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Machine learning has multiple applications in diverse fields, ranging from natural language processing to healthcare. Bioinformatics and biology-related disciplines have not been left behind in the revolution. Before machine learning emerged, these disciplines faced the problem of extracting valuable insights from large biological datasets. But as of today, ML techniques such as deep learning can learn the features of complex datasets and present them in a manner that is easy to understand.
In this article, we are going to take a closer look at machine learning in bioinformatics and biology. But before that, let’s begin by having a quick look at what machine learning in biology and bioinformatics really mean.
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Machine learning is a subset of artificial intelligence that gives systems the ability to learn from data and perform tasks without being explicitly programmed. While this technology has been around for years, it is a recent development to apply complex mathematical calculations to big data. Below are some widely-used machine learning applications that you might already be familiar with:
Of course, the list of examples is far longer, but that’s a different story.
There are three main branches of machine learning models. These include:
With the basics explained, let’s focus on bioinformatics.
Shortly put, bioinformatics is the application of computation and analysis techniques to capture and interpret biological data. It’s an interdisciplinry field between computer science, mathematics, statistics, biology, and genetics. Bioinformatics is mainly used to identify genes and nucleotides to understand genetic diseases better. It’s closely related to computational biology. Most people use the two terms interchangeably. But in the real sense, they are two distinct fields.
Let’s have a closer look at the two.
Computational biology and bioinformatics are interdisciplinary approaches to life sciences. They draw from empirical disciplines such as information science, computer science, physics, and mathematics.
Both fields have emerged from the rapid growth of bio enterprise around the globe and are often used in research centers, laboratories, and colleges.
While the two disciplines may sound similar, they are distinct in the kinds of needs they address.
Below are some of the main differences between them for reference and clarification.
Genomics is an essential domain of bioinformatics that focuses on studying genome mapping, evolution, and editing. A genome is a complete set of genetic material found in an organism. There are three main subsets of genomics;
Currently, the industry has a wide range of products and services in the commercial sector, thanks to machine learning. According to research, the industry is projected to reach a smashing 54.4 billion USD by 2025[1]. Some of the applications of the ML in genomics include:
It plays a pivotal role in medical diagnostics. Machine learning empowered DNA sequencing techniques such as next-generation sequencing[2] has made it possible for researchers to sequence human genomes in a day, as compared to the traditional Sanger Sequencing Technology that took over a decade to sequence a human genome.
Gene editing is the process of manipulating the genetic composition of an organism by inserting, deleting, or replacing a DNA sequence. It uses a technology called CRISPR[3], which is a faster and cheaper method of conducting the process.
However, researchers still need to do the legwork of selecting the right DNA sequence, which can be a long process susceptible to errors. Machine learning has come to the rescue by making it easier to identify the correct target audience, significantly reducing the cost and time required to perform gene editing.
Machine learning has hugely impacted the clinical workflow process. For example, healthcare personnel has always had problems accessing patient data, which lies within electronic records, paper charts, and other sources. But with the development of ML-enabled technologies such as Intel’s Analytics Toolkit, healthcare facilities can now make the most out of patient data.
Proteomics is the study of protein components, their interactions with each other, and their roles in an organism. Mass-spectrometry-enabled proteomics has made it possible to analyze thousands of human proteins. However, computational and experimental challenges have restricted its progress, requiring informatics solutions such as machine learning to analyze and interpret massive biological data sets. Mass spectrometry is an analytical tool used to characterize biological samples and is used in omics studies due to its high throughput activities.
Mass spectrometry does not measure proteins directly in their conventional form. Instead, it splits them up into smaller chunks of amino acid sequences of about 30 building blocks. It then compares them with the database and assigns the amino acids to specific proteins. The results are not entirely accurate because some proteins are not recognized correctly.
Machine learning methods can be applied to identify a wide range of proteins from a given sample. They can be used on:
These techniques have been helpful in the diagnosis of different types of diseases and have an obvious advantage over traditional methods such as enzyme-linked immunosorbent assays (ELISAs), protein arrays, affinity separation, 2D gel electrophoresis, among others.
Recent advancements in the use of Machine learning in proteomics include the development of a software called Prosit[4]. It was used successfully by a team of researchers in the Technical University of Munich (TUM) to quickly recognize protein patterns without errors.
Microarrays are laboratory tools used to detect multiple gene expressions at a go. With the increasing popularity of genetic studies in animals, plants, and microbes, this technology is helpful in studying genome organization, gene expression, and chromatin structures.
A microarray is made up of different probes (DNA, RNA, tissues, proteins, and peptides) that correspond to gene segments placed in a specific arrangement, mostly on a silicon microchip or glass slide. The theory behind this technology is that complementary sequences will bind to each other under the right conditions, while non-contemporary ones will not bind. The level of hybridization between contemporary probes is indicated by fluorescence.
The level of complexity in microarray data sets is increasing at a rapid pace. Large-scale experiments require thousands of probes to be monitored simultaneously. Machine learning has made it easier to spot significant interactions involved in complex experiments. It has been used widely in microarray analysis, with gene classification and clustering being some of the most cited examples.
Neural Designer, for example, has made it possible for researchers to discover intricate relationships and identify complex patterns in microarray data by use of machine learning methods. And public databases such as Array Express records all the information about a microarray experiment, making it readily available for reuse by the research community.
Some of the applications of machine learning methods on microarrays include:
Text mining is also referred to as text analytics. It’s a machine learning-powered technology that uses natural language processing to examine large volumes of documents and discover new information that helps answer research questions.
The increase in biological publications has made it difficult for researchers to search through different sources and compile relevant information on a given topic. Machine learning can work through different types of human-generated reports in databases to process and analyze data, reducing labor costs and speeding up the research process without compromising quality.
ML text analysis can be used in bioinformatics for:
Systems biology is the computational and mathematical analysis of the interactions and behavior of biological components such as molecules, cells, organs, and organisms. Computational modeling is a valuable tool used in this discipline. It uses mathematical modeling to capture the interactions between biological components and simulate the whole system’s behavior. However, it’s hard to build a steady mathematical model due to the complexity and lack of proper understanding of the underlying mechanisms.
But with the use of data-driven machine learning methods, it has become easier to model complex interactions in domains such as signal transduction networks, genetic networks, and metabolic pathways.
Machine learning is helpful in biological systems with sufficient biological data but not enough biological knowledge to develop theory-based models. A great example is the identification of the relationship between the phenotype and genotype of S. cerevisiae.
Even though there are many strains of characterized phonomes and genomes, there is still the unavailability of theory-based models that illustrate how the difference in genotypes dictates the strain phenotypes. Machine learning is used in this situation to establish the relationship between phenotypes and genotypes by training a supervised model with genomes as input and phenomes as an output. The interpretation of the resulting model gives hints on the critical genetic composition of the organism. It helps in the identification of the most crucial factors that contributes to the model’s predictive power.
One of the most used machine learning techniques in systems biology is the probabilistic graphical model. It figures out the structure between different variables and is used to model genetic networks. Another common technique is genetic algorithms. It’s based on the natural process of evolution and has also been used to model genetic networks and regulatory structures.
Machine learning is also used to solve systems biology problems such as the identification of transcription binding sites by the use of a technique called Markov chain optimization. A Markov Chain is a stochastic model that describes a sequence of possible events by relying on biological data obtained from previous events.
Machine learning and artificial intelligence are being used extensively in healthcare facilities to improve patient care and enhance the quality of life. Soon, hospitals might be able to use machine learning-based technology to obtain real-time data from multiple healthcare systems in different countries, increasing the efficiency of treatment. Some of the main applications of ML in healthcare include:
Machine learning is widely used in the early stages of drug discovery processes. Some of the research and development technologies used include precision medicine and next-generation sequencing. They have proven to be helpful in finding alternative options for multifactorial disease therapy.
Deep learning and machine learning have been used on a breakthrough technology known as computer vision. The technology has found acceptance in a wide range of applications. An example is Microsoft’s InnerEye project that builds innovative tools for quantitative analysis of 3D medical images.
Predictive analytics can be used on patient data to facilitate personalized treatment. Currently, doctors are limited to a specific set of diagnoses or are forced to estimate the risk of a disease on a patient based on their health history and limited genetic information. However, this could change soon because machine learning is making great strides in medicine by leveraging patient data to help generate a wide range of treatment options.
Machine learning uses pattern recognition to help diagnose, treat, and predict complications in various neurological diseases. Over the past few years, Acute Ischemic Stroke (AIS) treatment has experienced significant advancement. Machine learning algorithms are now being used to predict motor deficits in stroke patients. The most commonly used methods are Support Vector Machines (SVM), and 3D Conventional Neural Network (CNN).
This is a deep-learning tool that is used in genome data mining. It can predict common genetic variations more accurately as compared to previous classical methods. DeepVariant is one of the first biological tools that leverage machine learning and Google’s computing to provide a scalable, cloud-based solution that satisfies the needs of the most complex genomics data sets.
Atomwise is a biotech company based in San Francisco that developed the first deep learning-based algorithm that helps convert molecules to 3D pixels. This conversion helps in the study of the 3D structure of proteins and other molecules with atomic precision.
Also, it basically predicts molecules that can possibly interact with a specific protein. The algorithms are mainly used in drug discovery.
In the past, biological imaging software could only measure a single parameter of a group of images. However, that has changed, thanks to machine-learning methods. Scientists can now prepare and image a countless number of samples per day by using the CellProfiler software.
Moreover, the software can quantitatively measure individual features such as the number of fluorescent cells in a microscopy field. It can also point out thousands of cell features by the use of deep learning techniques.
Machine learning through deep learning algorithms extracts meaningful information from huge datasets such as genomes or a group of images and builds a model based on the extracted features. The model is then used to perform analysis on other biological datasets.
One of the most pressing issues in bioinformatics and biology as a whole is the processing of huge datasets generated by newly developed technologies into meaningful information. However, as we step into the era of artificial intelligence and big data, machine learning in bioinformatics is taking a central role in carrying out this transformation.
This article has highlighted some of the essential concepts of machine learning and its recent applications in biology and bioinformatics. We have seen that ML can be used to devise complex algorithms and models that help in the prediction of trends across different biological disciplines. Ultimately, for these models to succeed, they need quality data in terms of statistical power and sample sizes.
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Machine learning is a subset of artificial intelligence that enables systems to learn from data and perform tasks without explicit programming. Applications include personalized product recommendations, fraud detection, predictive algorithms, and online data analytics.
What is bioinformatics?
Bioinformatics involves applying computational and analytical techniques to capture and interpret biological data, focusing on identifying genes and nucleotides to understand genetic diseases.
Bioinformatics: Solves biological issues by analyzing biodata, developing codes, algorithms, and models.
Computational Biology: Finds solutions to problems arising from bioinformatics studies, focusing on stochastic models and genetic analysis.
Machine learning methods analyze mass spectral peaks and identify proteins from sequence databases, aiding in disease diagnosis and biological sample analysis.
Machine learning simplifies spotting significant interactions in complex experiments, aiding in gene analysis, differentiating gene stages, predicting future gene changes, and disease prevention.
Text mining uses natural language processing to examine large volumes of documents, discovering new information to answer research questions. It aids in large-scale protein interaction analysis, searching for novel drug targets, and gene function annotation.
Machine learning models complex interactions in biological systems with sufficient data but insufficient theoretical knowledge, using techniques like probabilistic graphical models and genetic algorithms.
Machine learning extracts meaningful information from large datasets, builds predictive models, and aids in the transformation of biological data into actionable insights, improving research and clinical outcomes.
This article is an updated version of the publication from Sep 21, 2021.
[1] Marketsandmarkets.com. Genomics Market by Product & Service. URL: https://bit.ly/3Am0N6I. Accessed Sep 20, 2021.
[2] NCBI.gov. What is next generation sequencing?. URL: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3841808/. Accessed Sep 20, 2021.
[3] Nature.com. CRISPR, the disruptor, issue 522, 2015. URL: https://www.nature.com/articles/522020a. Accessed Sep 20, 2021.
[4] ScienceDaily.com. Artificial intelligence boosts proteome research. URL: https://www.sciencedaily.com/releases/2019/05/190529113044.htm. Accessed Sep 20, 2021.
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