PURPOSE
To evaluate open-source large language models (LLMs) for extracting cancer-specific phenotypic data, benchmark their performance against GPT4 models, and assess the impact of fine-tuning with training data sizes.
METHODS
Open-source LLMs (Mistral, LLaMa, MAMBA, BioMistral) were evaluated in zero-/one-shot and fine-tuned setups against GPT4-turbo/GPT4o to extract the cancer presence, progression, response, and metastatic sites from radiology impressions of patients with solid tumors treated at Dana-Farber Cancer Institute. Performance metrics (accuracy, precision, recall, F1-score) were computed. McNemar's odds ratio (OR), measuring which model is more likely to be correct when they disagree, was computed with 95% CI. Statistical significance was assessed using the alpha of .000139.
RESULTS
This study included 2,623 patients (25,273 radiology impressions). In zero-/one-shot settings, GPT4-turbo/GPT4o outperformed open-source LLMs. However, fine-tuned open-source LLMs achieved higher F1-scores than GPT4 models. Compared with the best-performing GPT4 model, fine-tuned Mistral0.2-7.3B (OR, 0.27 [95% CI, 0.20 to 0.36]; P < .00001), Mistral0.3-7.3B (OR, 0.26 [95% CI, 0.19 to 0.36]; P < .00001), LLaMa2-6.7B (OR, 0.30 [95% CI, 0.22 to 0.40]; P < .00001), LLaMa3.1-8B (OR, 0.37 [95% CI, 0.28 to 0.48]; P < .00001), and MAMBA-2.8B (OR, 0.32 [95% CI, 0.24 to 0.42]; P < .00001) showed significantly better performance in ascertaining disease progression. Performance was consistently better for inferring overall response, any evidence of cancer, and sites of metastases, with no significant differences among fine-tuned open-source LLMs. Fine-tuning gains plateaued at 25% of training data (5,718 impressions) and remained comparable at 5% (1,144 impressions).
CONCLUSION
Open-source LLMs, when fine-tuned using labeled data, can effectively automate the ascertainment of key radiophenotypic variables using only the impression section of radiology reports, without the full report text. Their consistent performance in small training sets suggests that these models may provide a scalable approach for phenotypic characterization of patients with cancer in real-world clinical settings.
Syed Arsalan Ahmed Naqvi, I. Riaz, Amir Saeidi et al.· JCO Clinical Cancer Informat...· 0 citations
Large language model (LLM) agents are increasingly deployed in long-horizon, interactive, and stateful environments. In these settings, a single wrong action, such as refunding the wrong purchase, can cause irreversible task failure and must be intercepted before execution. Such failures may not appear in every single run, but can emerge across repeated trials, making reliability across steps and trials critical. However, ensuring agentic reliability is challenging: even frontier LLMs struggle to explain why an action may be wrong, especially in long, intertwined trajectories governed by domain-specific policies. Much recent work relies on prompt-based critique agents, while optimization-based methods lack a systematic way to produce rich verification rationales for training. We address this gap with CAST, a critique-aware training framework that converts sparse task outcomes into action-level supervision for critique learning and policy optimization. CAST analyzes agent trajectories to synthesize structured rationales explaining action validity under partial observability. The resulting critique model is used to construct critique-aware training data for optimizing the policy model. Fine-tuning Qwen3-family models on dynamic tool-calling benchmarks, CAST improves reliability across domains, outperforming GPT-OSS-120B by over 10% pass^4 on Retail tasks and yielding an additional 9% improvement on Telehealth in an out-of-domain setting. These results demonstrate that critique-aware training improves the robustness of LLM agents in realistic dynamic environments.
Amir Saeidi, Zeng Zhang, Rishitosh Singh et al.· 0 citations
Large Language Models (LLMs) trained on extensive scientific research are increasingly integrated as assistants for scientific discovery. However, most research papers omit the fine-grained cognitive process of examining constraints, failed alternatives, and iterative decisions required to achieve the desired goal. Such cognitive processes are vital for real-world scientists working toward specific goals under constraints. In this paper, we show that LLMs, when trained to produce such cognitive traces, perform better as scientific discovery assistants than when trained solely on scientific literature. We propose COGTRL, a trajectory-level reinforcement learning framework that trains LLMs to emulate cognitively grounded reasoning by jointly optimizing cognitive traces and the scientific steps produced in an interleaved manner. Across two 3B-parameter models and two scientific domains (AI and Materials Science), COGTRL improves method quality by an average of 7.85 points over comparable 3B model baselines and achieves competitive performance relative to 70B parameter models. Moreover, analysis by domain experts shows a preference for methods generated by COGTRL over the baselines.
Evaluating and monitoring reasoning fidelity should be a prerequisite for safe deployment of LLMs in oncology decision support, as endpoint accuracy alone may mask clinically meaningful reasoning failures.
Matthew Kenaston, U. Ayub, Mihir Parmar et al.· npj Digital Medicine· 0 citations