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restricted Boltzmann machine

Yiding Lu, Yufan Guo, Anna Korhonen
BACKGROUND: In silico drug-target interaction (DTI) prediction plays an integral role in drug repositioning: the discovery of new uses for existing drugs. One popular method of drug repositioning is network-based DTI prediction, which uses complex network theory to predict DTIs from a drug-target network. Currently, most network-based DTI prediction is based on machine learning - methods such as Restricted Boltzmann Machines (RBM) or Support Vector Machines (SVM). These methods require additional information about the characteristics of drugs, targets and DTIs, such as chemical structure, genome sequence, binding types, causes of interactions, etc...
January 17, 2017: BMC Bioinformatics
Fahimeh Ghasemi, Afshin Fassihi, Horacio Pérez-Sánchez, Alireza Mehri Dehnavi
Thousands of molecules and descriptors are available for a medicinal chemist thanks to the technological advancements in different branches of chemistry. This fact as well as the correlation between them has raised new problems in quantitative structure activity relationship studies. Proper parameter initialization in statistical modeling has merged as another challenge in recent years. Random selection of parameters leads to poor performance of deep neural network (DNN). In this research, deep belief network (DBN) was applied to initialize DNNs...
February 5, 2017: Journal of Computational Chemistry
Son N Tran, Artur S d'Avila Garcez
Developments in deep learning have seen the use of layerwise unsupervised learning combined with supervised learning for fine-tuning. With this layerwise approach, a deep network can be seen as a more modular system that lends itself well to learning representations. In this paper, we investigate whether such modularity can be useful to the insertion of background knowledge into deep networks, whether it can improve learning performance when it is available, and to the extraction of knowledge from trained deep networks, and whether it can offer a better understanding of the representations learned by such networks...
November 8, 2016: IEEE Transactions on Neural Networks and Learning Systems
Roshanak Farhoodi, Bahar Akbal-Delibas, Nurit Haspel
Discriminating native-like structures from false positives with high accuracy is one of the biggest challenges in protein-protein docking. While there is an agreement on the existence of a relationship between various favorable intermolecular interactions (e.g., Van der Waals, electrostatic, and desolvation forces) and the similarity of a conformation to its native structure, the precise nature of this relationship is not known. Existing protein-protein docking methods typically formulate this relationship as a weighted sum of selected terms and calibrate their weights by using a training set to evaluate and rank candidate complexes...
October 17, 2016: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
Stefan Elfwing, Eiji Uchibe, Kenji Doya
Free-energy based reinforcement learning (FERL) was proposed for learning in high-dimensional state and action spaces. However, the FERL method does only really work well with binary, or close to binary, state input, where the number of active states is fewer than the number of non-active states. In the FERL method, the value function is approximated by the negative free energy of a restricted Boltzmann machine (RBM). In our earlier study, we demonstrated that the performance and the robustness of the FERL method can be improved by scaling the free energy by a constant that is related to the size of network...
August 26, 2016: Neural Networks: the Official Journal of the International Neural Network Society
Zhizhong Han, Zhenbao Liu, Junwei Han, Chi-Man Vong, Shuhui Bu, Xuelong Li
Extracting local features from 3D shapes is an important and challenging task that usually requires carefully designed 3D shape descriptors. However, these descriptors are hand-crafted and require intensive human intervention with prior knowledge. To tackle this issue, we propose a novel deep learning model, namely Circle Convolutional Restricted Boltzmann Machine (CCRBM), for unsupervised 3D local feature learning. CCRBM is specially designed to learn from raw 3D representations. It effectively overcomes obstacles such as irregular vertex topology, orientation ambiguity on the 3D surface, and rigid or slightly non-rigid transformation invariance in the hierarchical learning of 3D data that cannot be resolved by the existing deep learning models...
September 2, 2016: IEEE Transactions on Image Processing: a Publication of the IEEE Signal Processing Society
Na Lu, Tengfei Li, Xiaodong Ren, Hongyu Miao
Motor imagery classification is an important topic in brain computer interface (BCI) research that enables the recognition of a subject's intension to, e.g., implement prosthesis control. The brain dynamics of motor imagery are usually measured by electroencephalography (EEG) as nonstationary time series of low signal-to-noise ratio. Although a variety of methods have been previously developed to learn EEG signal features, the deep learning idea has rarely been explored to generate new representation of EEG features and achieve further performance improvement for motor imagery classification...
August 17, 2016: IEEE Transactions on Neural Systems and Rehabilitation Engineering
Qi Zhang, Yang Xiao, Wei Dai, Jingfeng Suo, Congzhi Wang, Jun Shi, Hairong Zheng
This study aims to build a deep learning (DL) architecture for automated extraction of learned-from-data image features from the shear-wave elastography (SWE), and to evaluate the DL architecture in differentiation between benign and malignant breast tumors. We construct a two-layer DL architecture for SWE feature extraction, comprised of the point-wise gated Boltzmann machine (PGBM) and the restricted Boltzmann machine (RBM). The PGBM contains task-relevant and task-irrelevant hidden units, and the task-relevant units are connected to the RBM...
December 2016: Ultrasonics
Yajun Zhang, Zongtian Liu, Wen Zhou
Event recognition is the most fundamental and critical task in event-based natural language processing systems. Existing event recognition methods based on rules and shallow neural networks have certain limitations. For example, extracting features using methods based on rules is difficult; methods based on shallow neural networks converge too quickly to a local minimum, resulting in low recognition precision. To address these problems, we propose the Chinese emergency event recognition model based on deep learning (CEERM)...
2016: PloS One
Erik Gawehn, Jan A Hiss, Gisbert Schneider
Artificial neural networks had their first heyday in molecular informatics and drug discovery approximately two decades ago. Currently, we are witnessing renewed interest in adapting advanced neural network architectures for pharmaceutical research by borrowing from the field of "deep learning". Compared with some of the other life sciences, their application in drug discovery is still limited. Here, we provide an overview of this emerging field of molecular informatics, present the basic concepts of prominent deep learning methods and offer motivation to explore these techniques for their usefulness in computer-assisted drug discovery and design...
January 2016: Molecular Informatics
Lei Yang, Shuang Wang, Xiaoqian Jiang, Samuel Cheng, Hyeon-Eui Kim
BACKGROUND: Accurately assessing pain for those who cannot make self-report of pain, such as minimally responsive or severely brain-injured patients, is challenging. In this paper, we attempted to address this challenge by answering the following questions: (1) if the pain has dependency structures in electronic signals and if so, (2) how to apply this pattern in predicting the state of pain. To this end, we have been investigating and comparing the performance of several machine learning techniques...
2016: BMC Medical Informatics and Decision Making
Zhizhong Han, Zhenbao Liu, Junwei Han, Chi-Man Vong, Shuhui Bu, Chun Long Philip Chen
Discriminative features of 3-D meshes are significant to many 3-D shape analysis tasks. However, handcrafted descriptors and traditional unsupervised 3-D feature learning methods suffer from several significant weaknesses: 1) the extensive human intervention is involved; 2) the local and global structure information of 3-D meshes cannot be preserved, which is in fact an important source of discriminability; 3) the irregular vertex topology and arbitrary resolution of 3-D meshes do not allow the direct application of the popular deep learning models; 4) the orientation is ambiguous on the mesh surface; and 5) the effect of rigid and nonrigid transformations on 3-D meshes cannot be eliminated...
June 30, 2016: IEEE Transactions on Neural Networks and Learning Systems
Chuan Li, René-Vinicio Sánchez, Grover Zurita, Mariela Cerrada, Diego Cabrera
Fault diagnosis is important for the maintenance of rotating machinery. The detection of faults and fault patterns is a challenging part of machinery fault diagnosis. To tackle this problem, a model for deep statistical feature learning from vibration measurements of rotating machinery is presented in this paper. Vibration sensor signals collected from rotating mechanical systems are represented in the time, frequency, and time-frequency domains, each of which is then used to produce a statistical feature set...
2016: Sensors
Bruno U Pedroni, Srinjoy Das, John V Arthur, Paul A Merolla, Bryan L Jackson, Dharmendra S Modha, Kenneth Kreutz-Delgado, Gert Cauwenberghs
Stochastic neural networks such as Restricted Boltzmann Machines (RBMs) have been successfully used in applications ranging from speech recognition to image classification, and are particularly interesting because of their potential for generative tasks. Inference and learning in these algorithms use a Markov Chain Monte Carlo procedure called Gibbs sampling, where a logistic function forms the kernel of this sampler. On the other side of the spectrum, neuromorphic systems have shown great promise for low-power and parallelized cognitive computing, but lack well-suited applications and automation procedures...
August 2016: IEEE Transactions on Biomedical Circuits and Systems
Marc-Alexandre Côté, Hugo Larochelle
We present a mathematical construction for the restricted Boltzmann machine (RBM) that does not require specifying the number of hidden units. In fact, the hidden layer size is adaptive and can grow during training. This is obtained by first extending the RBM to be sensitive to the ordering of its hidden units. Then, with a carefully chosen definition of the energy function, we show that the limit of infinitely many hidden units is well defined. As with RBM, approximate maximum likelihood training can be performed, resulting in an algorithm that naturally and adaptively adds trained hidden units during learning...
July 2016: Neural Computation
Ryo Karakida, Masato Okada, Shun-Ichi Amari
The restricted Boltzmann machine (RBM) is an essential constituent of deep learning, but it is hard to train by using maximum likelihood (ML) learning, which minimizes the Kullback-Leibler (KL) divergence. Instead, contrastive divergence (CD) learning has been developed as an approximation of ML learning and widely used in practice. To clarify the performance of CD learning, in this paper, we analytically derive the fixed points where ML and CDn learning rules converge in two types of RBMs: one with Gaussian visible and Gaussian hidden units and the other with Gaussian visible and Bernoulli hidden units...
July 2016: Neural Networks: the Official Journal of the International Neural Network Society
Hojin Jang, Sergey M Plis, Vince D Calhoun, Jong-Hwan Lee
Feedforward deep neural networks (DNNs), artificial neural networks with multiple hidden layers, have recently demonstrated a record-breaking performance in multiple areas of applications in computer vision and speech processing. Following the success, DNNs have been applied to neuroimaging modalities including functional/structural magnetic resonance imaging (MRI) and positron-emission tomography data. However, no study has explicitly applied DNNs to 3D whole-brain fMRI volumes and thereby extracted hidden volumetric representations of fMRI that are discriminative for a task performed as the fMRI volume was acquired...
January 15, 2017: NeuroImage
Jun Li, Tong Zhang, Wei Luo, Jian Yang, Xiao-Tong Yuan, Jian Zhang
A major progress in deep multilayer neural networks (DNNs) is the invention of various unsupervised pretraining methods to initialize network parameters which lead to good prediction accuracy. This paper presents the sparseness analysis on the hidden unit in the pretraining process. In particular, we use the L₁-norm to measure sparseness and provide some sufficient conditions for that pretraining leads to sparseness with respect to the popular pretraining models--such as denoising autoencoders (DAEs) and restricted Boltzmann machines (RBMs)...
March 31, 2016: IEEE Transactions on Neural Networks and Learning Systems
Shuai Ma, Tao Shen, Rui-qi Wang, Hua Lai, Zheng-tao Yu
Feature extraction and classification are the key issues of terahertz spectroscopy identification. Because many materials have no apparent absorption peaks in the terahertz band, it is difficult to extract theirs terahertz spectroscopy feature and identify. To this end, a novel of identify terahertz spectroscopy approach with Deep Belief Network (DBN) was studied in this paper, which combines the advantages of DBN and K-Nearest Neighbors (KNN) classifier. Firstly, cubic spline interpolation and S-G filter were used to normalize the eight kinds of substances (ATP, Acetylcholine Bromide, Bifenthrin, Buprofezin, Carbazole, Bleomycin, Buckminster and Cylotriphosphazene) terahertz transmission spectra in the range of 0...
December 2015: Guang Pu Xue Yu Guang Pu Fen Xi, Guang Pu
Gijs van Tulder, Marleen de Bruijne
The choice of features greatly influences the performance of a tissue classification system. Despite this, many systems are built with standard, predefined filter banks that are not optimized for that particular application. Representation learning methods such as restricted Boltzmann machines may outperform these standard filter banks because they learn a feature description directly from the training data. Like many other representation learning methods, restricted Boltzmann machines are unsupervised and are trained with a generative learning objective; this allows them to learn representations from unlabeled data, but does not necessarily produce features that are optimal for classification...
May 2016: IEEE Transactions on Medical Imaging
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