arXiv subjects

Pratik Chakraborty

Publications and source records attributed to Pratik Chakraborty.

3 recordsLinked to original sources

arXiv2025

XAI-Driven Deep Learning for Protein Sequence Functional Group Classification

Proteins perform essential biological functions, and accurate classification of their sequences is critical for understanding structure-function relationships, enzyme mechanisms, and molecular interactions. This study presents a deep learning-based framework for functional group classification of protein sequences derived from the Protein Data Bank (PDB). Four architectures were implemented: Convolutional Neural Network (CNN), Bidirectional Long Short-Term Memory (BiLSTM), CNN-BiLSTM hybrid, and CNN with Attention. Each model was trained using k-mer integer encoding to capture both local and long-range dependencies. Among these, the CNN achieved the highest validation accuracy of 91.8%, demonstrating the effectiveness of localized motif detection. Explainable AI techniques, including Grad-CAM and Integrated Gradients, were applied to interpret model predictions and identify biologically meaningful sequence motifs. The discovered motifs, enriched in histidine, aspartate, glutamate, and lysine, represent amino acid residues commonly found in catalytic and metal-binding regions of transferase enzymes. These findings highlight that deep learning models can uncover functionally relevant biochemical signatures, bridging the gap between predictive accuracy and biological interpretability in protein sequence analysis.

q-bio.QM↗

arXiv2022

Cold Atoms in Space: Community Workshop Summary and Proposed Road-Map

We summarize the discussions at a virtual Community Workshop on Cold Atoms in Space concerning the status of cold atom technologies, the prospective scientific and societal opportunities offered by their deployment in space, and the developments needed before cold atoms could be operated in space. The cold atom technologies discussed include atomic clocks, quantum gravimeters and accelerometers, and atom interferometers. Prospective applications include metrology, geodesy and measurement of terrestrial mass change due to, e.g., climate change, and fundamental science experiments such as tests of the equivalence principle, searches for dark matter, measurements of gravitational waves and tests of quantum mechanics. We review the current status of cold atom technologies and outline the requirements for their space qualification, including the development paths and the corresponding technical milestones, and identifying possible pathfinder missions to pave the way for missions to exploit the full potential of cold atoms in space. Finally, we present a first draft of a possible road-map for achieving these goals, that we propose for discussion by the interested cold atom, Earth Observation, fundamental physics and other prospective scientific user communities, together with ESA and national space and research funding agencies.

astro-ph.IM↗

arXiv2017

Performance Optimization of Co-Existing Underlay Secondary Networks

In this paper, we analyze the throughput performance of two co-existing downlink multiuser underlay secondary networks that use fixed-rate transmissions. We assume that the interference temperature limit (ITL) is apportioned to accommodate two concurrent transmissions using an interference temperature apportioning parameter so as to ensure that the overall interference to the primary receiver does not exceed the ITL. Using the derived analytical expressions for throughput, when there is only one secondary user in each network, or when the secondary networks do not employ opportunistic user selection (use round robin scheduling for example), there exists a critical fixed-rate below which sum throughput with co-existing secondary networks is higher than the throughput with a single secondary network. We derive an expression for this critical fixed-rate. Below this critical rate, we show that careful apportioning of the ITL is critical to maximizing sum throughput of the co-existing networks. We derive an expression for this apportioning parameter. Throughput is seen to increase with increase in number of users in each of the secondary networks. Computer simulations demonstrate accuracy of the derived expressions.

cs.IT↗