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We introduce a set of useful expressions of Differential Privacy (DP) notions in terms of the Laplace transform of the privacy loss distribution. Its bare form expression appears in several related works on analyzing DP, either as an integral or an expectation. We show that recognizing the expression as a Laplace transform unlocks a new way to reason about DP properties by exploiting the duality between time and frequency domains. Leveraging our interpretation, we connect the $(q, \rho(q))$-R\'enyi DP curve and the $(\epsilon, \delta(\epsilon))$-DP curve as being the Laplace and inverse-Laplace transforms of one another. This connection shows that the R\'enyi divergence is well-defined for complex orders $q = \gamma + i \omega$. Using our Laplace transform-based analysis, we also prove an adaptive composition theorem for $(\epsilon, \delta)$-DP guarantees that is exactly tight (i.e., matches even in constants) for all values of $\epsilon$. Additionally, we resolve an issue regarding symmetry of $f$-DP on subsampling that prevented equivalence across all functional DP notions.

Federated Learning (FL) is a distributed learning technique that maintains data privacy by providing a decentralized training method for machine learning models using distributed big data. This promising Federated Learning approach has also gained popularity in bioinformatics, where the privacy of biomedical data holds immense importance, especially when patient data is involved. Despite the successful implementation of Federated learning in biological sequence analysis, rigorous consideration is still required to improve accuracy in a way that data privacy should not be compromised. Additionally, the optimal integration of federated learning, especially in protein sequence analysis, has not been fully explored. We propose a deep feed-forward neural network-based enhanced federated learning method for protein sequence classification to overcome these challenges. Our method introduces novel enhancements to improve classification accuracy. We introduce dynamic weighted federated learning (DWFL) which is a federated learning-based approach, where local model weights are adjusted using weighted averaging based on their performance metrics. By assigning higher weights to well-performing models, we aim to create a more potent initial global model for the federated learning process, leading to improved accuracy. We conduct experiments using real-world protein sequence datasets to assess the effectiveness of DWFL. The results obtained using our proposed approach demonstrate significant improvements in model accuracy, making federated learning a preferred, more robust, and privacy-preserving approach for collaborative machine-learning tasks., Comment: Accepted at SIMBig 2024

Advancements in genomics technology lead to a rising volume of viral (e.g., SARS-CoV-2) sequence data, resulting in increased usage of machine learning (ML) in bioinformatics. Traditional ML techniques require centralized data collection and processing, posing challenges in realistic healthcare scenarios. Additionally, privacy, ownership, and stringent regulation issues exist when pooling medical data into centralized storage to train a powerful deep learning (DL) model. The Federated learning (FL) approach overcomes such issues by setting up a central aggregator server and a shared global model. It also facilitates data privacy by extracting knowledge while keeping the actual data private. This work proposes a cutting-edge Privacy enhancement through Iterative Collaboration (EPIC) architecture. The network is divided and distributed between local and centralized servers. We demonstrate the EPIC approach to resolve a supervised classification problem to estimate SARS-CoV-2 genomic sequence data lineage without explicitly transferring raw sequence data. We aim to create a universal decentralized optimization framework that allows various data holders to work together and converge to a single predictive model. The findings demonstrate that privacy-preserving strategies can be successfully used with aggregation approaches without materially altering the degree of learning convergence. Finally, we highlight a few potential issues and prospects for study in FL-based approaches to healthcare applications., Comment: Accepted at SIMBig 2024

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.

Understanding the structural and functional characteristics of proteins are crucial for developing preventative and curative strategies that impact fields from drug discovery to policy development. An important and popular technique for examining how amino acids make up these characteristics of the protein sequences with position-specific scoring (PSS). While the string kernel is crucial in natural language processing (NLP), it is unclear if string kernels can extract biologically meaningful information from protein sequences, despite the fact that they have been shown to be effective in the general sequence analysis tasks. In this work, we propose a weighted PSS kernel matrix (or W-PSSKM), that combines a PSS representation of protein sequences, which encodes the frequency information of each amino acid in a sequence, with the notion of the string kernel. This results in a novel kernel function that outperforms many other approaches for protein sequence classification. We perform extensive experimentation to evaluate the proposed method. Our findings demonstrate that the W-PSSKM significantly outperforms existing baselines and state-of-the-art methods and achieves up to 45.1\% improvement in classification accuracy.

Cancer is a complex disease characterized by uncontrolled cell growth. T cell receptors (TCRs), crucial proteins in the immune system, play a key role in recognizing antigens, including those associated with cancer. Recent advancements in sequencing technologies have facilitated comprehensive profiling of TCR repertoires, uncovering TCRs with potent anti-cancer activity and enabling TCR-based immunotherapies. However, analyzing these intricate biomolecules necessitates efficient representations that capture their structural and functional information. T-cell protein sequences pose unique challenges due to their relatively smaller lengths compared to other biomolecules. An image-based representation approach becomes a preferred choice for efficient embeddings, allowing for the preservation of essential details and enabling comprehensive analysis of T-cell protein sequences. In this paper, we propose to generate images from the protein sequences using the idea of Chaos Game Representation (CGR) using the Kaleidoscopic images approach. This Deep Learning Assisted Analysis of Protein Sequences Using Chaos Enhanced Kaleidoscopic Images (called DANCE) provides a unique way to visualize protein sequences by recursively applying chaos game rules around a central seed point. we perform the classification of the T cell receptors (TCRs) protein sequences in terms of their respective target cancer cells, as TCRs are known for their immune response against cancer disease. The TCR sequences are converted into images using the DANCE method. We employ deep-learning vision models to perform the classification to obtain insights into the relationship between the visual patterns observed in the generated kaleidoscopic images and the underlying protein properties. By combining CGR-based image generation with deep learning classification, this study opens novel possibilities in the protein analysis domain.

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.

This study introduces a novel approach, combining substruct counting, $k$-mers, and Daylight-like fingerprints, to expand the representation of chemical structures in SMILES strings. The integrated method generates comprehensive molecular embeddings that enhance discriminative power and information content. Experimental evaluations demonstrate its superiority over traditional Morgan fingerprinting, MACCS, and Daylight fingerprint alone, improving chemoinformatics tasks such as drug classification. The proposed method offers a more informative representation of chemical structures, advancing molecular similarity analysis and facilitating applications in molecular design and drug discovery. It presents a promising avenue for molecular structure analysis and design, with significant potential for practical implementation., Comment: 12 Pages, 3 tables, Accepted at SimBig2023

Recently introduced magnetic materials called altermagnets (AM) feature zero net magnetization but a momentum dependent magnetic exchange field, which can have intriguing implications when combined with superconductivity. In our work, we use the quasiclassical framework to study the effects of such a material on a conventional superconductor (S) in an AM/S bilayer. We discuss the superconducting phase diagram and heat capacity of AM/S while making a comparison with a ferromagnet-superconductor bilayer. Furthermore, we examine the density of states and analyze the system's response to an external magnetic field. We illustrate the anisotropy of spin-susceptibility and magnetization of AM/S by considering an external field in the in-plane and out-of-plane direction, thereby facilitating the scope of experimental detection and characterization of an AM in an AM/S hybrid system., Comment: 6 pages, 6 figures

In the field of biological research, it is essential to comprehend the characteristics and functions of molecular sequences. The classification of molecular sequences has seen widespread use of neural network-based techniques. Despite their astounding accuracy, these models often require a substantial number of parameters and more data collection. In this work, we present a novel approach based on the compression-based Model, motivated from \cite{jiang2023low}, which combines the simplicity of basic compression algorithms like Gzip and Bz2, with Normalized Compression Distance (NCD) algorithm to achieve better performance on classification tasks without relying on handcrafted features or pre-trained models. Firstly, we compress the molecular sequence using well-known compression algorithms, such as Gzip and Bz2. By leveraging the latent structure encoded in compressed files, we compute the Normalized Compression Distance between each pair of molecular sequences, which is derived from the Kolmogorov complexity. This gives us a distance matrix, which is the input for generating a kernel matrix using a Gaussian kernel. Next, we employ kernel Principal Component Analysis (PCA) to get the vector representations for the corresponding molecular sequence, capturing important structural and functional information. The resulting vector representations provide an efficient yet effective solution for molecular sequence analysis and can be used in ML-based downstream tasks. The proposed approach eliminates the need for computationally intensive Deep Neural Networks (DNNs), with their large parameter counts and data requirements. Instead, it leverages a lightweight and universally accessible compression-based model., Comment: Accepted at The Pacific-Asia Conference on Knowledge Discovery and Data Mining (PAKDD) 2024

Proximity effect at superconductor/antiferromagnet (S/AF) interfaces, which manifests itself as generation of Neel-type triplet correlations, leads to sensitivity of the superconducting critical temperature to the mutual orientation of the AF Neel vectors in AF/S/AF trilayers, which is called the spin-valve effect. Here we predict that the spin-valve effect in AF/S/AF heterostructures crucially depends on the value of the chemical potential of the superconducting interlayer due to the occurrence of the finite-momentum Neel triplet correlations. In addition we investigate equal-spin triplet correlations, which appear in AF/S/AF structures for non-aligned Neel vectors of the AFs, and their role in the nonmonotonic dependence of the superconducting critical temperature of the AF/S/AF structure on the mutual orientation of the AF Neel vectors. The influence of impurities on the spin-valve effect is also investigated.

The rapid advancement of nanomaterials has paved the way for various technological breakthroughs, and MXenes, in particular, have gained substantial attention due to their unique properties such as high conductivity, broad-spectrum absorption strength, and tunable band gap. This article presents the impact of the process parameters on the structural and optical properties of Ti3C2Tx MXene for application in ultrafast dynamics. XRD along with Raman spectroscopy studies, confirmed the synthesis of a single phase from their MAX phase Ti3AlC2. The complete etching of Al and increase in the interplanar distance is also observed on centrifugation at very high speed. The ultrafast transient absorption spectroscopy used to understand the effect of centrifuge speed on the charge carrier dynamics and ultrafast spectrum of MXene displayed that the carrier lifetime is critically influenced by rotation per minute (rpm) e.g. faster decay lifetime at 10k rpm than 7k rpm. The electronic relaxation probed using the time-resolved photoluminescence (TRPL) technique exhibits an average decay time of 5.13 ns and 5.35 ns at the 7k and 10k rpm, respectively, which confirms that the optical properties of the MXene are strongly affected by the centrifuge speed. The synthesized MXene at 10k rpm typically suggests that radiative processes due to longer decay lifetime and experiences fewer nonradiative losses, resulting in enhanced luminescence properties., Comment: 21 pages , 6 figures

An antiferromagnetic insulator (AFI) bearing a compensated interface to an adjacent conventional superconductor (S) has recently been predicted to generate N\'eel triplet Cooper pairs, whose amplitude alternates sign in space. Here, we theoretically demonstrate that such N\'eel triplets enable control of the superconducting critical temperature in an S layer via the angle between the N\'eel vectors of two enclosing AFI layers. This angle dependence changes sign with the number of S monolayers providing a distinct signature of the N\'eel triplets. Furthermore, we show that the latter mediate a similarly distinct exchange interaction between the two AFIs' N\'eel vectors., Comment: 7 pages, 4 figures

Cancer is a complex disease characterized by uncontrolled cell growth and proliferation. T cell receptors (TCRs) are essential proteins for the adaptive immune system, and their specific recognition of antigens plays a crucial role in the immune response against diseases, including cancer. The diversity and specificity of TCRs make them ideal for targeting cancer cells, and recent advancements in sequencing technologies have enabled the comprehensive profiling of TCR repertoires. This has led to the discovery of TCRs with potent anti-cancer activity and the development of TCR-based immunotherapies. In this study, we investigate the use of sparse coding for the multi-class classification of TCR protein sequences with cancer categories as target labels. Sparse coding is a popular technique in machine learning that enables the representation of data with a set of informative features and can capture complex relationships between amino acids and identify subtle patterns in the sequence that might be missed by low-dimensional methods. We first compute the k-mers from the TCR sequences and then apply sparse coding to capture the essential features of the data. To improve the predictive performance of the final embeddings, we integrate domain knowledge regarding different types of cancer properties. We then train different machine learning (linear and non-linear) classifiers on the embeddings of TCR sequences for the purpose of supervised analysis. Our proposed embedding method on a benchmark dataset of TCR sequences significantly outperforms the baselines in terms of predictive performance, achieving an accuracy of 99.8\%. Our study highlights the potential of sparse coding for the analysis of TCR protein sequences in cancer research and other related fields., Comment: Accepted at ICONIP 2023