Position Specific Scoring Is All You Need? Revisiting Protein Sequence Classification Tasks

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.

Sequence-Based Nanobody-Antigen Binding Prediction

Nanobodies (Nb) are monomeric heavy-chain fragments derived from heavy-chain only antibodies naturally found in Camelids and Sharks. Their considerably small size (~3-4 nm; 13 kDa) and favorable biophysical properties make them attractive targets for recombinant production. Furthermore, their unique ability to bind selectively to specific antigens, such as toxins, chemicals, bacteria, and viruses, makes them powerful tools in cell biology, structural biology, medical diagnostics, and future therapeutic agents in treating cancer and other serious illnesses. However, a critical challenge in nanobodies production is the unavailability of nanobodies for a majority of antigens. Although some computational methods have been proposed to screen potential nanobodies for given target antigens, their practical application is highly restricted due to their reliance on 3D structures. Moreover, predicting nanobodyantigen interactions (binding) is a time-consuming and labor-intensive task. This study aims to develop a machine-learning method to predict Nanobody-Antigen binding solely based on the sequence data. We curated a comprehensive dataset of Nanobody-Antigen binding and nonbinding data and devised an embedding method based on gapped k-mers to predict binding based only on sequences of nanobody and antigen. Our approach achieves up to 90% accuracy in binding prediction and is significantly more efficient compared to the widely-used computational docking technique.

CAMP: A Context-Aware Cricket Players Performance Metric

Cricket is the second most popular sport after soccer in terms of viewership. However, the assessment of individual player performance, a fundamental task in team sports, is currently primarily based on aggregate performance statistics, including average runs and wickets taken. We propose Context-Aware Metric of player Performance, CAMP, to quantify individual players' contributions toward a cricket match outcome. CAMP employs data mining methods and enables effective data-driven decision-making for selection and drafting, coaching and training, team line-ups, and strategy development. CAMP incorporates the exact context of performance, such as opponents' strengths and specific circumstances of games, such as pressure situations. We empirically evaluate CAMP on data of limited-over cricket matches between 2001 and 2019. In every match, a committee of experts declares one player as the best player, called Man of the M}atch (MoM). The top two rated players by CAMP match with MoM in 83\% of the 961 games. Thus, the CAMP rating of the best player closely matches that of the domain experts. By this measure, CAMP significantly outperforms the current best-known players' contribution measure based on the Duckworth-Lewis-Stern (DLS) method.

Robust Brain Age Estimation via Regression Models and MRI-derived Features

The determination of biological brain age is a crucial biomarker in the assessment of neurological disorders and understanding of the morphological changes that occur during aging. Various machine learning models have been proposed for estimating brain age through Magnetic Resonance Imaging (MRI) of healthy controls. However, developing a robust brain age estimation (BAE) framework has been challenging due to the selection of appropriate MRI-derived features and the high cost of MRI acquisition. In this study, we present a novel BAE framework using the Open Big Healthy Brain (OpenBHB) dataset, which is a new multi-site and publicly available benchmark dataset that includes region-wise feature metrics derived from T1-weighted (T1-w) brain MRI scans of 3965 healthy controls aged between 6 to 86 years. Our approach integrates three different MRI-derived region-wise features and different regression models, resulting in a highly accurate brain age estimation with a Mean Absolute Error (MAE) of 3.25 years, demonstrating the framework's robustness. We also analyze our model's regression-based performance on gender-wise (male and female) healthy test groups. The proposed BAE framework provides a new approach for estimating brain age, which has important implications for the understanding of neurological disorders and age-related brain changes.

Virus2Vec: Viral Sequence Classification Using Machine Learning

Understanding the host-specificity of different families of viruses sheds light on the origin of, e.g., SARS-CoV-2, rabies, and other such zoonotic pathogens in humans. It enables epidemiologists, medical professionals, and policymakers to curb existing epidemics and prevent future ones promptly. In the family Coronaviridae (of which SARS-CoV-2 is a member), it is well-known that the spike protein is the point of contact between the virus and the host cell membrane. On the other hand, the two traditional mammalian orders, Carnivora (carnivores) and Chiroptera (bats) are recognized to be responsible for maintaining and spreading the Rabies Lyssavirus (RABV). We propose Virus2Vec, a feature-vector representation for viral (nucleotide or amino acid) sequences that enable vector-space-based machine learning models to identify viral hosts. Virus2Vec generates numerical feature vectors for unaligned sequences, allowing us to forego the computationally expensive sequence alignment step from the pipeline. Virus2Vec leverages the power of both the \emph{minimizer} and position weight matrix (PWM) to generate compact feature vectors. Using several classifiers, we empirically evaluate Virus2Vec on real-world spike sequences of Coronaviridae and rabies virus sequence data to predict the host (identifying the reservoirs of infection). Our results demonstrate that Virus2Vec outperforms the predictive accuracies of baseline and state-of-the-art methods.

BioSequence2Vec: Efficient Embedding Generation For Biological Sequences

Representation learning is an important step in the machine learning pipeline. Given the current biological sequencing data volume, learning an explicit representation is prohibitive due to the dimensionality of the resulting feature vectors. Kernel-based methods, e.g., SVM, are a proven efficient and useful alternative for several machine learning (ML) tasks such as sequence classification. Three challenges with kernel methods are (i) the computation time, (ii) the memory usage (storing an $n\times n$ matrix), and (iii) the usage of kernel matrices limited to kernel-based ML methods (difficult to generalize on non-kernel classifiers). While (i) can be solved using approximate methods, challenge (ii) remains for typical kernel methods. Similarly, although non-kernel-based ML methods can be applied to kernel matrices by extracting principal components (kernel PCA), it may result in information loss, while being computationally expensive. In this paper, we propose a general-purpose representation learning approach that embodies kernel methods' qualities while avoiding computation, memory, and generalizability challenges. This involves computing a low-dimensional embedding of each sequence, using random projections of its $k$-mer frequency vectors, significantly reducing the computation needed to compute the dot product and the memory needed to store the resulting representation. Our proposed fast and alignment-free embedding method can be used as input to any distance (e.g., $k$ nearest neighbors) and non-distance (e.g., decision tree) based ML method for classification and clustering tasks. Using different forms of biological sequences as input, we perform a variety of real-world classification tasks, such as SARS-CoV-2 lineage and gene family classification, outperforming several state-of-the-art embedding and kernel methods in predictive performance.

Efficient Classification of SARS-CoV-2 Spike Sequences Using Federated Learning

This paper presents a federated learning (FL) approach to train an AI model for SARS-Cov-2 coronavirus variant identification. We analyze the SARS-CoV-2 spike sequences in a distributed way, without data sharing, to detect different variants of the rapidly mutating coronavirus. A vast amount of sequencing data of SARS-CoV-2 is available due to various genomic monitoring initiatives by several nations. However, privacy concerns involving patient health information and national public health conditions could hinder openly sharing this data. In this work, we propose a lightweight FL paradigm to cooperatively analyze the spike protein sequences of SARS-CoV-2 privately, using the locally stored data to train a prediction model from remote nodes. Our method maintains the confidentiality of local data (that could be stored in different locations) yet allows us to reliably detect and identify different known and unknown variants of the novel coronavirus SARS-CoV-2. We compare the performance of our approach on spike sequence data with the recently proposed state-of-the-art methods for classification from spike sequences. Using the proposed approach, we achieve an overall accuracy of $93\%$ on the coronavirus variant identification task. To the best of our knowledge, this is the first work in the federated learning paradigm for biological sequence analysis. Since the proposed model is distributed in nature, it could scale on ``Big Data'' easily. We plan to use this proof-of-concept to implement a privacy-preserving pandemic response strategy.

Efficient Approximate Kernel Based Spike Sequence Classification

Machine learning (ML) models, such as SVM, for tasks like classification and clustering of sequences, require a definition of distance/similarity between pairs of sequences. Several methods have been proposed to compute the similarity between sequences, such as the exact approach that counts the number of matches between $k$-mers (sub-sequences of length $k$) and an approximate approach that estimates pairwise similarity scores. Although exact methods yield better classification performance, they pose high computational costs, limiting their applicability to a small number of sequences. The approximate algorithms are proven to be more scalable and perform comparably to (sometimes better than) the exact methods -- they are designed in a "general" way to deal with different types of sequences (e.g., music, protein, etc.). Although general applicability is a desired property of an algorithm, it is not the case in all scenarios. For example, in the current COVID-19 (coronavirus) pandemic, there is a need for an approach that can deal specifically with the coronavirus. To this end, we propose a series of ways to improve the performance of the approximate kernel (using minimizers and information gain) in order to enhance its predictive performance pm coronavirus sequences. More specifically, we improve the quality of the approximate kernel using domain knowledge (computed using information gain) and efficient preprocessing (using minimizers computation) to classify coronavirus spike protein sequences corresponding to different variants (e.g., Alpha, Beta, Gamma). We report results using different classification and clustering algorithms and evaluate their performance using multiple evaluation metrics. Using two datasets, we show that our proposed method helps improve the kernel's performance compared to the baseline and state-of-the-art approaches in the healthcare domain.