arXiv subjects

Sarwan Ali

Publications and source records attributed to Sarwan Ali.

At least 55 records · Page 3Linked to original sources

arXiv2023

ViralVectors: Compact and Scalable Alignment-free Virome Feature Generation

The amount of sequencing data for SARS-CoV-2 is several orders of magnitude larger than any virus. This will continue to grow geometrically for SARS-CoV-2, and other viruses, as many countries heavily finance genomic surveillance efforts. Hence, we need methods for processing large amounts of sequence data to allow for effective yet timely decision-making. Such data will come from heterogeneous sources: aligned, unaligned, or even unassembled raw nucleotide or amino acid sequencing reads pertaining to the whole genome or regions (e.g., spike) of interest. In this work, we propose \emph{ViralVectors}, a compact feature vector generation from virome sequencing data that allows effective downstream analysis. Such generation is based on \emph{minimizers}, a type of lightweight "signature" of a sequence, used traditionally in assembly and read mapping -- to our knowledge, the first use minimizers in this way. We validate our approach on different types of sequencing data: (a) 2.5M SARS-CoV-2 spike sequences (to show scalability); (b) 3K Coronaviridae spike sequences (to show robustness to more genomic variability); and (c) 4K raw WGS reads sets taken from nasal-swab PCR tests (to show the ability to process unassembled reads). Our results show that ViralVectors outperforms current benchmarks in most classification and clustering tasks.

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arXiv2023

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.

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arXiv2023

Exploring The Potential Of GANs In Biological Sequence Analysis

Biological sequence analysis is an essential step toward building a deeper understanding of the underlying functions, structures, and behaviors of the sequences. It can help in identifying the characteristics of the associated organisms, like viruses, etc., and building prevention mechanisms to eradicate their spread and impact, as viruses are known to cause epidemics that can become pandemics globally. New tools for biological sequence analysis are provided by machine learning (ML) technologies to effectively analyze the functions and structures of the sequences. However, these ML-based methods undergo challenges with data imbalance, generally associated with biological sequence datasets, which hinders their performance. Although various strategies are present to address this issue, like the SMOTE algorithm, which creates synthetic data, however, they focus on local information rather than the overall class distribution. In this work, we explore a novel approach to handle the data imbalance issue based on Generative Adversarial Networks (GANs) which use the overall data distribution. GANs are utilized to generate synthetic data that closely resembles the real one, thus this generated data can be employed to enhance the ML models' performance by eradicating the class imbalance problem for biological sequence analysis. We perform 3 distinct classification tasks by using 3 different sequence datasets (Influenza A Virus, PALMdb, VDjDB) and our results illustrate that GANs can improve the overall classification performance.

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arXiv2023

Efficient Data Analytics on Augmented Similarity Triplets

Data analysis require a pairwise proximity measure over objects. Recent work has extended this to situations where the distance information between objects is given as comparison results of distances between three objects (triplets). Humans find the comparison tasks much easier than the exact distance computation and such data can be easily obtained in big quantity via crowd-sourcing. In this work, we propose triplets augmentation, an efficient method to extend the triplets data by inferring the hidden implicit information form the existing data. Triplets augmentation improves the quality of kernel-based and kernel-free data analytics. We also propose a novel set of algorithms for common data analysis tasks based on triplets. These methods work directly with triplets and avoid kernel evaluations, thus are scalable to big data. We demonstrate that our methods outperform the current best-known techniques and are robust to noisy data.

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arXiv2022

Evaluating COVID-19 Sequence Data Using Nearest-Neighbors Based Network Model

The SARS-CoV-2 coronavirus is the cause of the COVID-19 disease in humans. Like many coronaviruses, it can adapt to different hosts and evolve into different lineages. It is well-known that the major SARS-CoV-2 lineages are characterized by mutations that happen predominantly in the spike protein. Understanding the spike protein structure and how it can be perturbed is vital for understanding and determining if a lineage is of concern. These are crucial to identifying and controlling current outbreaks and preventing future pandemics. Machine learning (ML) methods are a viable solution to this effort, given the volume of available sequencing data, much of which is unaligned or even unassembled. However, such ML methods require fixed-length numerical feature vectors in Euclidean space to be applicable. Similarly, euclidean space is not considered the best choice when working with the classification and clustering tasks for biological sequences. For this purpose, we design a method that converts the protein (spike) sequences into the sequence similarity network (SSN). We can then use SSN as an input for the classical algorithms from the graph mining domain for the typical tasks such as classification and clustering to understand the data. We show that the proposed alignment-free method is able to outperform the current SOTA method in terms of clustering results. Similarly, we are able to achieve higher classification accuracy using well-known Node2Vec-based embedding compared to other baseline embedding approaches.

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arXiv2022

Informative Initialization and Kernel Selection Improves t-SNE for Biological Sequences

The t-distributed stochastic neighbor embedding (t- SNE) is a method for interpreting high dimensional (HD) data by mapping each point to a low dimensional (LD) space (usually two-dimensional). It seeks to retain the structure of the data. An important component of the t-SNE algorithm is the initialization procedure, which begins with the random initialization of an LD vector. Points in this initial vector are then updated to minimize the loss function (the KL divergence) iteratively using gradient descent. This leads comparable points to attract one another while pushing dissimilar points apart. We believe that, by default, these algorithms should employ some form of informative initialization. Another essential component of the t-SNE is using a kernel matrix, a similarity matrix comprising the pairwise distances among the sequences. For t-SNE-based visualization, the Gaussian kernel is employed by default in the literature. However, we show that kernel selection can also play a crucial role in the performance of t-SNE. In this work, we assess the performance of t-SNE with various alternative initialization methods and kernels, using four different sets, out of which three are biological sequences (nucleotide, protein, etc.) datasets obtained from various sources, such as the well-known GISAID database for sequences of the SARS- CoV-2 virus. We perform subjective and objective assessments of these alternatives. We use the resulting t-SNE plots and k- ary neighborhood agreement (k-ANA) to evaluate and compare the proposed methods with the baselines. We show that by using different techniques, such as informed initialization and kernel matrix selection, that t-SNE performs significantly better. Moreover, we show that t-SNE also takes fewer iterations to converge faster with more intelligent initialization.

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arXiv2022

Reads2Vec: Efficient Embedding of Raw High-Throughput Sequencing Reads Data

The massive amount of genomic data appearing for SARS-CoV-2 since the beginning of the COVID-19 pandemic has challenged traditional methods for studying its dynamics. As a result, new methods such as Pangolin, which can scale to the millions of samples of SARS-CoV-2 currently available, have appeared. Such a tool is tailored to take as input assembled, aligned and curated full-length sequences, such as those found in the GISAID database. As high-throughput sequencing technologies continue to advance, such assembly, alignment and curation may become a bottleneck, creating a need for methods which can process raw sequencing reads directly. In this paper, we propose Reads2Vec, an alignment-free embedding approach that can generate a fixed-length feature vector representation directly from the raw sequencing reads without requiring assembly. Furthermore, since such an embedding is a numerical representation, it may be applied to highly optimized classification and clustering algorithms. Experiments on simulated data show that our proposed embedding obtains better classification results and better clustering properties contrary to existing alignment-free baselines. In a study on real data, we show that alignment-free embeddings have better clustering properties than the Pangolin tool and that the spike region of the SARS-CoV-2 genome heavily informs the alignment-free clusterings, which is consistent with current biological knowledge of SARS-CoV-2.

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arXiv2022

Impact Of Missing Data Imputation On The Fairness And Accuracy Of Graph Node Classifiers

Analysis of the fairness of machine learning (ML) algorithms recently attracted many researchers' interest. Most ML methods show bias toward protected groups, which limits the applicability of ML models in many applications like crime rate prediction etc. Since the data may have missing values which, if not appropriately handled, are known to further harmfully affect fairness. Many imputation methods are proposed to deal with missing data. However, the effect of missing data imputation on fairness is not studied well. In this paper, we analyze the effect on fairness in the context of graph data (node attributes) imputation using different embedding and neural network methods. Extensive experiments on six datasets demonstrate severe fairness issues in missing data imputation under graph node classification. We also find that the choice of the imputation method affects both fairness and accuracy. Our results provide valuable insights into graph data fairness and how to handle missingness in graphs efficiently. This work also provides directions regarding theoretical studies on fairness in graph data.

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arXiv2022

Characterizing SARS-CoV-2 Spike Sequences Based on Geographical Location

With the rapid spread of COVID-19 worldwide, viral genomic data is available in the order of millions of sequences on public databases such as GISAID. This Big Data creates a unique opportunity for analysis towards the research of effective vaccine development for current pandemics, and avoiding or mitigating future pandemics. One piece of information that comes with every such viral sequence is the geographical location where it was collected -- the patterns found between viral variants and geographical location surely being an important part of this analysis. One major challenge that researchers face is processing such huge, highly dimensional data to obtain useful insights as quickly as possible. Most of the existing methods face scalability issues when dealing with the magnitude of such data. In this paper, we propose an approach that first computes a numerical representation of the spike protein sequence of SARS-CoV-2 using $k$-mers (substrings) and then uses several machine learning models to classify the sequences based on geographical location. We show that our proposed model significantly outperforms the baselines. We also show the importance of different amino acids in the spike sequences by computing the information gain corresponding to the true class labels.

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arXiv2022

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.

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arXiv2022

Information We Can Extract About a User From 'One Minute Mobile Application Usage'

Understanding human behavior is an important task and has applications in many domains such as targeted advertisement, health analytics, security, and entertainment, etc. For this purpose, designing a system for activity recognition (AR) is important. However, since every human can have different behaviors, understanding and analyzing common patterns become a challenging task. Since smartphones are easily available to every human being in the modern world, using them to track the human activities becomes possible. In this paper, we extracted different human activities using accelerometer, magnetometer, and gyroscope sensors of android smartphones by building an android mobile applications. Using different social media applications, such as Facebook, Instagram, Whatsapp, and Twitter, we extracted the raw sensor values along with the attributes of $29$ subjects along with their attributes (class labels) such as age, gender, and left/right/both hands application usage. We extract features from the raw signals and use them to perform classification using different machine learning (ML) algorithms. Using statistical analysis, we show the importance of different features towards the prediction of class labels. In the end, we use the trained ML model on our data to extract unknown features from a well known activity recognition data from UCI repository, which highlights the potential of privacy breach using ML models. This security analysis could help researchers in future to take appropriate steps to preserve the privacy of human subjects.

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arXiv2022

Benchmarking Machine Learning Robustness in Covid-19 Genome Sequence Classification

The rapid spread of the COVID-19 pandemic has resulted in an unprecedented amount of sequence data of the SARS-CoV-2 genome -- millions of sequences and counting. This amount of data, while being orders of magnitude beyond the capacity of traditional approaches to understanding the diversity, dynamics, and evolution of viruses is nonetheless a rich resource for machine learning (ML) approaches as alternatives for extracting such important information from these data. It is of hence utmost importance to design a framework for testing and benchmarking the robustness of these ML models. This paper makes the first effort (to our knowledge) to benchmark the robustness of ML models by simulating biological sequences with errors. In this paper, we introduce several ways to perturb SARS-CoV-2 genome sequences to mimic the error profiles of common sequencing platforms such as Illumina and PacBio. We show from experiments on a wide array of ML models that some simulation-based approaches are more robust (and accurate) than others for specific embedding methods to certain adversarial attacks to the input sequences. Our benchmarking framework may assist researchers in properly assessing different ML models and help them understand the behavior of the SARS-CoV-2 virus or avoid possible future pandemics.

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arXiv2022

SsAG: Summarization and sparsification of Attributed Graphs

We present SsAG, an efficient and scalable lossy graph summarization method that retains the essential structure of the original graph. SsAG computes a sparse representation (summary) of the input graph and also caters to graphs with node attributes. The summary of a graph $G$ is stored as a graph on supernodes (subsets of vertices of $G$), and a weighted superedge connects two supernodes. The proposed method constructs a summary graph on $k$ supernodes that minimize the reconstruction error (difference between the original graph and the graph reconstructed from the summary) and maximum homogeneity with respect to attributes. We construct the summary by iteratively merging a pair of nodes. We derive a closed-form expression to efficiently compute the reconstruction error after merging a pair and approximate this score in constant time. To reduce the search space for selecting the best pair for merging, we assign a weight to each supernode that closely quantifies the contribution of the node in the score of the pairs containing it. We choose the best pair for merging from a random sample of supernodes selected with probability proportional to their weights. A logarithmic-sized sample yields a comparable summary based on various quality measures with weighted sampling. We propose a sparsification step for the constructed summary to reduce the storage cost to a given target size with a marginal increase in reconstruction error. Empirical evaluation on several real-world graphs and comparison with state-of-the-art methods shows that SsAG is up to $5\times$ faster and generates summaries of comparable quality.

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arXiv2022

Short-Term Load Forecasting Using AMI Data

Accurate short-term load forecasting is essential for the efficient operation of the power sector. Forecasting load at a fine granularity such as hourly loads of individual households is challenging due to higher volatility and inherent stochasticity. At the aggregate levels, such as monthly load at a grid, the uncertainties and fluctuations are averaged out; hence predicting load is more straightforward. This paper proposes a method called Forecasting using Matrix Factorization (\textsc{fmf}) for short-term load forecasting (\textsc{stlf}). \textsc{fmf} only utilizes historical data from consumers' smart meters to forecast future loads (does not use any non-calendar attributes, consumers' demographics or activity patterns information, etc.) and can be applied to any locality. A prominent feature of \textsc{fmf} is that it works at any level of user-specified granularity, both in the temporal (from a single hour to days) and spatial dimensions (a single household to groups of consumers). We empirically evaluate \textsc{fmf} on three benchmark datasets and demonstrate that it significantly outperforms the state-of-the-art methods in terms of load forecasting. The computational complexity of \textsc{fmf} is also substantially less than known methods for \textsc{stlf} such as long short-term memory neural networks, random forest, support vector machines, and regression trees.

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arXiv2022

PWM2Vec: An Efficient Embedding Approach for Viral Host Specification from Coronavirus Spike Sequences

COVID-19 pandemic, is still unknown and is an important open question. There are speculations that bats are a possible origin. Likewise, there are many closely related (corona-) viruses, such as SARS, which was found to be transmitted through civets. The study of the different hosts which can be potential carriers and transmitters of deadly viruses to humans is crucial to understanding, mitigating and preventing current and future pandemics. In coronaviruses, the surface (S) protein, or spike protein, is an important part of determining host specificity since it is the point of contact between the virus and the host cell membrane. In this paper, we classify the hosts of over five thousand coronaviruses from their spike protein sequences, segregating them into clusters of distinct hosts among avians, bats, camels, swines, humans and weasels, to name a few. We propose a feature embedding based on the well-known position-weight matrix (PWM), which we call PWM2Vec, and use to generate feature vectors from the spike protein sequences of these coronaviruses. While our embedding is inspired by the success of PWMs in biological applications such as determining protein function, or identifying transcription factor binding sites, we are the first (to the best of our knowledge) to use PWMs in the context of host classification from viral sequences to generate a fixed-length feature vector representation. The results on the real world data show that in using PWM2Vec, we are able to perform comparably well as compared to baseline models. We also measure the importance of different amino acids using information gain to show the amino acids which are important for predicting the host of a given coronavirus.

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arXiv2021

Spike2Vec: An Efficient and Scalable Embedding Approach for COVID-19 Spike Sequences

With the rapid global spread of COVID-19, more and more data related to this virus is becoming available, including genomic sequence data. The total number of genomic sequences that are publicly available on platforms such as GISAID is currently several million, and is increasing with every day. The availability of such \emph{Big Data} creates a new opportunity for researchers to study this virus in detail. This is particularly important with all of the dynamics of the COVID-19 variants which emerge and circulate. This rich data source will give us insights on the best ways to perform genomic surveillance for this and future pandemic threats, with the ultimate goal of mitigating or eliminating such threats. Analyzing and processing the several million genomic sequences is a challenging task. Although traditional methods for sequence classification are proven to be effective, they are not designed to deal with these specific types of genomic sequences. Moreover, most of the existing methods also face the issue of scalability. Previous studies which were tailored to coronavirus genomic data proposed to use spike sequences (corresponding to a subsequence of the genome), rather than using the complete genomic sequence, to perform different machine learning (ML) tasks such as classification and clustering. However, those methods suffer from scalability issues. In this paper, we propose an approach called Spike2Vec, an efficient and scalable feature vector representation for each spike sequence that can be used for downstream ML tasks. Through experiments, we show that Spike2Vec is not only scalable on several million spike sequences, but also outperforms the baseline models in terms of prediction accuracy, F1 score, etc.

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arXiv2021

Efficient Analysis of COVID-19 Clinical Data using Machine Learning Models

Because of the rapid spread of COVID-19 to almost every part of the globe, huge volumes of data and case studies have been made available, providing researchers with a unique opportunity to find trends and make discoveries like never before, by leveraging such big data. This data is of many different varieties, and can be of different levels of veracity e.g., precise, imprecise, uncertain, and missing, making it challenging to extract important information from such data. Yet, efficient analyses of this continuously growing and evolving COVID-19 data is crucial to inform -- often in real-time -- the relevant measures needed for controlling, mitigating, and ultimately avoiding viral spread. Applying machine learning based algorithms to this big data is a natural approach to take to this aim, since they can quickly scale to such data, and extract the relevant information in the presence of variety and different levels of veracity. This is important for COVID-19, and for potential future pandemics in general. In this paper, we design a straightforward encoding of clinical data (on categorical attributes) into a fixed-length feature vector representation, and then propose a model that first performs efficient feature selection from such representation. We apply this approach on two clinical datasets of the COVID-19 patients and then apply different machine learning algorithms downstream for classification purposes. We show that with the efficient feature selection algorithm, we can achieve a prediction accuracy of more than 90\% in most cases. We also computed the importance of different attributes in the dataset using information gain. This can help the policy makers to focus on only certain attributes for the purposes of studying this disease rather than focusing on multiple random factors that may not be very informative to patient outcomes.

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arXiv2021

Robust Representation and Efficient Feature Selection Allows for Effective Clustering of SARS-CoV-2 Variants

The widespread availability of large amounts of genomic data on the SARS-CoV-2 virus, as a result of the COVID-19 pandemic, has created an opportunity for researchers to analyze the disease at a level of detail unlike any virus before it. One one had, this will help biologists, policy makers and other authorities to make timely and appropriate decisions to control the spread of the coronavirus. On the other hand, such studies will help to more effectively deal with any possible future pandemic. Since the SARS-CoV-2 virus contains different variants, each of them having different mutations, performing any analysis on such data becomes a difficult task. It is well known that much of the variation in the SARS-CoV-2 genome happens disproportionately in the spike region of the genome sequence -- the relatively short region which codes for the spike protein(s). Hence, in this paper, we propose an approach to cluster spike protein sequences in order to study the behavior of different known variants that are increasing at very high rate throughout the world. We use a k-mers based approach to first generate a fixed-length feature vector representation for the spike sequences. We then show that with the appropriate feature selection, we can efficiently and effectively cluster the spike sequences based on the different variants. Using a publicly available set of SARS-CoV-2 spike sequences, we perform clustering of these sequences using both hard and soft clustering methods and show that with our feature selection methods, we can achieve higher F1 scores for the clusters.

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