Ziaurrehman Tanoli

Asifullah Khan, Anabia Sohail, Mustansar Fiaz et al.

Advances in deep learning are re-defining how visual data is processed and understand by the machines. Vision Transformers (ViTs) have recently demonstrated prominent performance in computer vision related tasks. However, their performance improves with increasing numbers of labeled data, indicating reliance on labeled data. Humanly annotated data are difficult to acquire and thus shifted the focus from traditional annotations to unsupervised learning strategies that learn structures inside the data. In response to this challenge, self-supervised learning (SSL) has emerged as a promising technique. SSL utilize inherent relationships within the data as a form of supervision. This technique can reduce the dependence on manual annotations and offers a more scalable and resource-effective approach to training models. Taking these strengths into account, it is necessary to assess the combination of SSL methods with ViTs, especially in the cases of limited labeled data. Inspired by this evolving trend, this survey aims to systematically review SSL mechanisms tailored for ViTs. We propose a comprehensive taxonomy to classify SSL techniques based on their representations and pre-training tasks. Furthermore, we highlighted the motivations behind the study of SSL, reviewed prominent pre-training tasks, and highlight advancements and challenges in this field. Furthermore, we conduct a comparative analysis of various SSL methods designed for ViTs, evaluating their strengths, limitations, and applicability to different scenarios.

Jehad Aldahdooh, Ziaurrehman Tanoli, Jing Tang

In this research, we present our work participation for the DrugProt task of BioCreative VII challenge. Drug-target interactions (DTIs) are critical for drug discovery and repurposing, which are often manually extracted from the experimental articles. There are >32M biomedical articles on PubMed and manually extracting DTIs from such a huge knowledge base is challenging. To solve this issue, we provide a solution for Track 1, which aims to extract 10 types of interactions between drug and protein entities. We applied an Ensemble Classifier model that combines BioMed-RoBERTa, a state of art language model, with Convolutional Neural Networks (CNN) to extract these relations. Despite the class imbalances in the BioCreative VII DrugProt test corpus, our model achieves a good performance compared to the average of other submissions in the challenge, with the micro F1 score of 55.67% (and 63% on BioCreative VI ChemProt test corpus). The results show the potential of deep learning in extracting various types of DTIs.