scholarly journals DeePaC: Predicting pathogenic potential of novel DNA with a universal framework for reverse-complement neural networks

2019 ◽  
Author(s):  
Jakub M. Bartoszewicz ◽  
Anja Seidel ◽  
Robert Rentzsch ◽  
Bernhard Y. Renard
Keyword(s):  
Machine Learning ◽  
Neural Networks ◽  
Pathogen Detection ◽  
State Of The Art ◽  
Model Performance ◽  
Pathogenic Potential ◽  
Reverse Complement ◽  
Recent Developments ◽  
Undesirable Property ◽  
Simple Character

AbstractMotivation:We expect novel pathogens to arise due to their fast-paced evolution, and new species to be discovered thanks to advances in DNA sequencing and metagenomics. What is more, recent developments in synthetic biology raise concerns that some strains of bacteria could be modified for malicious purposes. Traditional approaches to open-view pathogen detection depend on databases of known organisms, limiting their performance on unknown, unrecognized, and unmapped sequences. In contrast, machine learning methods can infer pathogenic phenotypes from single NGS reads even though the biological context is unavailable. However, modern neural architectures treat DNA as a simple character string and may predict conflicting labels for a given sequence and its reverse-complement. This undesirable property may impact model performance.Results:We present DeePaC, a Deep Learning Approach to Pathogenicity Classification. It includes a universal, extensible framework for neural architectures ensuring identical predictions for any given DNA sequence and its reverse-complement. We implement reverse-complement convolutional neural networks and LSTMs, which outperform the state-of-the-art methods based on both sequence homology and machine learning. Combining a reverse-complement architecture with integrating the predictions for both mates in a read pair results in cutting the error rate almost in half in comparison to the previous state-of-the-art.Availability:The code and the models are available at: https://gitlab.com/rki_bioinformatics/DeePaC

scholarly journals DeePaC: predicting pathogenic potential of novel DNA with reverse-complement neural networks

2019 ◽  
Author(s):  
Jakub M Bartoszewicz ◽  
Anja Seidel ◽  
Robert Rentzsch ◽  
Bernhard Y Renard
Keyword(s):  
Machine Learning ◽  
Neural Networks ◽  
Deep Learning ◽  
Pathogen Detection ◽  
State Of The Art ◽  
Supplementary Information ◽  
Learning Approach ◽  
Pathogenic Potential ◽  
Reverse Complement ◽  
Recent Developments

Abstract Motivation We expect novel pathogens to arise due to their fast-paced evolution, and new species to be discovered thanks to advances in DNA sequencing and metagenomics. Moreover, recent developments in synthetic biology raise concerns that some strains of bacteria could be modified for malicious purposes. Traditional approaches to open-view pathogen detection depend on databases of known organisms, which limits their performance on unknown, unrecognized and unmapped sequences. In contrast, machine learning methods can infer pathogenic phenotypes from single NGS reads, even though the biological context is unavailable. Results We present DeePaC, a Deep Learning Approach to Pathogenicity Classification. It includes a flexible framework allowing easy evaluation of neural architectures with reverse-complement parameter sharing. We show that convolutional neural networks and LSTMs outperform the state-of-the-art based on both sequence homology and machine learning. Combining a deep learning approach with integrating the predictions for both mates in a read pair results in cutting the error rate almost in half in comparison to the previous state-of-the-art. Availability and implementation The code and the models are available at: https://gitlab.com/rki_bioinformatics/DeePaC. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Representing Deep Neural Networks Latent Space Geometries with Graphs

Algorithms ◽  
2021 ◽  
Vol 14 (2) ◽  
pp. 39
Author(s):  
Carlos Lassance ◽  
Vincent Gripon ◽  
Antonio Ortega
Keyword(s):  
Machine Learning ◽  
Neural Networks ◽  
Deep Learning ◽  
Objective Function ◽  
Learning Process ◽  
Deep Neural Networks ◽  
State Of The Art ◽  
The Core ◽  
Learning Tasks ◽  
Latent Space

Deep Learning (DL) has attracted a lot of attention for its ability to reach state-of-the-art performance in many machine learning tasks. The core principle of DL methods consists of training composite architectures in an end-to-end fashion, where inputs are associated with outputs trained to optimize an objective function. Because of their compositional nature, DL architectures naturally exhibit several intermediate representations of the inputs, which belong to so-called latent spaces. When treated individually, these intermediate representations are most of the time unconstrained during the learning process, as it is unclear which properties should be favored. However, when processing a batch of inputs concurrently, the corresponding set of intermediate representations exhibit relations (what we call a geometry) on which desired properties can be sought. In this work, we show that it is possible to introduce constraints on these latent geometries to address various problems. In more detail, we propose to represent geometries by constructing similarity graphs from the intermediate representations obtained when processing a batch of inputs. By constraining these Latent Geometry Graphs (LGGs), we address the three following problems: (i) reproducing the behavior of a teacher architecture is achieved by mimicking its geometry, (ii) designing efficient embeddings for classification is achieved by targeting specific geometries, and (iii) robustness to deviations on inputs is achieved via enforcing smooth variation of geometry between consecutive latent spaces. Using standard vision benchmarks, we demonstrate the ability of the proposed geometry-based methods in solving the considered problems.

Framework for TCAD augmented machine learning on multi- I–V characteristics using convolutional neural network and multiprocessing

2021 ◽  
Vol 42 (12) ◽  
pp. 124101
Author(s):  
Thomas Hirtz ◽  
Steyn Huurman ◽  
He Tian ◽  
Yi Yang ◽  
Tian-Ling Ren
Keyword(s):  
Machine Learning ◽  
Neural Networks ◽  
Information Technologies ◽  
Deep Neural Networks ◽  
State Of The Art ◽  
Data Driven ◽  
Sufficient Data ◽  
Learning Models ◽  
Simulation Tools ◽  
New Information

Abstract In a world where data is increasingly important for making breakthroughs, microelectronics is a field where data is sparse and hard to acquire. Only a few entities have the infrastructure that is required to automate the fabrication and testing of semiconductor devices. This infrastructure is crucial for generating sufficient data for the use of new information technologies. This situation generates a cleavage between most of the researchers and the industry. To address this issue, this paper will introduce a widely applicable approach for creating custom datasets using simulation tools and parallel computing. The multi-I–V curves that we obtained were processed simultaneously using convolutional neural networks, which gave us the ability to predict a full set of device characteristics with a single inference. We prove the potential of this approach through two concrete examples of useful deep learning models that were trained using the generated data. We believe that this work can act as a bridge between the state-of-the-art of data-driven methods and more classical semiconductor research, such as device engineering, yield engineering or process monitoring. Moreover, this research gives the opportunity to anybody to start experimenting with deep neural networks and machine learning in the field of microelectronics, without the need for expensive experimentation infrastructure.

scholarly journals Using machine-learning risk prediction models to triage the acuity of undifferentiated patients entering the emergency care system: a systematic review

2020 ◽  
Vol 4 (1) ◽  
Author(s):  
Jamie Miles ◽  
Janette Turner ◽  
Richard Jacques ◽  
Julia Williams ◽  
Suzanne Mason
Keyword(s):  
Machine Learning ◽  
Systematic Review ◽  
Neural Networks ◽  
Logistic Regression ◽  
Emergency Care ◽  
Model Performance ◽  
Machine Learning Methods ◽  
C Statistic ◽  
Emergency Care System ◽  
Care System

Abstract Background The primary objective of this review is to assess the accuracy of machine learning methods in their application of triaging the acuity of patients presenting in the Emergency Care System (ECS). The population are patients that have contacted the ambulance service or turned up at the Emergency Department. The index test is a machine-learning algorithm that aims to stratify the acuity of incoming patients at initial triage. This is in comparison to either an existing decision support tool, clinical opinion or in the absence of these, no comparator. The outcome of this review is the calibration, discrimination and classification statistics. Methods Only derivation studies (with or without internal validation) were included. MEDLINE, CINAHL, PubMed and the grey literature were searched on the 14th December 2019. Risk of bias was assessed using the PROBAST tool and data was extracted using the CHARMS checklist. Discrimination (C-statistic) was a commonly reported model performance measure and therefore these statistics were represented as a range within each machine learning method. The majority of studies had poorly reported outcomes and thus a narrative synthesis of results was performed. Results There was a total of 92 models (from 25 studies) included in the review. There were two main triage outcomes: hospitalisation (56 models), and critical care need (25 models). For hospitalisation, neural networks and tree-based methods both had a median C-statistic of 0.81 (IQR 0.80-0.84, 0.79-0.82). Logistic regression had a median C-statistic of 0.80 (0.74-0.83). For critical care need, neural networks had a median C-statistic of 0.89 (0.86-0.91), tree based 0.85 (0.84-0.88), and logistic regression 0.83 (0.79-0.84). Conclusions Machine-learning methods appear accurate in triaging undifferentiated patients entering the Emergency Care System. There was no clear benefit of using one technique over another; however, models derived by logistic regression were more transparent in reporting model performance. Future studies should adhere to reporting guidelines and use these at the protocol design stage. Registration and funding This systematic review is registered on the International prospective register of systematic reviews (PROSPERO) and can be accessed online at the following URL: https://www.crd.york.ac.uk/PROSPERO/display_record.php?ID=CRD42020168696 This study was funded by the NIHR as part of a Clinical Doctoral Research Fellowship.

scholarly journals Detecting Emotions in English and Arabic Tweets

Information ◽  
2019 ◽  
Vol 10 (3) ◽  
pp. 98 ◽  
Author(s):  
Tariq Ahmad ◽  
Allan Ramsay ◽  
Hanady Ahmed
Keyword(s):  
Machine Learning ◽  
Neural Networks ◽  
Deep Neural Networks ◽  
State Of The Art ◽  
Learning Algorithms ◽  
General Purpose ◽  
Machine Learning Algorithms ◽  
Current State ◽  
Optimal Thresholds ◽  
Alternative Approach

Assigning sentiment labels to documents is, at first sight, a standard multi-label classification task. Many approaches have been used for this task, but the current state-of-the-art solutions use deep neural networks (DNNs). As such, it seems likely that standard machine learning algorithms, such as these, will provide an effective approach. We describe an alternative approach, involving the use of probabilities to construct a weighted lexicon of sentiment terms, then modifying the lexicon and calculating optimal thresholds for each class. We show that this approach outperforms the use of DNNs and other standard algorithms. We believe that DNNs are not a universal panacea and that paying attention to the nature of the data that you are trying to learn from can be more important than trying out ever more powerful general purpose machine learning algorithms.

scholarly journals Single-Cell Phenotype Classification Using Deep Convolutional Neural Networks

2016 ◽  
Vol 21 (9) ◽  
pp. 998-1003 ◽  
Author(s):  
Oliver Dürr ◽  
Beate Sick
Keyword(s):  
Machine Learning ◽  
Neural Networks ◽  
Deep Learning ◽  
Single Cell ◽  
Convolutional Neural Networks ◽  
State Of The Art ◽  
Misclassification Rate ◽  
Support Vector ◽  
Learning Methods ◽  
Phenotype Classification

Deep learning methods are currently outperforming traditional state-of-the-art computer vision algorithms in diverse applications and recently even surpassed human performance in object recognition. Here we demonstrate the potential of deep learning methods to high-content screening–based phenotype classification. We trained a deep learning classifier in the form of convolutional neural networks with approximately 40,000 publicly available single-cell images from samples treated with compounds from four classes known to lead to different phenotypes. The input data consisted of multichannel images. The construction of appropriate feature definitions was part of the training and carried out by the convolutional network, without the need for expert knowledge or handcrafted features. We compare our results against the recent state-of-the-art pipeline in which predefined features are extracted from each cell using specialized software and then fed into various machine learning algorithms (support vector machine, Fisher linear discriminant, random forest) for classification. The performance of all classification approaches is evaluated on an untouched test image set with known phenotype classes. Compared to the best reference machine learning algorithm, the misclassification rate is reduced from 8.9% to 6.6%.

scholarly journals State of the Art in Computational Bioacoustics and Machine Learning: How far have we come?

2019 ◽  
Vol 3 ◽  
Author(s):  
Dan Stowell
Keyword(s):  
Machine Learning ◽  
Big Data ◽  
Deep Learning ◽  
State Of The Art ◽  
Learning Networks ◽  
Recent Developments ◽  
Audio Data ◽  
Ecological Applications ◽  
Near Future ◽  
Statistical Ecology

Terrestrial bioacoustics, like many other domains, has recently witnessed some transformative results from the application of deep learning and big data (Stowell 2017, Mac Aodha et al. 2018, Fairbrass et al. 2018, Mercado III and Sturdy 2017). Generalising over specific projects, which bioacoustic tasks can we consider "solved"? What can we expect in the near future, and what remains hard to do? What does a bioacoustician need to understand about deep learning? This contribution will address these questions, giving the audience a concise summary of recent developments and ways forward. It builds on recent projects and evaluation campaigns led by the author (Stowell et al. 2015, Stowell et al. 2018), as well as broader developments in signal processing, machine learning and bioacoustic applications of these. We will discuss which type of deep learning networks are appropriate for audio data, how to address zoological/ecological applications which often have few available data, and issues in integrating deep learning predictions with existing workflows in statistical ecology.

scholarly journals Convolutional Neural Networks Inference Memory Optimization with Receptive Field-Based InputTiling

2021 ◽  
Author(s):  
Weihao Zhuang ◽  
Tristan Hascoet ◽  
Xunquan Chen ◽  
Ryoichi Takashima ◽  
Tetsuya Takiguchi ◽  
...  
Keyword(s):  
Neural Networks ◽  
Computer Vision ◽  
Convolutional Neural Networks ◽  
Language Processing ◽  
State Of The Art ◽  
Input Image ◽  
Memory Consumption ◽  
Excellent Performance ◽  
Conceptual Approach ◽  
Recent Developments

Abstract Currently, deep learning plays an indispensable role in many fields, including computer vision, natural language processing, and speech recognition. Convolutional Neural Networks (CNNs) have demonstrated excellent performance in computer vision tasks thanks to their powerful feature extraction capability. However, as the larger models have shown higher accuracy, recent developments have led to state-of-the-art CNN models with increasing resource consumption. This paper investigates a conceptual approach to reduce the memory consumption of CNN inference. Our method consists of processing the input image in a sequence of carefully designed tiles within the lower subnetwork of the CNN, so as to minimize its peak memory consumption, while keeping the end-to-end computation unchanged. This method introduces a trade-off between memory consumption and computations, which is particularly suitable for high-resolution inputs. Our experimental results show that MobileNetV2 memory consumption can be reduced by up to 5.3 times with our proposed method. For ResNet50, one of the most commonly used CNN models in computer vision tasks, memory can be optimized by up to 2.3 times.

scholarly journals Quantification of the suitable rooftop area for solar panel installation from overhead imagery using Convolutional Neural Networks

2021 ◽  
Vol 2042 (1) ◽  
pp. 012002
Author(s):  
Roberto Castello ◽  
Alina Walch ◽  
Raphaël Attias ◽  
Riccardo Cadei ◽  
Shasha Jiang ◽  
...  
Keyword(s):  
Neural Network ◽  
Machine Learning ◽  
Neural Networks ◽  
Computer Vision ◽  
State Of The Art ◽  
Solar Panel ◽  
Post Processing ◽  
Processing Step ◽  
Recent Method

Abstract The integration of solar technology in the built environment is realized mainly through rooftop-installed panels. In this paper, we leverage state-of-the-art Machine Learning and computer vision techniques applied on overhead images to provide a geo-localization of the available rooftop surfaces for solar panel installation. We further exploit a 3D building database to associate them to the corresponding roof geometries by means of a geospatial post-processing approach. The stand-alone Convolutional Neural Network used to segment suitable rooftop areas reaches an intersection over union of 64% and an accuracy of 93%, while a post-processing step using building database improves the rejection of false positives. The model is applied to a case study area in the canton of Geneva and the results are compared with another recent method used in the literature to derive the realistic available area.

scholarly journals ColNet: Embedding the Semantics of Web Tables for Column Type Prediction

2019 ◽  
Vol 33 ◽  
pp. 29-36 ◽  
Author(s):  
Jiaoyan Chen ◽  
Ernesto Jiménez-Ruiz ◽  
Ian Horrocks ◽  
Charles Sutton
Keyword(s):  
Neural Network ◽  
Machine Learning ◽  
Neural Networks ◽  
State Of The Art ◽  
Column Type ◽  
Basic Understanding ◽  
Word Representation ◽  
Meta Information ◽  
A Cell ◽  
Multiple Cells

Automatically annotating column types with knowledge base (KB) concepts is a critical task to gain a basic understanding of web tables. Current methods rely on either table metadata like column name or entity correspondences of cells in the KB, and may fail to deal with growing web tables with incomplete meta information. In this paper we propose a neural network based column type annotation framework named ColNet which is able to integrate KB reasoning and lookup with machine learning and can automatically train Convolutional Neural Networks for prediction. The prediction model not only considers the contextual semantics within a cell using word representation, but also embeds the semantics of a column by learning locality features from multiple cells. The method is evaluated with DBPedia and two different web table datasets, T2Dv2 from the general Web and Limaye from Wikipedia pages, and achieves higher performance than the state-of-the-art approaches.

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