scholarly journals DeepCapTail: A Deep Learning Framework to Predict Capsid and Tail Proteins of Phage Genomes

2018 ◽  
Author(s):  
Dhoha Abid ◽  
Liqing Zhang
Keyword(s):  
Neural Networks ◽  
Deep Learning ◽  
Deep Neural Networks ◽  
State Of The Art ◽  
Sequence Conservation ◽  
Structural Proteins ◽  
Genomic Sequences ◽  
Learning Framework ◽  
Art Methods ◽  
Tail Proteins

AbstractThe capsid and tail proteins are considered the main structural proteins for phages and also their footprint since they exist only in phage genomes. These proteins are known to lack sequence conservation, making them extremely diverse and thus posing a major challenge to identify and annotate them in genomic sequences. In this study, we aim to overcome this challenge and predict these proteins by using deep neural networks with composition-based features. We develop two models trained with k-mer features to predict capsid and tail proteins respectively. Evaluating the models on two different testing sets shows that they outperform state-of-the-art methods with improved F-1 scores.

scholarly journals Enabling deeper learning on big data for materials informatics applications

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Dipendra Jha ◽  
Vishu Gupta ◽  
Logan Ward ◽  
Zijiang Yang ◽  
Christopher Wolverton ◽  
...  
Keyword(s):  
Neural Networks ◽  
Big Data ◽  
Deep Learning ◽  
Deep Neural Networks ◽  
Materials Science ◽  
Prediction Models ◽  
Model Performance ◽  
Materials Informatics ◽  
Learning Framework ◽  
Significant Attention

AbstractThe application of machine learning (ML) techniques in materials science has attracted significant attention in recent years, due to their impressive ability to efficiently extract data-driven linkages from various input materials representations to their output properties. While the application of traditional ML techniques has become quite ubiquitous, there have been limited applications of more advanced deep learning (DL) techniques, primarily because big materials datasets are relatively rare. Given the demonstrated potential and advantages of DL and the increasing availability of big materials datasets, it is attractive to go for deeper neural networks in a bid to boost model performance, but in reality, it leads to performance degradation due to the vanishing gradient problem. In this paper, we address the question of how to enable deeper learning for cases where big materials data is available. Here, we present a general deep learning framework based on Individual Residual learning (IRNet) composed of very deep neural networks that can work with any vector-based materials representation as input to build accurate property prediction models. We find that the proposed IRNet models can not only successfully alleviate the vanishing gradient problem and enable deeper learning, but also lead to significantly (up to 47%) better model accuracy as compared to plain deep neural networks and traditional ML techniques for a given input materials representation in the presence of big data.

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.

scholarly journals CapsTM: capsule network for Chinese medical text matching

2021 ◽  
Vol 21 (S2) ◽  
Author(s):  
Xiaoming Yu ◽  
Yedan Shen ◽  
Yuan Ni ◽  
Xiaowei Huang ◽  
Xiaolong Wang ◽  
...  
Keyword(s):  
Neural Network ◽  
Neural Networks ◽  
Deep Learning ◽  
Network Architecture ◽  
State Of The Art ◽  
Interaction Matrix ◽  
Application Systems ◽  
Input Layer ◽  
Art Methods ◽  
Text Matching

Abstract Background Text Matching (TM) is a fundamental task of natural language processing widely used in many application systems such as information retrieval, automatic question answering, machine translation, dialogue system, reading comprehension, etc. In recent years, a large number of deep learning neural networks have been applied to TM, and have refreshed benchmarks of TM repeatedly. Among the deep learning neural networks, convolutional neural network (CNN) is one of the most popular networks, which suffers from difficulties in dealing with small samples and keeping relative structures of features. In this paper, we propose a novel deep learning architecture based on capsule network for TM, called CapsTM, where capsule network is a new type of neural network architecture proposed to address some of the short comings of CNN and shows great potential in many tasks. Methods CapsTM is a five-layer neural network, including an input layer, a representation layer, an aggregation layer, a capsule layer and a prediction layer. In CapsTM, two pieces of text are first individually converted into sequences of embeddings and are further transformed by a highway network in the input layer. Then, Bidirectional Long Short-Term Memory (BiLSTM) is used to represent each piece of text and attention-based interaction matrix is used to represent interactive information of the two pieces of text in the representation layer. Subsequently, the two kinds of representations are fused together by BiLSTM in the aggregation layer, and are further represented with capsules (vectors) in the capsule layer. Finally, the prediction layer is a connected network used for classification. CapsTM is an extension of ESIM by adding a capsule layer before the prediction layer. Results We construct a corpus of Chinese medical question matching, which contains 36,360 question pairs. This corpus is randomly split into three parts: a training set of 32,360 question pairs, a development set of 2000 question pairs and a test set of 2000 question pairs. On this corpus, we conduct a series of experiments to evaluate the proposed CapsTM and compare it with other state-of-the-art methods. CapsTM achieves the highest F-score of 0.8666. Conclusion The experimental results demonstrate that CapsTM is effective for Chinese medical question matching and outperforms other state-of-the-art methods for comparison.

scholarly journals Medical Knowledge Graph in Chinese Using Deep Semantic Mobile Computation Based on IoT and WoT

2021 ◽  
Vol 2021 ◽  
pp. 1-13
Author(s):  
Wanheng Liu ◽  
Ling Yin ◽  
Cong Wang ◽  
Fulin Liu ◽  
Zhiyu Ni
Keyword(s):  
Neural Networks ◽  
Deep Learning ◽  
Deep Neural Networks ◽  
State Of The Art ◽  
Medical Knowledge ◽  
Disease Diagnosis ◽  
Knowledge Graph ◽  
Great Success ◽  
Smart Healthcare ◽  
Made In

In this paper, a novel medical knowledge graph in Chinese approach applied in smart healthcare based on IoT and WoT is presented, using deep neural networks combined with self-attention to generate medical knowledge graph to make it more convenient for performing disease diagnosis and providing treatment advisement. Although great success has been made in the medical knowledge graph in recent studies, the issue of comprehensive medical knowledge graph in Chinese appropriate for telemedicine or mobile devices have been ignored. In our study, it is a working theory which is based on semantic mobile computing and deep learning. When several experiments have been carried out, it is demonstrated that it has better performance in generating various types of medical knowledge graph in Chinese, which is similar to that of the state-of-the-art. Also, it works well in the accuracy and comprehensive, which is much higher and highly consisted with the predictions of the theoretical model. It proves to be inspiring and encouraging that our work involving studies of medical knowledge graph in Chinese, which can stimulate the smart healthcare development.

scholarly journals Tri-net for Semi-Supervised Deep Learning

2018 ◽  
Author(s):  
Dong-Dong Chen ◽  
Wei Wang ◽  
Wei Gao ◽  
Zhi-Hua Zhou
Keyword(s):  
Neural Network ◽  
Neural Networks ◽  
Deep Learning ◽  
Error Rate ◽  
Deep Neural Network ◽  
Deep Neural Networks ◽  
State Of The Art ◽  
Fine Tuning ◽  
Learning Methods ◽  
Model Initialization

Deep neural networks have witnessed great successes in various real applications, but it requires a large number of labeled data for training. In this paper, we propose tri-net, a deep neural network which is able to use massive unlabeled data to help learning with limited labeled data. We consider model initialization, diversity augmentation and pseudo-label editing simultaneously. In our work, we utilize output smearing to initialize modules, use fine-tuning on labeled data to augment diversity and eliminate unstable pseudo-labels to alleviate the influence of suspicious pseudo-labeled data. Experiments show that our method achieves the best performance in comparison with state-of-the-art semi-supervised deep learning methods. In particular, it achieves 8.30% error rate on CIFAR-10 by using only 4000 labeled examples.

scholarly journals When the state of the art is ahead of the state of understanding: Unintuitive properties of deep neural networks

2018 ◽  
Author(s):  
Joan Serrà
Keyword(s):  
Neural Networks ◽  
Deep Learning ◽  
Recent Work ◽  
Deep Neural Networks ◽  
State Of The Art ◽  
The State ◽  
Computing Power ◽  
The Media ◽  
Insight Into ◽  
Empirical Means

Deep learning is an undeniably hot topic, not only within both academia and industry, but also among society and the media. The reasons for the advent of its popularity are manifold: unprecedented availability of data and computing power, some innovative methodologies, minor but significant technical tricks, etc. However, interestingly, the current success and practice of deep learning seems to be uncorrelated with its theoretical, more formal understanding. And with that, deep learning’s state-of-the-art presents a number of unintuitive properties or situations. In this note, I highlight some of these unintuitive properties, trying to show relevant recent work, and expose the need to get insight into them, either by formal or more empirical means.

End-to-end, sequence-to-sequence probabilistic visual odometry through deep neural networks

2017 ◽  
Vol 37 (4-5) ◽  
pp. 513-542 ◽  
Author(s):  
Sen Wang ◽  
Ronald Clark ◽  
Hongkai Wen ◽  
Niki Trigoni
Keyword(s):  
Neural Networks ◽  
Deep Learning ◽  
Convolutional Neural Networks ◽  
Deep Neural Networks ◽  
State Of The Art ◽  
Visual Odometry ◽  
Feature Representation ◽  
Geometric Information ◽  
Geometric Problem ◽  
End To End

This paper studies visual odometry (VO) from the perspective of deep learning. After tremendous efforts in the robotics and computer vision communities over the past few decades, state-of-the-art VO algorithms have demonstrated incredible performance. However, since the VO problem is typically formulated as a pure geometric problem, one of the key features still missing from current VO systems is the capability to automatically gain knowledge and improve performance through learning. In this paper, we investigate whether deep neural networks can be effective and beneficial to the VO problem. An end-to-end, sequence-to-sequence probabilistic visual odometry (ESP-VO) framework is proposed for the monocular VO based on deep recurrent convolutional neural networks. It is trained and deployed in an end-to-end manner, that is, directly inferring poses and uncertainties from a sequence of raw images (video) without adopting any modules from the conventional VO pipeline. It can not only automatically learn effective feature representation encapsulating geometric information through convolutional neural networks, but also implicitly model sequential dynamics and relation for VO using deep recurrent neural networks. Uncertainty is also derived along with the VO estimation without introducing much extra computation. Extensive experiments on several datasets representing driving, flying and walking scenarios show competitive performance of the proposed ESP-VO to the state-of-the-art methods, demonstrating a promising potential of the deep learning technique for VO and verifying that it can be a viable complement to current VO systems.

scholarly journals Computer-Aided Diagnosis of Skin Diseases Using Deep Neural Networks

2020 ◽  
Vol 10 (7) ◽  
pp. 2488 ◽  
Author(s):  
Muhammad Naseer Bajwa ◽  
Kaoru Muta ◽  
Muhammad Imran Malik ◽  
Shoaib Ahmed Siddiqui ◽  
Stephan Alexander Braun ◽  
...  
Keyword(s):  
Neural Networks ◽  
Deep Learning ◽  
Deep Neural Networks ◽  
Skin Diseases ◽  
State Of The Art ◽  
Disease Diagnosis ◽  
Classification Performance ◽  
Computer Aided Diagnosis ◽  
Computer Aided ◽  
Aided Diagnosis

Propensity of skin diseases to manifest in a variety of forms, lack and maldistribution of qualified dermatologists, and exigency of timely and accurate diagnosis call for automated Computer-Aided Diagnosis (CAD). This study aims at extending previous works on CAD for dermatology by exploring the potential of Deep Learning to classify hundreds of skin diseases, improving classification performance, and utilizing disease taxonomy. We trained state-of-the-art Deep Neural Networks on two of the largest publicly available skin image datasets, namely DermNet and ISIC Archive, and also leveraged disease taxonomy, where available, to improve classification performance of these models. On DermNet we establish new state-of-the-art with 80% accuracy and 98% Area Under the Curve (AUC) for classification of 23 diseases. We also set precedence for classifying all 622 unique sub-classes in this dataset and achieved 67% accuracy and 98% AUC. On ISIC Archive we classified all 7 diseases with 93% average accuracy and 99% AUC. This study shows that Deep Learning has great potential to classify a vast array of skin diseases with near-human accuracy and far better reproducibility. It can have a promising role in practical real-time skin disease diagnosis by assisting physicians in large-scale screening using clinical or dermoscopic images.

scholarly journals DeepQGHO: Quantized Greedy Hyperparameter Optimization in Deep Neural Networks for on-the-fly Learning

2021 ◽  
Author(s):  
Anjir Ahmed Chowdhury ◽  
Md Abir Hossen ◽  
Md Ali Azam ◽  
Md. Hafizur Rahman
Keyword(s):  
Neural Networks ◽  
Deep Learning ◽  
Energy Consumption ◽  
Deep Neural Networks ◽  
State Of The Art ◽  
Optimization Algorithms ◽  
Computation Time ◽  
Hyperparameter Optimization ◽  
Computationally Expensive ◽  
Time And Energy

Abstract Hyperparameter optimization or tuning plays a significant role in the performance and reliability of deep learning (DL). Many hyperparameter optimization algorithms have been developed for obtaining better validation accuracy in DL training. Most state-of-the-art hyperparameters are computationally expensive due to a focus on validation accuracy. Therefore, they are unsuitable for online or on-the-fly training applications which require computational efficiency. In this paper, we develop a novel greedy approach-based hyperparameter optimization (GHO) algorithm for faster training applications, e.g., on-the-fly training. We perform an empirical study to compute the performance such as computation time and energy consumption of the GHO and compare it with two state-of-the-art hyperparameter optimization algorithms. We also deploy the GHO algorithm in an edge device to validate the performance of our algorithm. We perform post-training quantization to the GHO algorithm to reduce inference time and latency.

scholarly journals Adversarial Attacks for Deep Learning-Based Infrared Object Detection

2021 ◽  
Vol 24 (6) ◽  
pp. 591-601
Author(s):  
Hoseong Kim ◽  
Jaeguk Hyun ◽  
Hyunjung Yoo ◽  
Chunho Kim ◽  
Hyunho Jeon
Keyword(s):  
Neural Networks ◽  
Deep Learning ◽  
Object Detection ◽  
Image Recognition ◽  
Rapid Growth ◽  
Deep Neural Networks ◽  
State Of The Art ◽  
Visible Image ◽  
Adversarial Attack

Recently, infrared object detection(IOD) has been extensively studied due to the rapid growth of deep neural networks(DNN). Adversarial attacks using imperceptible perturbation can dramatically deteriorate the performance of DNN. However, most adversarial attack works are focused on visible image recognition(VIR), and there are few methods for IOD. We propose deep learning-based adversarial attacks for IOD by expanding several state-of-the-art adversarial attacks for VIR. We effectively validate our claim through comprehensive experiments on two challenging IOD datasets, including FLIR and MSOD.

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