SynerGPT: In-Context Learning for Personalized Drug Synergy Prediction and Drug Design

• URL: http://arxiv.org/abs/2307.11694v2
• Date: Tue, 24 Oct 2023 23:51:57 GMT
• Title: SynerGPT: In-Context Learning for Personalized Drug Synergy Prediction and Drug Design
• Authors: Carl Edwards and Aakanksha Naik and Tushar Khot and Martin Burke and Heng Ji and Tom Hope
• Abstract summary: We propose a novel setting and models for in-context drug synergy learning. We are given a small "personalized dataset" of 10-20 drug synergy relationships in the context of specific cancer cell targets. Our goal is to predict additional drug synergy relationships in that context.
• Score: 64.69434941796904
• License: http://arxiv.org/licenses/nonexclusive-distrib/1.0/
• Abstract: Predicting synergistic drug combinations can help accelerate discovery of cancer treatments, particularly therapies personalized to a patient's specific tumor via biopsied cells. In this paper, we propose a novel setting and models for in-context drug synergy learning. We are given a small "personalized dataset" of 10-20 drug synergy relationships in the context of specific cancer cell targets. Our goal is to predict additional drug synergy relationships in that context. Inspired by recent work that pre-trains a GPT language model (LM) to "in-context learn" common function classes, we devise novel pre-training schemes that enable a GPT model to in-context learn "drug synergy functions". Our model -- which does not use any textual corpora, molecular fingerprints, protein interaction or any other domain-specific knowledge -- is able to achieve competitive results. We further integrate our in-context approach with a genetic algorithm to optimize model prompts and select synergy candidates to test after conducting a patient biopsy. Finally, we explore a novel task of inverse drug design which can potentially enable the design of drugs that synergize specifically to target a given patient's "personalized dataset". Our findings can potentially have an important impact on precision cancer medicine, and also raise intriguing questions on non-textual pre-training for LMs.

Related papers

• Multiscale Topology in Interactomic Network: From Transcriptome to Antiaddiction Drug Repurposing [0.3683202928838613]
  The escalating drug addiction crisis in the United States underscores the urgent need for innovative therapeutic strategies. This study embarked on an innovative and rigorous strategy to unearth potential drug repurposing candidates for opioid and cocaine addiction treatment.
  arXiv  Detail & Related papers  (2023-12-03T04:01:38Z)
• Emerging Drug Interaction Prediction Enabled by Flow-based Graph Neural Network with Biomedical Network [69.16939798838159]
  We propose EmerGNN, a graph neural network (GNN) that can effectively predict interactions for emerging drugs. EmerGNN learns pairwise representations of drugs by extracting the paths between drug pairs, propagating information from one drug to the other, and incorporating the relevant biomedical concepts on the paths. Overall, EmerGNN has higher accuracy than existing approaches in predicting interactions for emerging drugs and can identify the most relevant information on the biomedical network.
  arXiv  Detail & Related papers  (2023-11-15T06:34:00Z)
• PGraphDTA: Improving Drug Target Interaction Prediction using Protein Language Models and Contact Maps [4.590060921188914]
  Key aspect of drug discovery involves identifying novel drug-target (DT) interactions. Protein-ligand interactions exhibit a continuum of binding strengths, known as binding affinity. We propose novel enhancements to enhance their performance.
  arXiv  Detail & Related papers  (2023-10-06T05:00:25Z)
• Drug Synergistic Combinations Predictions via Large-Scale Pre-Training and Graph Structure Learning [82.93806087715507]
  Drug combination therapy is a well-established strategy for disease treatment with better effectiveness and less safety degradation. Deep learning models have emerged as an efficient way to discover synergistic combinations. Our framework achieves state-of-the-art results in comparison with other deep learning-based methods.
  arXiv  Detail & Related papers  (2023-01-14T15:07:43Z)
• MOOMIN: Deep Molecular Omics Network for Anti-Cancer Drug Combination Therapy [2.446672595462589]
  We propose a multimodal graph neural network that can predict the synergistic effect of drug combinations for cancer treatment. Our model captures the representation based on the context of drugs at multiple scales based on a drug-protein interaction network and metadata. We demonstrate that the model makes high-quality predictions over a wide range of cancer cell line tissues.
  arXiv  Detail & Related papers  (2021-10-28T13:10:25Z)
• Scientific Language Models for Biomedical Knowledge Base Completion: An Empirical Study [62.376800537374024]
  We study scientific LMs for KG completion, exploring whether we can tap into their latent knowledge to enhance biomedical link prediction. We integrate the LM-based models with KG embedding models, using a router method that learns to assign each input example to either type of model and provides a substantial boost in performance.
  arXiv  Detail & Related papers  (2021-06-17T17:55:33Z)
• Discovering Synergistic Drug Combinations for COVID with Biological Bottleneck Models [38.637412590671865]
  We propose a emphbiological bottleneck model that jointly learns drug-target interaction and synergy. The model consists of two parts: a drug-target interaction and target-disease association module. We experimentally tested the model predictions in the U.S. National Center for Advancing Translational Sciences.
  arXiv  Detail & Related papers  (2020-11-09T03:30:44Z)
• Text Mining to Identify and Extract Novel Disease Treatments From Unstructured Datasets [56.38623317907416]
  We use Google Cloud to transcribe podcast episodes of an NPR radio show. We then build a pipeline for systematically pre-processing the text. Our model successfully identified that Omeprazole can help treat heartburn.
  arXiv  Detail & Related papers  (2020-10-22T19:52:49Z)
• Ensemble Transfer Learning for the Prediction of Anti-Cancer Drug Response [49.86828302591469]
  In this paper, we apply transfer learning to the prediction of anti-cancer drug response. We apply the classic transfer learning framework that trains a prediction model on the source dataset and refines it on the target dataset. The ensemble transfer learning pipeline is implemented using LightGBM and two deep neural network (DNN) models with different architectures.
  arXiv  Detail & Related papers  (2020-05-13T20:29:48Z)

This list is automatically generated from the titles and abstracts of the papers in this site.

This site does not guarantee the quality of this site (including all information) and is not responsible for any consequences.