CLDR: Contrastive Learning Drug Response Models from Natural Language
  Supervision
Kun Li Wenbin Hu
Deep learning-based drug response prediction (DRP) methods can accelerate the
drug discovery process and reduce R\&D costs. Although the mainstream methods
achieve high accuracy in predicting response regression values, the
regression-aware representations of these methods are fragmented and fail to
capture the continuity of the sample order. This phenomenon leads to models
optimized to sub-optimal solution spaces, reducing generalization ability and
may result in significant wasted costs in the drug discovery phase. In this
paper, we propose \MN, a contrastive learning framework with natural language
supervision for the DRP. The \MN~converts regression labels into text, which is
merged with the captions text of the drug response as a second modality of the
samples compared to the traditional modalities (graph, sequence). In each
batch, two modalities of one sample are considered positive pairs and the other
pairs are considered negative pairs. At the same time, in order to enhance the
continuous representation capability of the numerical text, a common-sense
numerical knowledge graph is introduced. We validated several hundred thousand
samples from the Genomics of Drug Sensitivity in Cancer dataset, observing the
average improvement of the DRP method ranges from 7.8\% to 31.4\% with the
application of our framework. The experiments prove that the \MN~effectively
constrains the samples to a continuous distribution in the representation
space, and achieves impressive prediction performance with only a few epochs of
fine-tuning after pre-training. The code is available at:
\url{https://gitee.com/xiaoyibang/clipdrug.git}.