Identification of protein-protein interactions (PPIs) helps derive cellular mechanistic understanding, particularly in the context of complex conditions such as neurodegenerative disorders, metabolic syndromes, and cancer. Large Language Models (LLMs) have demonstrated remarkable potential in predicting protein structures and interactions via automated mining of vast biomedical literature; yet their inherent uncertainty remains a key challenge for deriving reproducible findings, critical for biomedical applications. In this study, we present an uncertainty-aware adaptation of LLMs for PPI analysis, leveraging fine-tuned LLaMA-3 and BioMedGPT models. To enhance prediction reliability, we integrate LoRA ensembles and Bayesian LoRA models for uncertainty quantification (UQ), ensuring confidence-calibrated insights into protein behavior. Our approach achieves competitive performance in PPI identification across diverse disease contexts while addressing model uncertainty, thereby enhancing trustworthiness and reproducibility in computational biology. These findings underscore the potential of uncertainty-aware LLM adaptation for advancing precision medicine and biomedical research.

Fine-tuning large language models can improve task specific performance, although a general understanding of what the fine-tuned model has learned, forgotten and how to trust its predictions is still missing. We derive principled uncertainty quantification for fine-tuned LLMs with posterior approximations using computationally efficient low-rank adaptation ensembles. We analyze three common multiple-choice datasets using low-rank adaptation ensembles based on Mistral-7b, and draw quantitative and qualitative conclusions on their perceived complexity and model efficacy on the different target domains during and after fine-tuning. In particular, backed by the numerical experiments, we hypothesise about signals from entropic uncertainty measures for data domains that are inherently difficult for a given architecture to learn.

Reinforcement learning from human feedback (RLHF) emerges as a promising paradigm for aligning large language models (LLMs). However, a notable challenge in RLHF is overoptimization, where beyond a certain threshold, the pursuit of higher rewards leads to a decline in human preferences. In this paper, we observe the weakness of KL regularization which is commonly employed in existing RLHF methods to address overoptimization. To mitigate this limitation, we scrutinize the RLHF objective in the offline dataset and propose uncertainty-penalized RLHF (UP-RLHF), which incorporates uncertainty regularization during RL-finetuning. To enhance the uncertainty quantification abilities for reward models, we first propose a diverse low-rank adaptation (LoRA) ensemble by maximizing the nuclear norm of LoRA matrix concatenations. Then we optimize policy models utilizing penalized rewards, determined by both rewards and uncertainties provided by the diverse reward LoRA ensembles. Our experimental results, based on two real human preference datasets, showcase the effectiveness of diverse reward LoRA ensembles in quantifying reward uncertainty. Additionally, uncertainty regularization in UP-RLHF proves to be pivotal in mitigating overoptimization, thereby contributing to the overall performance.

Finetuned LLMs often exhibit poor uncertainty quantification, manifesting as overconfidence, poor calibration, and unreliable prediction results on test data or out-of-distribution samples. One approach commonly used in vision for alleviating this issue is a deep ensemble, which constructs an ensemble by training the same model multiple times using different random initializations. However, there is a huge challenge to ensembling LLMs: the most effective LLMs are very, very large. Keeping a single LLM in memory is already challenging enough: keeping an ensemble of e.g. 5 LLMs in memory is impossible in many settings. To address these issues, we propose an ensemble approach using Low-Rank Adapters (LoRA), a parameter-efficient fine-tuning technique. Critically, these low-rank adapters represent a very small number of parameters, orders of magnitude less than the underlying pre-trained model. Thus, it is possible to construct large ensembles of LoRA adapters with almost the same computational overhead as using the original model. We find that LoRA ensembles, applied on its own or on top of pre-existing regularization techniques, gives consistent improvements in predictive accuracy and uncertainty quantification.