A Enhanced Approach for Identification of Tuberculosis for Chest X-Ray Image using Machine Learning

Lungs are the primary organs affected by the infectious illness tuberculosis (TB). Mycobacterium tuberculosis, often known as Mtb, is the bacterium that causes tuberculosis. When a person speaks, spits, coughs, or breathes in, active tuberculosis can quickly spread through the air. Early TB diagnosis takes some time. Early detection of the bacilli allows for straightforward therapy. Chest X-ray images, sputum images, computer-assisted identification, feature selection, neural networks, and active contour technologies are used to diagnose human tuberculosis. Even when several approaches are used in conjunction, a more accurate early TB diagnosis can still be made. Worldwide, this leads to a large number of fatalities. An efficient technology known as the Deep Learning approach is used to diagnose tuberculosis microorganisms. Because this technology outperforms the present methods for early TB diagnosis, Despite the fact that death cannot be prevented, it is possible to lessen its effects

Diagnosis of Smear-Negative Pulmonary Tuberculosis using Ensemble Method: A Preliminary Research

Indonesia is one of 22 countries with the highest burden of Tuberculosis in the world. According to WHO’s 2015 report, Indonesia was estimated to have one million new tuberculosis (TB) cases per year. Unfortunately, only one-third of new TB cases are detected. Diagnosis of TB is difficult, especially in the case of smear-negative pulmonary tuberculosis (SNPT). The SNPT is diagnosed by TB trained doctors based on physical and laboratory examinations. This study is preliminary research that aims to determine the ensemble method with the highest level of accuracy in the diagnosis model of SNPT. This model is expected to be a reference in the development of the diagnosis of new pulmonary tuberculosis cases using input in the form of symptoms and physical examination in accordance with the guidelines for tuberculosis management in Indonesia. The proposed SNPT diagnosis model can be used as a cost-effective tool in conditions of limited resources. Data were obtained from medical records of tuberculosis patients from the Jakarta Respiratory Center. The results show that the Random Forest has the best accuracy, which is 90.59%, then Adaboost of 90.54% and Bagging of 86.91%

Automatic Chest X-rays Analysis using Statistical Machine Learning Strategies

Tuberculosis (TB) is a disease responsible for the deaths of more than one million people worldwide every year. Even though it is preventable and curable, it remains a major threat to humanity that needs to be taken care of. It is often diagnosed in developed countries using approaches such as sputum smear microscopy and culture methods. However, since these approaches are rather expensive, they are not commonly used in poor regions of the globe such as India, Africa, and Bangladesh. Instead, the well known and affordable chest x-ray (CXR) interpretation by radiologists is the technique employed in those places. Nevertheless, if this method is obsolete in other parts of the world nowadays it is because of its many flaws including: i) it is a tedious task that requires experienced medical personnel --which is scarce given the high demand for it--, ii) it is manual and difficult when executed for a large population, and iii) it is prone to human error depending on the proficiency and aptitude of the interpreter. Researchers have thus been trying to overcome these challenges over the years by proposing software solutions that mainly involve computer vision, artificial intelligence, and machine learning. The problems with these existing solutions are that they are either complex or not reliable enough. The need for better solutions in this specific domain as well as my desire to bring my contribution to something meaningful are what led us to investigate in this direction. In this manuscript, I propose a simple fully automatic software solution that uses only machine learning and image processing to analyze and detect anomalies related to TB in CXR scans. My system starts by extracting the region of interest from the incoming images, then performs a computationally inexpensive yet efficient feature extraction that involves edge detection using Laplacian of Gaussian and positional information retention. The extracted features are then fed to a regular random forest classifier for discrimination. I tested the system on two benchmark data collections --Montgomery and Shenzhen-- and obtained state-of-the-art results that reach up to 97% classification accuracy

Protein Fold Recognition Using Neural Networks

To predict accurately the three-dimensional (3D) structures of proteins from their amino acid sequences alone remains a challenging problem. However, using protein fold recognition tools, it is often possible to achieve good models or at least to gain some more information, to aid scientists in their research. This thesis describes development of TUNE (Threading Using Neural Networks), a fold recognition program using artificial neural network (ANN) models. A new method to generate amino acid substitution matrices is described in chapter two. It uses an ANN to generalise amino acid substitutions observed in protein structure alignments. Matrices for alignment scoring from this approach were compared with classic alignment scoring schemes. From these neural network models, a series of encoding schemes were constructed. These schemes describe the amino acid types with a few numbers. They were generated to replace the orthogonal encoding scheme, so that smaller, faster and more accurate neural network models can be applied on bioinformatic problems. The TUNE model was introduced in chapter four to measure protein sequence-structure compatibility. Given the integrated residue structural environment descriptions, the model predicts probabilities of observing amino acid types in such environments. Using this model, a scoring function to measure the fitness of a residue in a protein structure model can be made for protein threading programs. The model in chapter two was extended by including the residue structural environment descriptions for predictions. A simple protein fold recognition program with a dynamic programming algorithm was developed using this model. The program was then tested in the fourth round of the Critical Assessment of protein Structure Prediction methods (CASP4) and produced reasonably good results

Tackling complexity in biological systems: Multi-scale approaches to tuberculosis infection

Tuberculosis is an ancient disease responsible for more than a million deaths per year worldwide, whose complex infection cycle involves dynamical processes that take place at different spatial and temporal scales, from single pathogenic cells to entire hosts' populations. In this thesis we study TB disease at different levels of description from the perspective of complex systems sciences. On the one hand, we use complex networks theory for the analysis of cell interactomes of the causative agent of the disease: the bacillus Mycobacterium tuberculosis. Here, we analyze the gene regulatory network of the bacterium, as well as its network of protein interactions and the way in which it is transformed as a consequence of gene expression adaptation to disparate environments. On the other hand, at the level of human societies, we develop new models for the description of TB spreading on complex populations. First, we develop mathematical models aimed at addressing, from a conceptual perspective, the interplay between complexity of hosts' populations and certain dynamical traits characteristic of TB spreading, like long latency periods and syndemic associations with other diseases. On the other hand, we develop a novel data-driven model for TB spreading with the objective of providing faithful impact evaluations for novel TB vaccines of different types

The application of biomedical engineering techniques to the diagnosis and management of tropical diseases: A review

This paper reviews a number of biomedical engineering approaches to help aid in the detection and treatment of tropical diseases such as dengue, malaria, cholera, schistosomiasis, lymphatic filariasis, ebola, leprosy, leishmaniasis, and American trypanosomiasis (Chagas). Many different forms of non-invasive approaches such as ultrasound, echocardiography and electrocardiography, bioelectrical impedance, optical detection, simplified and rapid serological tests such as lab-on-chip and micro-/nano-fluidic platforms and medical support systems such as artificial intelligence clinical support systems are discussed. The paper also reviewed the novel clinical diagnosis and management systems using artificial intelligence and bioelectrical impedance techniques for dengue clinical applications

Protein interface prediction using graph convolutional networks

2017 Fall.Includes bibliographical references.Proteins play a critical role in processes both within and between cells, through their interactions with each other and other molecules. Proteins interact via an interface forming a protein complex, which is difficult, expensive, and time consuming to determine experimentally, giving rise to computational approaches. These computational approaches utilize known electrochemical properties of protein amino acid residues in order to predict if they are a part of an interface or not. Prediction can occur in a partner independent fashion, where amino acid residues are considered independently of their neighbor, or in a partner specific fashion, where pairs of potentially interacting residues are considered together. Ultimately, prediction of protein interfaces can help illuminate cellular biology, improve our understanding of diseases, and aide pharmaceutical research. Interface prediction has historically been performed with a variety of methods, to include docking, template matching, and more recently, machine learning approaches. The field of machine learning has undergone a revolution of sorts with the emergence of convolutional neural networks as the leading method of choice for a wide swath of tasks. Enabled by large quantities of data and the increasing power and availability of computing resources, convolutional neural networks efficiently detect patterns in grid structured data and generate hierarchical representations that prove useful for many types of problems. This success has motivated the work presented in this thesis, which seeks to improve upon state of the art interface prediction methods by incorporating concepts from convolutional neural networks. Proteins are inherently irregular, so they don't easily conform to a grid structure, whereas a graph representation is much more natural. Various convolution operations have been proposed for graph data, each geared towards a particular application. We adapted these convolutions for use in interface prediction, and proposed two new variants. Neural networks were trained on the Docking Benchmark Dataset version 4.0 complexes and tested on the new complexes added in version 5.0. Results were compared against the state of the art method partner specific method, PAIRpred [1]. Results show that multiple variants of graph convolution outperform PAIRpred, with no method emerging as the clear winner. In the future, additional training data may be incorporated from other sources, unsupervised pretraining such as autoencoding may be employed, and a generalization of convolution to simplicial complexes may also be explored. In addition, the various graph convolution approaches may be applied to other applications with graph structured data, such as Quantitative Structure Activity Relationship (QSAR) learning, and knowledge base inference

Deep Learning in Medical Image Analysis

The accelerating power of deep learning in diagnosing diseases will empower physicians and speed up decision making in clinical environments. Applications of modern medical instruments and digitalization of medical care have generated enormous amounts of medical images in recent years. In this big data arena, new deep learning methods and computational models for efficient data processing, analysis, and modeling of the generated data are crucially important for clinical applications and understanding the underlying biological process. This book presents and highlights novel algorithms, architectures, techniques, and applications of deep learning for medical image analysis

The dynamics of complex systems. Studies and applications in computer science and biology

Our research has focused on the study of complex dynamics and on their use in both information security and bioinformatics. Our first work has been on chaotic discrete dynamical systems, and links have been established between these dynamics on the one hand, and either random or complex behaviors. Applications on information security are on the pseudorandom numbers generation, hash functions, informationhiding, and on security aspects on wireless sensor networks. On the bioinformatics level, we have applied our studies of complex systems to theevolution of genomes and to protein folding