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https://www.readbyqxmd.com/read/28645845/the-feature-weighted-receptive-field-an-interpretable-encoding-model-for-complex-feature-spaces
#1
REVIEW
Ghislain St-Yves, Thomas Naselaris
We introduce the feature-weighted receptive field (fwRF), an encoding model designed to balance expressiveness, interpretability and scalability. The fwRFis organized around the notion of a feature map-a transformation of visual stimuli into visual features that preserves the topology of visual space (but not necessarily the native resolution of the stimulus). The key assumption of the fwRFmodel is that activity in each voxel encodes variation in a spatially localized region across multiple feature maps. This region is fixed for all feature maps; however, the contribution of each feature map to voxel activity is weighted...
June 20, 2017: NeuroImage
https://www.readbyqxmd.com/read/28643394/incorporating-deep-learning-with-convolutional-neural-networks-and-position-specific-scoring-matrices-for-identifying-electron-transport-proteins
#2
Nguyen-Quoc-Khanh Le, Quang-Thai Ho, Yu-Yen Ou
In several years, deep learning is a modern machine learning technique using in a variety of fields with state-of-the-art performance. Therefore, utilization of deep learning to enhance performance is also an important solution for current bioinformatics field. In this study, we try to use deep learning via convolutional neural networks and position specific scoring matrices to identify electron transport proteins, which is an important molecular function in transmembrane proteins. Our deep learning method can approach a precise model for identifying of electron transport proteins with achieved sensitivity of 80...
June 22, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/28641250/deep-convolutional-neural-network-for-inverse-problems-in-imaging
#3
Kyong Hwan Jin, Michael T McCann, Emmanuel Froustey, Michael Unser
In this paper, we propose a novel deep convolutional neural network (CNN)-based algorithm for solving ill-posed inverse problems. Regularized iterative algorithms have emerged as the standard approach to ill-posed inverse problems in the past few decades. These methods produce excellent results, but can be challenging to deploy in practice due to factors including the high computational cost of the forward and adjoint operators and the difficulty of hyper parameter selection. The starting point of our work is the observation that unrolled iterative methods have the form of a CNN (filtering followed by point-wise nonlinearity) when the normal operator ( H*H where H* is the adjoint of the forward imaging operator, H ) of the forward model is a convolution...
June 15, 2017: IEEE Transactions on Image Processing: a Publication of the IEEE Signal Processing Society
https://www.readbyqxmd.com/read/28641247/modeling-task-fmri-data-via-deep-convolutional-autoencoder
#4
Heng Huang, Xintao Hu, Yu Zhao, Milad Makkie, Qinglin Dong, Shijie Zhao, Lei Guo, Tianming Liu
Task-based fMRI (tfMRI) has been widely used to study functional brain networks under task performance. Modeling tfMRI data is challenging due to at least two problems: the lack of the ground truth of underlying neural activity and the highly complex intrinsic structure of tfMRI data. To better understand brain networks based on fMRI data, data-driven approaches have been proposed, for instance, Independent Component Analysis (ICA) and Sparse Dictionary Learning (SDL). However, both ICA and SDL only build shallow models, and they are under the strong assumption that original fMRI signal could be linearly decomposed into time series components with their corresponding spatial maps...
June 15, 2017: IEEE Transactions on Medical Imaging
https://www.readbyqxmd.com/read/28641239/automatic-recognition-of-fmri-derived-functional-networks-using-3d-convolutional-neural-networks
#5
Yu Zhao, Qinglin Dong, Shu Zhang, Wei Zhang, Hanbo Chen, Xi Jiang, Lei Guo, Xintao Hu, Junwei Han, Tianming Liu
Current fMRI data modeling techniques such as Independent Component Analysis (ICA) and Sparse Coding methods can effectively reconstruct dozens or hundreds of concurrent interacting functional brain networks simultaneously from the whole brain fMRI signals. However, such reconstructed networks have no correspondences across different subjects. Thus, automatic, effective and accurate classification and recognition of these large numbers of fMRI-derived functional brain networks are very important for subsequent steps of functional brain analysis in cognitive and clinical neuroscience applications...
June 15, 2017: IEEE Transactions on Bio-medical Engineering
https://www.readbyqxmd.com/read/28630866/cnndel-calling-structural-variations-on-low-coverage-data-based-on-convolutional-neural-networks
#6
Jing Wang, Cheng Ling, Jingyang Gao
Many structural variations (SVs) detection methods have been proposed due to the popularization of next-generation sequencing (NGS). These SV calling methods use different SV-property-dependent features; however, they all suffer from poor accuracy when running on low coverage sequences. The union of results from these tools achieves fairly high sensitivity but still produces low accuracy on low coverage sequence data. That is, these methods contain many false positives. In this paper, we present CNNdel, an approach for calling deletions from paired-end reads...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28622676/training-dcnn-by-combining-max-margin-max-correlation-objectives-and-correntropy-loss-for-multilabel-image-classification
#7
Weiwei Shi, Yihong Gong, Xiaoyu Tao, Nanning Zheng
In this paper, we build a multilabel image classifier using a general deep convolutional neural network (DCNN). We propose a novel objective function that consists of three parts, i.e., max-margin objective, max-correlation objective, and correntropy loss. The max-margin objective explicitly enforces that the minimum score of positive labels must be larger than the maximum score of negative labels by a predefined margin, which not only improves accuracies of the multilabel classifier, but also eases the threshold determination...
June 13, 2017: IEEE Transactions on Neural Networks and Learning Systems
https://www.readbyqxmd.com/read/28622671/low-dose-ct-with-a-residual-encoder-decoder-convolutional-neural-network-red-cnn
#8
Hu Chen, Yi Zhang, Mannudeep K Kalra, Feng Lin, Yang Chen, Peixo Liao, Jiliu Zhou, Ge Wang
Given the potential risk of X-ray radiation to the patient, low-dose CT has attracted a considerable interest in the medical imaging field. Currently, the main stream low-dose CT methods include vendor-specific sinogram domain filtration and iterative reconstruction algorithms, but they need to access raw data whose formats are not transparent to most users. Due to the difficulty of modeling the statistical characteristics in the image domain, the existing methods for directly processing reconstructed images cannot eliminate image noise very well while keeping structural details...
June 13, 2017: IEEE Transactions on Medical Imaging
https://www.readbyqxmd.com/read/28622667/netvlad-cnn-architecture-for-weakly-supervised-place-recognition
#9
Relja Arandjelovic, Petr Gronat, Akihiko Torii, Tomas Pajdla, Josef Sivic
We tackle the problem of large scale visual place recognition, where the task is to quickly and accurately recognize the location of a given query photograph. We present the following four principal contributions. First, we develop a convolutional neural network (CNN) architecture that is trainable in an end-to-end manner directly for the place recognition task. The main component of this architecture, NetVLAD, is a new generalized VLAD layer, inspired by the "Vector of Locally Aggregated Descriptors" image representation commonly used in image retrieval...
June 1, 2017: IEEE Transactions on Pattern Analysis and Machine Intelligence
https://www.readbyqxmd.com/read/28618815/convolutional-neural-network-based-automatic-classification-of-midsagittal-tongue-gestural-targets-using-b-mode-ultrasound-images
#10
Kele Xu, Pierre Roussel, Tamás Gábor Csapó, Bruce Denby
Tongue gestural target classification is of great interest to researchers in the speech production field. Recently, deep convolutional neural networks (CNN) have shown superiority to standard feature extraction techniques in a variety of domains. In this letter, both CNN-based speaker-dependent and speaker-independent tongue gestural target classification experiments are conducted to classify tongue gestures during natural speech production. The CNN-based method achieves state-of-the-art performance, even though no pre-training of the CNN (with the exception of a data augmentation preprocessing) was carried out...
June 2017: Journal of the Acoustical Society of America
https://www.readbyqxmd.com/read/28618812/auditory-feature-representation-using-convolutional-restricted-boltzmann-machine-and-teager-energy-operator-for-speech-recognition
#11
Hardik B Sailor, Hemant A Patil
In this letter, authors propose an auditory feature representation technique with the filterbank learned using an annealing dropout convolutional restricted Boltzmann machine (ConvRBM) and noise-robust energy estimation using the Teager energy operator (TEO). TEO is applied on each subband of ConvRBM filterbank and pooled later to get the short-term spectral features. Experiments on AURORA 4 database show that the proposed features perform better than the Mel filterbank features. The relative improvement of 2...
June 2017: Journal of the Acoustical Society of America
https://www.readbyqxmd.com/read/28615793/classification-of-clinical-significance-of-mri-prostate-findings-using-3d-convolutional-neural-networks
#12
Alireza Mehrtash, Alireza Sedghi, Mohsen Ghafoorian, Mehdi Taghipour, Clare M Tempany, William M Wells, Tina Kapur, Parvin Mousavi, Purang Abolmaesumi, Andriy Fedorov
Prostate cancer (PCa) remains a leading cause of cancer mortality among American men. Multi-parametric magnetic resonance imaging (mpMRI) is widely used to assist with detection of PCa and characterization of its aggressiveness. Computer-aided diagnosis (CADx) of PCa in MRI can be used as clinical decision support system to aid radiologists in interpretation and reporting of mpMRI. We report on the development of a convolution neural network (CNN) model to support CADx in PCa based on the appearance of prostate tissue in mpMRI, conducted as part of the SPIE-AAPM-NCI PROSTATEx challenge...
February 11, 2017: Proceedings of SPIE
https://www.readbyqxmd.com/read/28615003/3d-deep-convolutional-neural-networks-for-amino-acid-environment-similarity-analysis
#13
Wen Torng, Russ B Altman
BACKGROUND: Central to protein biology is the understanding of how structural elements give rise to observed function. The surfeit of protein structural data enables development of computational methods to systematically derive rules governing structural-functional relationships. However, performance of these methods depends critically on the choice of protein structural representation. Most current methods rely on features that are manually selected based on knowledge about protein structures...
June 14, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28613185/improving-cnn-performance-accuracies-with-min-max-objective
#14
Weiwei Shi, Yihong Gong, Xiaoyu Tao, Jinjun Wang, Nanning Zheng
We propose a novel method for improving performance accuracies of convolutional neural network (CNN) without the need to increase the network complexity. We accomplish the goal by applying the proposed Min-Max objective to a layer below the output layer of a CNN model in the course of training. The Min-Max objective explicitly ensures that the feature maps learned by a CNN model have the minimum within-manifold distance for each object manifold and the maximum between-manifold distances among different object manifolds...
June 9, 2017: IEEE Transactions on Neural Networks and Learning Systems
https://www.readbyqxmd.com/read/28613168/convolution-neural-networks-with-two-pathways-for-image-style-recognition
#15
Tiancheng Sun, Yulong Wang, Jian Yang, Xiaolin Hu
Automatic recognition of an image's style is important for many applications including artwork analysis, photo organization and image retrieval. Traditional convolution neural network (CNN) approach uses only object features for image style recognition. This approach may not be optimal because the same object in two images may have different styles. We propose a CNN architecture with two pathways extracting object features and texture features, respectively. The object pathway represents the standard CNN architecture and the texture pathway intermixes the object pathway by outputting the gram matrices of intermediate features in the object pathway...
June 9, 2017: IEEE Transactions on Image Processing: a Publication of the IEEE Signal Processing Society
https://www.readbyqxmd.com/read/28611583/pattern-recognition-of-momentary-mental-workload-based-on-multi-channel-electrophysiological-data-and-ensemble-convolutional-neural-networks
#16
Jianhua Zhang, Sunan Li, Rubin Wang
In this paper, we deal with the Mental Workload (MWL) classification problem based on the measured physiological data. First we discussed the optimal depth (i.e., the number of hidden layers) and parameter optimization algorithms for the Convolutional Neural Networks (CNN). The base CNNs designed were tested according to five classification performance indices, namely Accuracy, Precision, F-measure, G-mean, and required training time. Then we developed an Ensemble Convolutional Neural Network (ECNN) to enhance the accuracy and robustness of the individual CNN model...
2017: Frontiers in Neuroscience
https://www.readbyqxmd.com/read/28608811/simple-smartphone-based-guiding-system-for-visually-impaired-people
#17
Bor-Shing Lin, Cheng-Che Lee, Pei-Ying Chiang
Visually impaired people are often unaware of dangers in front of them, even in familiar environments. Furthermore, in unfamiliar environments, such people require guidance to reduce the risk of colliding with obstacles. This study proposes a simple smartphone-based guiding system for solving the navigation problems for visually impaired people and achieving obstacle avoidance to enable visually impaired people to travel smoothly from a beginning point to a destination with greater awareness of their surroundings...
June 13, 2017: Sensors
https://www.readbyqxmd.com/read/28606869/predicting-mental-conditions-based-on-history-of-present-illness-in-psychiatric-notes-with-deep-neural-networks
#18
Tung Tran, Ramakanth Kavuluru
BACKGROUND: Applications of natural language processing to mental health notes are not common given the sensitive nature of the associated narratives. The CEGS N-GRID 2016 Shared Task in Clinical Natural Language Processing (NLP) changed this scenario by providing the first set of neuropsychiatric notes to participants. This study summarizes our efforts and results in proposing a novel data use case for this dataset as part of the third track in this shared task. OBJECTIVE: We explore the feasibility and effectiveness of predicting a set of common mental conditions a patient has based on the short textual description of patient's history of present illness typically occurring in the beginning of a psychiatric initial evaluation note...
June 9, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28605776/exploring-convolutional-neural-networks-for-drug-drug-interaction-extraction
#19
Víctor Suárez-Paniagua, Isabel Segura-Bedmar, Paloma Martínez
Drug-drug interaction (DDI), which is a specific type of adverse drug reaction, occurs when a drug influences the level or activity of another drug. Natural language processing techniques can provide health-care professionals with a novel way of reducing the time spent reviewing the literature for potential DDIs. The current state-of-the-art for the extraction of DDIs is based on feature-engineering algorithms (such as support vector machines), which usually require considerable time and effort. One possible alternative to these approaches includes deep learning...
January 1, 2017: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/28604624/convolutional-neural-network-based-robot-navigation-using-uncalibrated-spherical-images
#20
Lingyan Ran, Yanning Zhang, Qilin Zhang, Tao Yang
Vision-based mobile robot navigation is a vibrant area of research with numerous algorithms having been developed, the vast majority of which either belong to the scene-oriented simultaneous localization and mapping (SLAM) or fall into the category of robot-oriented lane-detection/trajectory tracking. These methods suffer from high computational cost and require stringent labelling and calibration efforts. To address these challenges, this paper proposes a lightweight robot navigation framework based purely on uncalibrated spherical images...
June 12, 2017: Sensors
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