# Uncertainty-Aware Adaptation of Large Language Models for Protein-Protein Interaction Analysis

arXiv: https://arxiv.org/abs/2502.06173 · HTML: https://mlsanity.com/paper/2502.06173/

## Key facts

- Cited by 2 papers in the map (data through 14 Oct 2026).
- Builds on 36 of its 62 references that are in the map.
- First posted on arXiv 10 Feb 2025.

## Builds on (most cited first, 30 of 36)

- [Language Models are Few-Shot Learners](https://mlsanity.com/paper/2005.14165/) (2020)
- [GPT-4 Technical Report](https://mlsanity.com/paper/2303.08774/) (2023)
- [The Llama 3 Herd of Models](https://mlsanity.com/paper/2407.21783/) (2024)
- [LoRA: Low-Rank Adaptation of Large Language Models](https://mlsanity.com/paper/2106.09685/) (2021)
- [Llama 2: Open Foundation and Fine-Tuned Chat Models](https://mlsanity.com/paper/2307.09288/) (2023)
- [Evaluating Large Language Models Trained on Code](https://mlsanity.com/paper/2107.03374/) (2021)
- [Simple and Scalable Predictive Uncertainty Estimation using Deep Ensembles](https://mlsanity.com/paper/1612.01474/) (2016)
- [Delving Deep into Rectifiers: Surpassing Human-Level Performance on ImageNet Classification](https://mlsanity.com/paper/1502.01852/) (2015)
- [Large Language Models Encode Clinical Knowledge](https://mlsanity.com/paper/2212.13138/) (2022)
- [Can LLMs Express Their Uncertainty? An Empirical Evaluation of Confidence Elicitation in LLMs](https://mlsanity.com/paper/2306.13063/) (2023)
- [BloombergGPT: A Large Language Model for Finance](https://mlsanity.com/paper/2303.17564/) (2023)
- [Galactica: A Large Language Model for Science](https://mlsanity.com/paper/2211.09085/) (2022)
- [ChemCrow: Augmenting large-language models with chemistry tools](https://mlsanity.com/paper/2304.05376/) (2023)
- [A Simple Baseline for Bayesian Uncertainty in Deep Learning](https://mlsanity.com/paper/1902.02476/) (2019)
- [BioGPT: Generative Pre-trained Transformer for Biomedical Text Generation and Mining](https://mlsanity.com/paper/2210.10341/) (2022)
- [Large Language Models: A Survey](https://mlsanity.com/paper/2402.06196/) (2024)
- [Laplace Redux -- Effortless Bayesian Deep Learning](https://mlsanity.com/paper/2106.14806/) (2021)
- [What Are Bayesian Neural Network Posteriors Really Like?](https://mlsanity.com/paper/2104.14421/) (2021)
- [GatorTron: A Large Clinical Language Model to Unlock Patient Information from Unstructured Electronic Health Records](https://mlsanity.com/paper/2203.03540/) (2022)
- [A Survey on Uncertainty Quantification of Large Language Models: Taxonomy, Open Research Challenges, and Future Directions](https://mlsanity.com/paper/2412.05563/) (2024)
- [Bayesian Low-rank Adaptation for Large Language Models](https://mlsanity.com/paper/2308.13111/) (2023)
- [Taming Overconfidence in LLMs: Reward Calibration in RLHF](https://mlsanity.com/paper/2410.09724/) (2024)
- [BioMedGPT: Open Multimodal Generative Pre-trained Transformer for BioMedicine](https://mlsanity.com/paper/2308.09442/) (2023)
- [LoRA ensembles for large language model fine-tuning](https://mlsanity.com/paper/2310.00035/) (2023)
- [BLoB: Bayesian Low-Rank Adaptation by Backpropagation for Large Language Models](https://mlsanity.com/paper/2406.11675/) (2024)
- [ClimateGPT: Towards AI Synthesizing Interdisciplinary Research on Climate Change](https://mlsanity.com/paper/2401.09646/) (2024)
- [Think Twice Before Trusting: Self-Detection for Large Language Models through Comprehensive Answer Reflection](https://mlsanity.com/paper/2403.09972/) (2024)
- [Uncertainty quantification in fine-tuned LLMs using LoRA ensembles](https://mlsanity.com/paper/2402.12264/) (2024)
- [Adapting the Linearised Laplace Model Evidence for Modern Deep Learning](https://mlsanity.com/paper/2206.08900/) (2022)
- [Preserving Pre-trained Features Helps Calibrate Fine-tuned Language Models](https://mlsanity.com/paper/2305.19249/) (2023)

## Built on by (most cited first, 2 of 2)

- [C-LoRA: Contextual Low-Rank Adaptation for Uncertainty Estimation in Large Language Models](https://mlsanity.com/paper/2505.17773/) (2025)
- [Compressed Active Subspaces for Scalable Bayesian Inference](https://mlsanity.com/paper/2609.19539/) (2026)

## Abstract (arXiv)

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.