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

arXiv: https://arxiv.org/abs/2211.10546 · HTML: https://mlsanity.com/paper/2211.10546/

## Key facts

- Cited by 3 papers in the map (data through 14 Oct 2026).
- Builds on 16 of its 39 references that are in the map.
- First posted on arXiv 19 Nov 2022.

## Builds on (most cited first, 16 of 16)

- [node2vec: Scalable Feature Learning for Networks](https://mlsanity.com/paper/1607.00653/) (2016)
- [DeepWalk: Online Learning of Social Representations](https://mlsanity.com/paper/1403.6652/) (2014)
- [Spike2Vec: An Efficient and Scalable Embedding Approach for COVID-19 Spike Sequences](https://mlsanity.com/paper/2109.05019/) (2021)
- [A k-mer Based Approach for SARS-CoV-2 Variant Identification](https://mlsanity.com/paper/2108.03465/) (2021)
- [PWM2Vec: An Efficient Embedding Approach for Viral Host Specification from Coronavirus Spike Sequences](https://mlsanity.com/paper/2201.02273/) (2022)
- [Efficient Approximate Kernel Based Spike Sequence Classification](https://mlsanity.com/paper/2209.04952/) (2022)
- [Predicting Attributes of Nodes Using Network Structure](https://mlsanity.com/paper/1912.12264/) (2019)
- [Effective and scalable clustering of SARS-CoV-2 sequences](https://mlsanity.com/paper/2108.08143/) (2021)
- [Detecting DDoS Attack on SDN Due to Vulnerabilities in OpenFlow](https://mlsanity.com/paper/1912.12221/) (2019)
- [Effect of Analysis Window and Feature Selection on Classification of Hand Movements Using EMG Signal](https://mlsanity.com/paper/2002.00461/) (2020)
- [Robust Representation and Efficient Feature Selection Allows for Effective Clustering of SARS-CoV-2 Variants](https://mlsanity.com/paper/2110.09622/) (2021)
- [Short-Term Load Forecasting Using AMI Data](https://mlsanity.com/paper/1912.12479/) (2019)
- [Reads2Vec: Efficient Embedding of Raw High-Throughput Sequencing Reads Data](https://mlsanity.com/paper/2211.08267/) (2022)
- [Efficient Analysis of COVID-19 Clinical Data using Machine Learning Models](https://mlsanity.com/paper/2110.09606/) (2021)
- [Benchmarking Machine Learning Robustness in Covid-19 Genome Sequence Classification](https://mlsanity.com/paper/2207.08898/) (2022)
- [Impact Of Missing Data Imputation On The Fairness And Accuracy Of Graph Node Classifiers](https://mlsanity.com/paper/2211.00783/) (2022)

## Built on by (most cited first, 3 of 3)

- [BioSequence2Vec: Efficient Embedding Generation For Biological Sequences](https://mlsanity.com/paper/2304.00291/) (2023)
- [ViralVectors: Compact and Scalable Alignment-free Virome Feature Generation](https://mlsanity.com/paper/2304.02891/) (2023)
- [Breaking the Euclidean Barrier: Hyperboloid-Based Biological Sequence Analysis](https://mlsanity.com/paper/2510.01118/) (2025)

## Abstract (arXiv)

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.