Naeem Akhter

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.

Adiba Yaseen, Imran Amin, Naeem Akhter et al.

Motivation: Machine learning based prediction of compound-protein interactions (CPIs) is important for drug design, screening and repurposing studies and can improve the efficiency and cost-effectiveness of wet lab assays. Despite the publication of many research papers reporting CPI predictors in the recent years, we have observed a number of fundamental issues in experiment design that lead to over optimistic estimates of model performance. Results: In this paper, we analyze the impact of several important factors affecting generalization perfor-mance of CPI predictors that are overlooked in existing work: 1. Similarity between training and test examples in cross-validation 2. The strategy for generating negative examples, in the absence of experimentally verified negative examples. 3. Choice of evaluation protocols and performance metrics and their alignment with real-world use of CPI predictors in screening large compound libraries. Using both an existing state-of-the-art method (CPI-NN) and a proposed kernel based approach, we have found that assessment of predictive performance of CPI predictors requires careful con-trol over similarity between training and test examples. We also show that random pairing for gen-erating synthetic negative examples for training and performance evaluation results in models with better generalization performance in comparison to more sophisticated strategies used in existing studies. Furthermore, we have found that our kernel based approach, despite its simple design, exceeds the prediction performance of CPI-NN. We have used the proposed model for compound screening of several proteins including SARS-CoV-2 Spike and Human ACE2 proteins and found strong evidence in support of its top hits. Availability: Code and raw experimental results available at https://github.com/adibayaseen/HKRCPI Contact: Fayyaz.minhas@warwick.ac.uk

Minhaj Uddin Ansari, Talha Bilal, Naeem Akhter

Deep learning based 3D reconstruction of single view 2D image is becoming increasingly popular due to their wide range of real-world applications, but this task is inherently challenging because of the partial observability of an object from a single perspective. Recently, state of the art probability based Occupancy Networks reconstructed 3D surfaces from three different types of input domains: single view 2D image, point cloud and voxel. In this study, we extend the work on Occupancy Networks by exploiting cross-domain learning of image and point cloud domains. Specifically, we first convert the single view 2D image into a simpler point cloud representation, and then reconstruct a 3D surface from it. Our network, the Double Occupancy Network (D-OccNet) outperforms Occupancy Networks in terms of visual quality and details captured in the 3D reconstruction.