aftabhussain / gene-subseq-analysis

An ML Framework for Gene Subsequence Analysis

In this exploratory work, we try to build an approach to investigate the relationship between gene subsequences and gene families.

Synthetic Dataset Details

We apply the approach on a synthetic dataset, where each sample has the following construct:

{
	gene_sequence: <>,
        gene_family: <>
}

A gene sequence is represented as a sequence of characters, where each character represents a neocleotide. For our exploratory study, we consider the following neocleotides: A, C, G, T, where each of them correspond to the four nucleotide bases of a DNA strand. We consider the following gene families: INS, TP53, HBB.

The synthetic dataset consists of 50,000 samples (40k train, 5k validation, and 5k test samples). Each gene sequence consists of 150 characters. Here is an example:

{
	gene_sequence: ["A","T",...,"C"],
        gene_family: "INS"
}

Motivation behind Building the Framework

We want to create a machine-learning framework to check if there are relationships between certain features of gene subsequences and the families of genes.

Construction of Nucleotide-Count Subsequence Feature from Dataset

We construct the feature Subs_k_N, the number of subsequences in a gene sequence where the total number of neocleotides of type N is k. We find this feature for each nucleotide using a hash-map-based prefix-sum approach. The complexity of the approach is O(n) where n is the number of characters in the given sample.

After adding a feature for each nucleotide for each sample, our sample has the following fields (a dummy example for k=3):

{
	gene_sequence: ["A","T",...,"C"],
        gene_family: "INS",
        subseqs_A_k3: 12,
        subseqs_T_k3: 84,
        subseqs_G_k3: 7,
        subseqs_C_k3: 4
}

Applying ML Algorithms to Analyze Relationship between Gene Subsequence and Family

We build a tool using which different machine learning algorithms can be applied to predict gene family from nucleotide-count subsequence feature.

References

• Wikipedia, Nucleic Acid Sequence (link)