Aims and Scope

The Open Bioinformatics Journal is an Open Access online journal, which publishes research articles, reviews/mini-reviews, letters, clinical trial and guest edited single topic issues in all areas of bioinformatics and computational biology. The coverage includes biomedicine, focusing on large data acquisition, analysis and curation, computational and statistical methods for the modeling and analysis of biological data, and descriptions of new algorithms and databases.


The Open Bioinformatics Journal, a peer reviewed journal, is an important and reliable source of current information on the developments in the field. The emphasis will be on publishing quality articles rapidly and freely available worldwide.


Recent Articles

Machine Learning Techniques used for the Histopathological Image Analysis of Oral Cancer-A Review

Santisudha Panigrahi, Tripti Swarnkar

Oral diseases are the 6th most revealed malignancy happening in head and neck regions found mainly in south Asian countries. It is the most common cancer with fourteen deaths in an hour on a yearly basis, as per the WHO oral cancer incidence in India. Due to the cost of tests, mistakes in the recognition procedure, and the enormous remaining task at hand of the cytopathologist, oral growths cannot be diagnosed promptly. This area is open to be looked into by biomedical analysts to identify it at an early stage. At present, with the advent of entire slide computerized scanners and tissue histopathology, there is a gigantic aggregation of advanced digital histopathological images, which has prompted the necessity for their analysis. A lot of computer aided analysis techniques have been developed by utilizing machine learning strategies for prediction and prognosis of cancer. In this review paper, first various steps of obtaining histopathological images, followed by the visualization and classification done by the doctors are discussed. As machine learning techniques are well known, in the second part of this review, the works done for histopathological image analysis as well as other oral datasets using these strategies for growth prognosis and anticipation are discussed. Comparing the pitfalls of machine learning and how it has overcome by deep learning mostly for image recognition tasks are also discussed subsequently. The third part of the manuscript describes how deep learning is beneficial and widely used in different cancer domains. Due to the remarkable growth of deep learning and wide applicability, it is best suited for the prognosis of oral disease. The aim of this review is to provide insight to the researchers opting to work for oral cancer by implementing deep learning and artificial neural networks.


November 30, 2020
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Editor's Choice

Data Mining Approach to Identify Disease Cohorts from Primary Care Electronic Medical Records: A Case of Diabetes Mellitus

Ebenezer S. Owusu Adjah, Olga Montvida, Julius Agbeve, Sanjoy K. Paul

Background:

Identification of diseased patients from primary care based electronic medical records (EMRs) has methodological challenges that may impact epidemiologic inferences.

Objective:

To compare deterministic clinically guided selection algorithms with probabilistic machine learning (ML) methodologies for their ability to identify patients with type 2 diabetes mellitus (T2DM) from large population based EMRs from nationally representative primary care database.

Methods:

Four cohorts of patients with T2DM were defined by deterministic approach based on disease codes. The database was mined for a set of best predictors of T2DM and the performance of six ML algorithms were compared based on cross-validated true positive rate, true negative rate, and area under receiver operating characteristic curve.

Results:

In the database of 11,018,025 research suitable individuals, 379 657 (3.4%) were coded to have T2DM. Logistic Regression classifier was selected as best ML algorithm and resulted in a cohort of 383,330 patients with potential T2DM. Eighty-three percent (83%) of this cohort had a T2DM code, and 16% of the patients with T2DM code were not included in this ML cohort. Of those in the ML cohort without disease code, 52% had at least one measure of elevated glucose level and 22% had received at least one prescription for antidiabetic medication.

Conclusion:

Deterministic cohort selection based on disease coding potentially introduces significant mis-classification problem. ML techniques allow testing for potential disease predictors, and under meaningful data input, are able to identify diseased cohorts in a holistic way.


December 12, 2017
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