# TCR: A Transformer Based Deep Network for Predicting Cancer Drugs Response

arXiv: https://arxiv.org/abs/2207.04457 · HTML: https://mlsanity.com/paper/2207.04457/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 16 of its 53 references that are in the map.
- First posted on arXiv 10 Jul 2022.

## Builds on (most cited first, 16 of 16)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [Adam: A Method for Stochastic Optimization](https://mlsanity.com/paper/1412.6980/) (2014)
- [Language Models are Few-Shot Learners](https://mlsanity.com/paper/2005.14165/) (2020)
- [Swin Transformer: Hierarchical Vision Transformer using Shifted Windows](https://mlsanity.com/paper/2103.14030/) (2021)
- [Semi-Supervised Classification with Graph Convolutional Networks](https://mlsanity.com/paper/1609.02907/) (2016)
- [End-to-End Object Detection with Transformers](https://mlsanity.com/paper/2005.12872/) (2020)
- [Batch Normalization: Accelerating Deep Network Training by Reducing Internal Covariate Shift](https://mlsanity.com/paper/1502.03167/) (2015)
- [Training Region-based Object Detectors with Online Hard Example Mining](https://mlsanity.com/paper/1604.03540/) (2016)
- [Learning to Plan Chemical Syntheses](https://mlsanity.com/paper/1708.04202/) (2017)
- [Deep Reinforcement Learning for De-Novo Drug Design](https://mlsanity.com/paper/1711.10907/) (2017)
- [Ranked List Loss for Deep Metric Learning](https://mlsanity.com/paper/1903.03238/) (2019)
- [AttentiveNAS: Improving Neural Architecture Search via Attentive Sampling](https://mlsanity.com/paper/2011.09011/) (2020)
- [Drug cell line interaction prediction](https://mlsanity.com/paper/1812.11178/) (2018)
- [Discovering Molecular Functional Groups Using Graph Convolutional Neural Networks](https://mlsanity.com/paper/1812.00265/) (2018)
- [Drug response prediction by ensemble learning and drug-induced gene expression signatures](https://mlsanity.com/paper/1802.03800/) (2018)

## Abstract (arXiv)

Predicting clinical outcomes to anti-cancer drugs on a personalized basis is challenging in cancer treatment due to the heterogeneity of tumors. Traditional computational efforts have been made to model the effect of drug response on individual samples depicted by their molecular profile, yet overfitting occurs because of the high dimension for omics data, hindering models from clinical application. Recent research shows that deep learning is a promising approach to build drug response models by learning alignment patterns between drugs and samples. However, existing studies employed the simple feature fusion strategy and only considered the drug features as a whole representation while ignoring the substructure information that may play a vital role when aligning drugs and genes. Hereby in this paper, we propose TCR (Transformer based network for Cancer drug Response) to predict anti-cancer drug response. By utilizing an attention mechanism, TCR is able to learn the interactions between drug atom/sub-structure and molecular signatures efficiently in our study. Furthermore, a dual loss function and cross sampling strategy were designed to improve the prediction power of TCR. We show that TCR outperformed all other methods under various data splitting strategies on all evaluation matrices (some with significant improvement). Extensive experiments demonstrate that TCR shows significantly improved generalization ability on independent in-vitro experiments and in-vivo real patient data. Our study highlights the prediction power of TCR and its potential value for cancer drug repurpose and precision oncology treatment.