Advances in neural network language models have demonstrated that these models can effectively learn representations of words meaning. In this paper, we explore a variation of neural language models that can learn on concepts taken from structured ontologies and extracted from free-text, rather than directly from terms in free-text. 

This model is employed for the task of measuring semantic similarity between medical concepts, a task that is central to a number of techniques in medical informatics and information retrieval. The model is built with two medical corpora (journal abstracts and patient records) and empirically validated on two ground-truth datasets of human-judged concept pairs assessed by medical professionals. Empirically, our approach correlates closely with expert human assessors ($\approx$ 0.9) and outperforms a number of state-of-the-art benchmarks for medical semantic similarity. 

The demonstrated superiority of this model for providing an effective semantic similarity measure is promising in that this may translate into effectiveness gains for techniques in medical information retrieval and medical informatics (e.g., query expansion and literature-based discovery).

Medical semantic similarity with a neural language model

Parallel Scientific Computation: A Structured Approach using BSP and MPI Rob H. Bisseling Hardcover: 324 pages Oxford University Press, USA (May 6, 2004) Language: English ISBN: 0198529392 In spite of many efforts, no solid framework exists for developing parallel software that is portable and efficient across various parallel architectures. The lack of such framework is mostly due to the absence of a universal model of parallel computation, which can play a role similar to that which Von Neumann’s model plays for the sequential computing, and inhibit the diversity of the existing parallel architecture and parallel programming models. Bulk Synchronous Parallel (BSP) is a parallel computing model proposed by Valiant in 1989, which provides a useful and elegant theoretical framework for bridging the gap between parallel hardware and software. This model comprises a computer archicture (BSP computer), a class of algorithms (BSP algorithm), and a performance model (BSP cost function). The attraction of BSP model lays in its simplicity. A BSP computer consists of collection of processors, each with private memory, and a communication network. A BSP algorithm consists of a sequence of supersteps. A superstep contains either a number of computation steps or a number of communication steps, followed by global barrier synchronization. A BSP performance cost function is based on four parameters: number of processors (p), processor computing rate (r), the ratio between the computation time and communication time (g), and the synchronization cost (l). In Parallel Scientific Computation: A Structured Approach using BSP and MPI, Rob Bisseling provides a practical introduction to the area of numerical scientific computation by using BSPlib communication library in parallel algorithm design and parallel programming. Each chapter contains: an abstract; a brief discussion of sequential algorithm included to make the material self-contain; the design and analysis of a parallel algorithm; an annotated program text; illustrative experimental results of an implementation on a particular parallel computer; bibliographic notes; theoretical and practical exercises. The source files of the printed program texts, together with a set of test programs that demonstrate their use, form a package called BSPedupack, which is available at the official home page of the book. Researchers, students, and savvy professionals, schooled in hardware or software, will value Bisseling's self-study approach to parallel scientific programming. After all, this is the first textbook provides a comprehensive overview of the technical aspects of building parallel programs using BSP. The book opens with an overview of BSP model and BSPlib, which tell you how to get started with writing BSP programs, and how to benchmark your computer as a BSP computer. Chapter 2 on dense LU decomposition presents a regular computation with communication patterns that are common in matrix computations. Chapter 3 on the FFT also treats a regular computation but one with a more complex flow of data. Chapter 4 presents the multiplication of a sparse matrix and dense vector. Appendix C presents MPI programs in the order of the corresponding BSP programs appear in the main text. The book includes a reasonable amount of real world examples, which support the theoretical aspects of the discussions. It is easy to follow and includes logical and consistent exposition and clear descriptions of basic and advanced techniques. Being a textbook, it contains various exercises and project assignments at the end of each chapter. However, sample solutions for these exercises are still not available. Perhaps an accompanying CD carrying the sample solutions and tutorials for use in the classroom would have added to the academic value of the book. However, the bibliographic notes given at the ends of each chapter, as well as the references at the end of the book, are quite useful for those interested in exploring the subject of BSP development further. The book is contemporary, well presented, and balanced between concepts and the technical depth required for developing parallel algorithms. Although the book takes a simple performance view of parallel algorithms design, readers should have some basic knowledge of parallel computing, data structures, and C programming. Overall, the book is suitable as a textbook for one-term undergraduate or graduate courses, as a self-study book, or as technical training material for professionals. Ami Marowka Department of Software Engineering Shenkar College of Engineering and Design Ramat-Gan, Israel.

Parallel Scientific Computation: A Structured Approach using BSP and MPI

Deep learning (DL) algorithms have recently emerged from machine learning and soft computing techniques. Since then, several deep learning (DL) algorithms have been recently introduced to scientific communities and are applied in various application domains. Today the usage of DL has become essential due to their intelligence, efficient learning, accuracy and robustness in model building. However, in the scientific literature, a comprehensive list of DL algorithms has not been introduced yet. This paper provides a list of the most popular DL algorithms, along with their applications domains.

/pdf/list-of-deep-learning-models-3zmxfdu43q.pdf

List of Deep Learning Models

BARF: A new direct and cross-based binary residual feature fusion with uncertainty-aware module for medical image classification

A deep learning approach to the screening of malaria infection: Automated and rapid cell counting, object detection and instance segmentation using Mask R-CNN.

In the last few years, there has been a growing expectation created about the analysis of large amounts of data often available in organizations, which has been both scrutinized by the academic world and successfully exploited by industry. Nowadays, two of the most common terms heard in scientific circles are Big Data and Deep Learning. In this double review, we aim to shed some light on the current state of these different, yet somehow related branches of Data Science, in order to understand the current state and future evolution within the healthcare area. We start by giving a simple description of the technical elements of Big Data technologies, as well as an overview of the elements of Deep Learning techniques, according to their usual description in scientific literature. Then, we pay attention to the application fields that can be said to have delivered relevant real-world success stories, with emphasis on examples from large technology companies and financial institutions, among others. The academic effort that has been put into bringing these technologies to the healthcare sector are then summarized and analyzed from a twofold view as follows: first, the landscape of application examples is globally scrutinized according to the varying nature of medical data, including the data forms in electronic health recordings, medical time signals, and medical images; second, a specific application field is given special attention, in particular the electrocardiographic signal analysis, where a number of works have been published in the last two years. A set of toy application examples are provided with the publicly-available MIMIC dataset, aiming to help the beginners start with some principled, basic, and structured material and available code. Critical discussion is provided for current and forthcoming challenges on the use of both sets of techniques in our future healthcare.

https://www.mdpi.com/2076-3417/9/11/2331/pdf

Alicia Gerrero-Curieses

Papers

Deep Learning and Big Data in Healthcare: A Double Review for Critical Beginners