impactful in the metamaterial field.