Machine learning methods for histopathological image analysis

Abundant accumulation of digital histopathological images has led to the increased demand for their analysis, such as computer-aided diagnosis using machine learning techniques. However, digital pathological images and related tasks have some issues to be considered. In this mini-review, we introduce the application of digital pathological image analysis using machine learning algorithms, address some problems specific to such analysis, and propose possible solutions.Comment: 23 pages, 4 figure

An incremental approach to automated protein localisation

Tscherepanow M, Jensen N, Kummert F. An incremental approach to automated protein localisation. BMC Bioinformatics. 2008;9(1): 445.Background: The subcellular localisation of proteins in intact living cells is an important means for gaining information about protein functions. Even dynamic processes can be captured, which can barely be predicted based on amino acid sequences. Besides increasing our knowledge about intracellular processes, this information facilitates the development of innovative therapies and new diagnostic methods. In order to perform such a localisation, the proteins under analysis are usually fused with a fluorescent protein. So, they can be observed by means of a fluorescence microscope and analysed. In recent years, several automated methods have been proposed for performing such analyses. Here, two different types of approaches can be distinguished: techniques which enable the recognition of a fixed set of protein locations and methods that identify new ones. To our knowledge, a combination of both approaches – i.e. a technique, which enables supervised learning using a known set of protein locations and is able to identify and incorporate new protein locations afterwards – has not been presented yet. Furthermore, associated problems, e.g. the recognition of cells to be analysed, have usually been neglected. Results: We introduce a novel approach to automated protein localisation in living cells. In contrast to well-known techniques, the protein localisation technique presented in this article aims at combining the two types of approaches described above: After an automatic identification of unknown protein locations, a potential user is enabled to incorporate them into the pre-trained system. An incremental neural network allows the classification of a fixed set of protein location as well as the detection, clustering and incorporation of additional patterns that occur during an experiment. Here, the proposed technique achieves promising results with respect to both tasks. In addition, the protein localisation procedure has been adapted to an existing cell recognition approach. Therefore, it is especially well-suited for high-throughput investigations where user interactions have to be avoided. Conclusion: We have shown that several aspects required for developing an automatic protein localisation technique – namely the recognition of cells, the classification of protein distribution patterns into a set of learnt protein locations, and the detection and learning of new locations – can be combined successfully. So, the proposed method constitutes a crucial step to render image-based protein localisation techniques amenable to large-scale experiments

Recognition of Characters from Streaming Videos

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Multimodal Machine Learning-based Knee Osteoarthritis Progression Prediction from Plain Radiographs and Clinical Data

Knee osteoarthritis (OA) is the most common musculoskeletal disease without a cure, and current treatment options are limited to symptomatic relief. Prediction of OA progression is a very challenging and timely issue, and it could, if resolved, accelerate the disease modifying drug development and ultimately help to prevent millions of total joint replacement surgeries performed annually. Here, we present a multi-modal machine learning-based OA progression prediction model that utilizes raw radiographic data, clinical examination results and previous medical history of the patient. We validated this approach on an independent test set of 3,918 knee images from 2,129 subjects. Our method yielded area under the ROC curve (AUC) of 0.79 (0.78-0.81) and Average Precision (AP) of 0.68 (0.66-0.70). In contrast, a reference approach, based on logistic regression, yielded AUC of 0.75 (0.74-0.77) and AP of 0.62 (0.60-0.64). The proposed method could significantly improve the subject selection process for OA drug-development trials and help the development of personalized therapeutic plans

Document Layout Analysis and Recognition Systems

Automatic extraction of relevant knowledge to domain-specific questions from Optical Character Recognition (OCR) documents is critical for developing intelligent systems, such as document search engines, sentiment analysis, and information retrieval, since hands-on knowledge extraction by a domain expert with a large volume of documents is intensive, unscalable, and time-consuming. There have been a number of studies that have automatically extracted relevant knowledge from OCR documents, such as ABBY and Sandford Natural Language Processing (NLP). Despite the progress, there are still limitations yet-to-be solved. For instance, NLP often fails to analyze a large document. In this thesis, we propose a knowledge extraction framework, which takes domain-specific questions as input and provides the most relevant sentence/paragraph to the given questions in the document. Overall, our proposed framework has two phases. First, an OCR document is reconstructed into a semi-structured document (a document with hierarchical structure of (sub)sections and paragraphs). Then, relevant sentence/paragraph for a given question is identified from the reconstructed semi structured document. Specifically, we proposed (1) a method that converts an OCR document into a semi structured document using text attributes such as font size, font height, and boldface (in Chapter 2), (2) an image-based machine learning method that extracts Table of Contents (TOC) to provide an overall structure of the document (in Chapter 3), (3) a document texture-based deep learning method (DoT-Net) that classifies types of blocks such as text, image, and table (in Chapter 4), and (4) a Question & Answer (Q&A) system that retrieves most relevant sentence/paragraph for a domain-specific question. A large number of document intelligent systems can benefit from our proposed automatic knowledge extraction system to construct a Q&A system for OCR documents. Our Q&A system has applied to extract domain specific information from business contracts at GE Power

Pedestrian Attribute Recognition: A Survey

Recognizing pedestrian attributes is an important task in computer vision community due to it plays an important role in video surveillance. Many algorithms has been proposed to handle this task. The goal of this paper is to review existing works using traditional methods or based on deep learning networks. Firstly, we introduce the background of pedestrian attributes recognition (PAR, for short), including the fundamental concepts of pedestrian attributes and corresponding challenges. Secondly, we introduce existing benchmarks, including popular datasets and evaluation criterion. Thirdly, we analyse the concept of multi-task learning and multi-label learning, and also explain the relations between these two learning algorithms and pedestrian attribute recognition. We also review some popular network architectures which have widely applied in the deep learning community. Fourthly, we analyse popular solutions for this task, such as attributes group, part-based, \emph{etc}. Fifthly, we shown some applications which takes pedestrian attributes into consideration and achieve better performance. Finally, we summarized this paper and give several possible research directions for pedestrian attributes recognition. The project page of this paper can be found from the following website: \url{https://sites.google.com/view/ahu-pedestrianattributes/}.Comment: Check our project page for High Resolution version of this survey: https://sites.google.com/view/ahu-pedestrianattributes

Machine Learning Techniques, Detection and Prediction of Glaucoma– A Systematic Review

Globally, glaucoma is the most common factor in both permanent blindness and impairment. However, the majority of patients are unaware they have the condition, and clinical practise continues to face difficulties in detecting glaucoma progression using current technology. An expert ophthalmologist examines the retinal portion of the eye to see how the glaucoma is progressing. This method is quite time-consuming, and doing it manually takes more time. Therefore, using deep learning and machine learning techniques, this problem can be resolved by automatically diagnosing glaucoma. This systematic review involved a comprehensive analysis of various automated glaucoma prediction and detection techniques. More than 100 articles on Machine learning (ML) techniques with understandable graph and tabular column are reviewed considering summery, method, objective, performance, advantages and disadvantages. In the ML techniques such as support vector machine (SVM), and K-means. Fuzzy c-means clustering algorithm are widely used in glaucoma detection and prediction. Through the systematic review, the most accurate technique to detect and predict glaucoma can be determined which can be utilized for future betterment

Biometric Systems

Biometric authentication has been widely used for access control and security systems over the past few years. The purpose of this book is to provide the readers with life cycle of different biometric authentication systems from their design and development to qualification and final application. The major systems discussed in this book include fingerprint identification, face recognition, iris segmentation and classification, signature verification and other miscellaneous systems which describe management policies of biometrics, reliability measures, pressure based typing and signature verification, bio-chemical systems and behavioral characteristics. In summary, this book provides the students and the researchers with different approaches to develop biometric authentication systems and at the same time includes state-of-the-art approaches in their design and development. The approaches have been thoroughly tested on standard databases and in real world applications