arXiv subjects

Artem Bisliouk

Publications and source records attributed to Artem Bisliouk.

3 recordsLinked to original sources

arXiv2026

Aligning Biomedical Texts and Knowledge Graphs: A Systematic Comparison of Lightweight Alignment Strategies

Biomedical knowledge exists in two complementary but distinct forms: unstructured scientific literature and structured knowledge graphs (KGs). Aligning them is essential for knowledge grounding, evidence retrieval, and KG completion, yet existing methods do not explicitly align free-text evidence with KG triples. We present a unified framework for systematically studying design choices for aligning biomedical text and KGs. With a text encoder and a KG embedding model both frozen, we learn only a lightweight projection between their spaces via a contrastive objective. This enables a fair comparison across six design dimensions: text encoder, KG embedding model, projection head, triple composition, training direction, and hard-negatives sampling. We construct CTD-Align, a corpus of over 22K one-to-one tripledocument pairs linking chemical-gene interactions from the Comparative Toxicogenomics Database to supporting PubMed passages. We evaluate alignment on it in two retrieval settings: document-to-triple and triple-to-document. We find that the triple composition and the training direction (i.e., shared retrieval space) have the greatest impact, whereas the text encoder and hard-negatives sampling matter little. Overall, simple choices win: projecting text into the KG space with a linear head over concatenated subject, predicate, and object embeddings performs best. These findings establish lightweight contrastive alignment as an effective, practical foundation for bridging biomedical text and KGs.

cs.CL↗

arXiv2026

Confidence over Time: Confidence Calibration with Temporal Logic for Large Language Model Reasoning

Large Language Models (LLMs) increasingly rely on long-form, multi-step reasoning to solve complex tasks such as mathematical problem solving and scientific question answering. Despite strong performance, existing confidence estimation methods typically reduce an entire reasoning process to a single scalar score, ignoring how confidence evolves throughout the generation. As a result, these methods are often sensitive to superficial factors such as response length or verbosity, and struggle to distinguish correct reasoning from confidently stated errors. We propose to characterize the stepwise confidence signal using Signal Temporal Logic (STL). Using a discriminative STL mining procedure, we discover temporal formulas that distinguish confidence signals of correct and incorrect responses. Our analysis found that the STL patterns generalize across tasks, and numeric parameters exhibit sensitivity to individual questions. Based on these insights, we develop a confidence estimation approach that informs STL blocks with parameter hypernetworks. Experiments on multiple reasoning tasks show our confidence scores are more calibrated than the baselines.

cs.CL↗

arXiv2025

Temporalizing Confidence: Evaluation of Chain-of-Thought Reasoning with Signal Temporal Logic

Large Language Models (LLMs) have shown impressive performance in mathematical reasoning tasks when guided by Chain-of-Thought (CoT) prompting. However, they tend to produce highly confident yet incorrect outputs, which poses significant risks in domains like education, where users may lack the expertise to assess reasoning steps. To address this, we propose a structured framework that models stepwise confidence as a temporal signal and evaluates it using Signal Temporal Logic (STL). In particular, we define formal STL-based constraints to capture desirable temporal properties and compute robustness scores that serve as structured, interpretable confidence estimates. Our approach also introduces a set of uncertainty reshaping strategies to enforce smoothness, monotonicity, and causal consistency across the reasoning trajectory. Experiments show that our approach consistently improves calibration metrics and provides more reliable uncertainty estimates than conventional confidence aggregation and post-hoc calibration.

cs.LG↗