# DPTM-DT: Dual-Pretrained Transformer Multitask Representation Learning for Drug-Target Prediction

arXiv: https://arxiv.org/abs/2609.22184 · HTML: https://mlsanity.com/paper/2609.22184/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 4 of its 40 references that are in the map.
- First posted on arXiv 28 Aug 2026.

## Builds on (most cited first, 4 of 4)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [Multimodal Transformer for Unaligned Multimodal Language Sequences](https://mlsanity.com/paper/1906.00295/) (2019)
- [DeepDTA: Deep Drug-Target Binding Affinity Prediction](https://mlsanity.com/paper/1801.10193/) (2018)
- [WideDTA: prediction of drug-target binding affinity](https://mlsanity.com/paper/1902.04166/) (2019)

## Abstract (arXiv)

Drug-target relation prediction supports candidate screening, drug repositioning, and mechanism analysis. Existing models often use incomplete drug or protein representations, model cross-modal interactions shallowly, or train affinity regression and interaction classification separately, although these tasks describe closely related views of the same drug-target pair. This paper presents DPTM-DT, a dual-pretrained Transformer framework for multitask drug-target prediction. DPTM-DT combines GROVER molecular graph embeddings, ESM protein language-model embeddings, and CTD physicochemical descriptors, then exchanges drug-target information through bidirectional cross-modal attention. A shared pair representation is used for continuous affinity regression, high-affinity binary classification, and six-level affinity classification. Experiments on Davis and KIBA cover random 80/20 and DeepDTA-style standard splits. On the random 80/20 split, DPTM-DT achieves MSE/CI values of 0.193/0.917 on Davis and 0.120/0.918 on KIBA. It also reports binary AUPR/MCC values of 0.727/0.654 and 0.798/0.689, and six-class Macro-F1/Top-2 values of 0.800/0.932 and 0.815/0.962 on Davis and KIBA, respectively. Across the reported regression, binary classification, and multiclass classification settings, DPTM-DT achieves the best overall performance among the compared methods. Results under the standard split show the same relative trend. Ablations indicate that dual target representation, gated fusion, and cross-modal attention each contribute to the final performance. Code and supplementary materials are available at: anonymous.4open.science/r/DPCM-DT-74E0.