Lawrence Phillips

Josefa Lia Stoisser, Marc Boubnovski Martell, Lawrence Phillips et al.

We propose STRuCT-LLM, a unified framework for training large language models (LLMs) to perform structured reasoning over both relational and graph-structured data. Our approach jointly optimizes Text-to-SQL and Text-to-Cypher tasks using reinforcement learning (RL) combined with Chain-of-Thought (CoT) supervision. To support fine-grained optimization in graph-based parsing, we introduce a topology-aware reward function based on graph edit distance. Unlike prior work that treats relational and graph formalisms in isolation, STRuCT-LLM leverages shared abstractions between SQL and Cypher to induce cross-formalism transfer, enabling SQL training to improve Cypher performance and vice versa - even without shared schemas. Our largest model (QwQ-32B) achieves substantial relative improvements across tasks: on semantic parsing, Spider improves by 13.5\% and Text2Cypher by 73.1\%. The model also demonstrates strong zero-shot generalization, improving performance on downstream tabular QA (TableBench: 8.5\%) and knowledge graph QA (CR-LT-KGQA: 1.7\%) without any QA-specific supervision. These results demonstrate both the effectiveness of executable queries as scaffolds for structured reasoning and the synergistic benefits of jointly training on SQL and Cypher (code available at https://github.com/bouv/STRuCT-LLM).

Josefa Lia Stoisser, Lawrence Phillips, Aditya Misra et al.

Synthetic chain-of-thought (CoT) traces are widely used to train large reasoning models (LRMs), improving generalization by providing step-level supervision. Yet most approaches require ground-truth labels to seed or filter these traces - an expensive bottleneck in domains like biology where wet-lab data are scarce. We propose a label-free alternative: uncertainty-based filtering, which uses a model's own confidence - quantified through established uncertainty metrics like self-consistency and predictive perplexity - as a substitute for external labels. We sample multiple reasoning traces and retain only low-uncertainty subsets. Applied to biological perturbation prediction, a domain where wet-lab labels are especially costly, we show that the filtered subset has higher accuracy, and that supervised fine-tuning (SFT) on uncertainty-filtered data outperforms unfiltered synthetic data, narrows the gap to ground-truth training, and surpasses strong LRM baselines. Ablations show that per-class filtering corrects for class-specific uncertainty scales and that hybrid uncertainty metrics yield higher-quality datasets. Our results suggest that model-internal confidence is a powerful signal for efficient reasoning dataset creation, enabling LRMs in domains where supervision is expensive.

Lawrence G. Phillips, David B. Grimes, Yihan Jessie Li

We present an approach to domain adaptation, addressing the case where data from the source domain is abundant, labelled data from the target domain is limited or non-existent, and a small amount of paired source-target data is available. The method is designed for developing deep learning models that detect the presence of medical conditions based on data from consumer-grade portable biosensors. It addresses some of the key problems in this area, namely, the difficulty of acquiring large quantities of clinically labelled data from the biosensor, and the noise and ambiguity that can affect the clinical labels. The idea is to pre-train an expressive model on a large dataset of labelled recordings from a sensor modality for which data is abundant, and then to adapt the model's lower layers so that its predictions on the target modality are similar to the original model's on paired examples from the source modality. We show that the pre-trained model's predictions provide a substantially better learning signal than the clinician-provided labels, and that this teacher-student technique significantly outperforms both a naive application of supervised deep learning and a label-supervised version of domain adaptation on a synthetic dataset and in a real-world case study on sleep apnea. By reducing the volume of data required and obviating the need for labels, our approach should reduce the cost associated with developing high-performance deep learning models for biosensors.