Bipin Koirala

Sarwan Ali, Prakash Chourasia, Bipin Koirala et al.

Molecular sequence analysis is crucial for comprehending several biological processes, including protein-protein interactions, functional annotation, and disease classification. The large number of sequences and the inherently complicated nature of protein structures make it challenging to analyze such data. Finding patterns and enhancing subsequent research requires the use of dimensionality reduction and feature selection approaches. Recently, a method called Correlated Clustering and Projection (CCP) has been proposed as an effective method for biological sequencing data. The CCP technique is still costly to compute even though it is effective for sequence visualization. Furthermore, its utility for classifying molecular sequences is still uncertain. To solve these two problems, we present a Nearest Neighbor Correlated Clustering and Projection (CCP-NN)-based technique for efficiently preprocessing molecular sequence data. To group related molecular sequences and produce representative supersequences, CCP makes use of sequence-to-sequence correlations. As opposed to conventional methods, CCP doesn't rely on matrix diagonalization, therefore it can be applied to a range of machine-learning problems. We estimate the density map and compute the correlation using a nearest-neighbor search technique. We performed molecular sequence classification using CCP and CCP-NN representations to assess the efficacy of our proposed approach. Our findings show that CCP-NN considerably improves classification task accuracy as well as significantly outperforms CCP in terms of computational runtime.

Mahesh Shakya, Bijay Adhikari, Nirsara Shrestha et al.

Vision- and hearing-threatening diseases cause preventable disability, especially in resource-constrained settings(RCS) with few specialists and limited screening setup. Large scale AI-assisted screening and telehealth has potential to expand early detection, but practical deployment is challenging in paper-based workflows and limited documented field experience exist to build upon. We provide insights on challenges and ways forward in development to adoption of scalable AI-assisted Telehealth and screening in such settings. Specifically, we find that iterative, interdisciplinary collaboration through early prototyping, shadow deployment and continuous feedback is important to build shared understanding as well as reduce usability hurdles when transitioning from paper-based to AI-ready workflows. We find public datasets and AI models highly useful despite poor performance due to domain shift. In addition, we find the need for automated AI-based image quality check to capture gradable images for robust screening in high-volume camps. Our field learning stress the importance of treating AI development and workflow digitization as an end-to-end, iterative co-design process. By documenting these practical challenges and lessons learned, we aim to address the gap in contextual, actionable field knowledge for building real-world AI-assisted telehealth and mass-screening programs in RCS.

Sarwan Ali, Prakash Chourasia, Haris Mansoor et al.

The t-Distributed Stochastic Neighbor Embedding (t-SNE) has emerged as a popular dimensionality reduction technique for visualizing high-dimensional data. It computes pairwise similarities between data points by default using an RBF kernel and random initialization (in low-dimensional space), which successfully captures the overall structure but may struggle to preserve the local structure efficiently. This research proposes a novel approach called the Modified Isolation Kernel (MIK) as an alternative to the Gaussian kernel, which is built upon the concept of the Isolation Kernel. MIK uses adaptive density estimation to capture local structures more accurately and integrates robustness measures. It also assigns higher similarity values to nearby points and lower values to distant points. Comparative research using the normal Gaussian kernel, the isolation kernel, and several initialization techniques, including random, PCA, and random walk initializations, are used to assess the proposed approach (MIK). Additionally, we compare the computational efficiency of all $3$ kernels with $3$ different initialization methods. Our experimental results demonstrate several advantages of the proposed kernel (MIK) and initialization method selection. It exhibits improved preservation of the local and global structure and enables better visualization of clusters and subclusters in the embedded space. These findings contribute to advancing dimensionality reduction techniques and provide researchers and practitioners with an effective tool for data exploration, visualization, and analysis in various domains.