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https://www.readbyqxmd.com/read/28748400/reconstructing-genetic-regulatory-networks-using-two-step-algorithms-with-the-differential-equation-models-of-neural-networks
#1
Chi-Kan Chen
BACKGROUND: The identification of genetic regulatory networks (GRNs) provides insights into complex cellular processes. A class of recurrent neural networks (RNNs) captures the dynamics of GRN. Algorithms combining the RNN and machine learning schemes were proposed to reconstruct small-scale GRNs using gene expression time series. RESULTS: We present new GRN reconstruction methods with neural networks. The RNN is extended to a class of recurrent multilayer perceptrons (RMLPs) with latent nodes...
July 26, 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/28720701/de-novo-peptide-sequencing-by-deep-learning
#2
Ngoc Hieu Tran, Xianglilan Zhang, Lei Xin, Baozhen Shan, Ming Li
De novo peptide sequencing from tandem MS data is the key technology in proteomics for the characterization of proteins, especially for new sequences, such as mAbs. In this study, we propose a deep neural network model, DeepNovo, for de novo peptide sequencing. DeepNovo architecture combines recent advances in convolutional neural networks and recurrent neural networks to learn features of tandem mass spectra, fragment ions, and sequence patterns of peptides. The networks are further integrated with local dynamic programming to solve the complex optimization task of de novo sequencing...
July 18, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28712570/electron-microscopic-reconstruction-of-functionally-identified-cells-in-a-neural-integrator
#3
Ashwin Vishwanathan, Kayvon Daie, Alexandro D Ramirez, Jeff W Lichtman, Emre R F Aksay, H Sebastian Seung
Neural integrators are involved in a variety of sensorimotor and cognitive behaviors. The oculomotor system contains a simple example, a hindbrain neural circuit that takes velocity signals as inputs and temporally integrates them to control eye position. Here we investigated the structural underpinnings of temporal integration in the larval zebrafish by first identifying integrator neurons using two-photon calcium imaging and then reconstructing the same neurons through serial electron microscopic analysis...
July 24, 2017: Current Biology: CB
https://www.readbyqxmd.com/read/28707626/performance-of-neural-networks-for-localizing-moving-objects-with-an-artificial-lateral-line
#4
Luuk H Boulogne, Ben J Wolf, Marco A Wiering, Sietse M van Netten
Fish are able to sense water flow velocities relative to their body with their mechanoreceptive lateral line organ. This organ consists of an array of flow detectors distributed along the fish body. Using the excitation of these individual detectors, fish can determine the location of nearby moving objects. Inspired by this sensory modality, it is shown here how neural networks can be used to extract an object's location from simulated excitation patterns, such as can be measured along arrays of stationary artificial flow velocity sensors...
July 14, 2017: Bioinspiration & Biomimetics
https://www.readbyqxmd.com/read/28699566/entity-recognition-from-clinical-texts-via-recurrent-neural-network
#5
Zengjian Liu, Ming Yang, Xiaolong Wang, Qingcai Chen, Buzhou Tang, Zhe Wang, Hua Xu
BACKGROUND: Entity recognition is one of the most primary steps for text analysis and has long attracted considerable attention from researchers. In the clinical domain, various types of entities, such as clinical entities and protected health information (PHI), widely exist in clinical texts. Recognizing these entities has become a hot topic in clinical natural language processing (NLP), and a large number of traditional machine learning methods, such as support vector machine and conditional random field, have been deployed to recognize entities from clinical texts in the past few years...
July 5, 2017: BMC Medical Informatics and Decision Making
https://www.readbyqxmd.com/read/28696758/local-dynamics-in-trained-recurrent-neural-networks
#6
Alexander Rivkind, Omri Barak
Learning a task induces connectivity changes in neural circuits, thereby changing their dynamics. To elucidate task-related neural dynamics, we study trained recurrent neural networks. We develop a mean field theory for reservoir computing networks trained to have multiple fixed point attractors. Our main result is that the dynamics of the network's output in the vicinity of attractors is governed by a low-order linear ordinary differential equation. The stability of the resulting equation can be assessed, predicting training success or failure...
June 23, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/28694119/recurrent-neural-networks-for-classifying-relations-in-clinical-notes
#7
Yuan Luo
We proposed the first models based on recurrent neural networks (more specifically Long Short-Term Memory - LSTM) for classifying relations from clinical notes. We tested our models on the i2b2/VA relation classification challenge dataset. We showed that our segment LSTM model, with only word embedding feature and no manual feature engineering, achieved a micro-averaged f-measure of 0.661 for classifying medical problem-treatment relations, 0.800 for medical problem-test relations, and 0.683 for medical problem-medical problem relations...
July 7, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28692993/pth-moment-exponential-input-to-state-stability-of-delayed-recurrent-neural-networks-with-markovian-switching-via-vector-lyapunov-function
#8
Lei Liu, Jinde Cao, Cheng Qian
In this paper, the pth moment input-to-state exponential stability for delayed recurrent neural networks (DRNNs) with Markovian switching is studied. By using stochastic analysis techniques and classical Razumikhin techniques, a generalized vector L-operator differential inequality including cross item is obtained. Without additional restrictive conditions on the time-varying delay, the sufficient criteria on the pth moment input-to-state exponential stability for DRNNs with Markovian switching are derived by means of the vector L-operator differential inequality...
July 6, 2017: IEEE Transactions on Neural Networks and Learning Systems
https://www.readbyqxmd.com/read/28692680/recurrent-myocardial-infarction-mechanisms-of-free-floating-adaptation-and-autonomic-derangement-in-networked-cardiac-neural-control
#9
Guy Kember, Jeffrey L Ardell, Kalyanam Shivkumar, J Andrew Armour
The cardiac nervous system continuously controls cardiac function whether or not pathology is present. While myocardial infarction typically has a major and catastrophic impact, population studies have shown that longer-term risk for recurrent myocardial infarction and the related potential for sudden cardiac death depends mainly upon standard atherosclerotic variables and autonomic nervous system maladaptations. Investigative neurocardiology has demonstrated that autonomic control of cardiac function includes local circuit neurons for networked control within the peripheral nervous system...
2017: PloS One
https://www.readbyqxmd.com/read/28682271/multiobjective-evolution-of-biped-robot-gaits-using-advanced-continuous-ant-colony-optimized-recurrent-neural-networks
#10
Chia-Feng Juang, Yen-Ting Yeh
This paper proposes the optimization of a fully connected recurrent neural network (FCRNN) using advanced multiobjective continuous ant colony optimization (AMO-CACO) for the multiobjective gait generation of a biped robot (the NAO). The FCRNN functions as a central pattern generator and is optimized to generate angles of the hip roll and pitch, the knee pitch, and the ankle pitch and roll. The performance of the FCRNN-generated gait is evaluated according to the walking speed, trajectory straightness, oscillations of the body in the pitch and yaw directions, and walking posture, subject to the basic constraints that the robot cannot fall down and must walk forward...
June 30, 2017: IEEE Transactions on Cybernetics
https://www.readbyqxmd.com/read/28680506/an-investigation-of-the-dynamical-transitions-in-harmonically-driven-random-networks-of-firing-rate-neurons
#11
Kyriacos Nikiforou, Pedro A M Mediano, Murray Shanahan
Continuous-time recurrent neural networks are widely used as models of neural dynamics and also have applications in machine learning. But their dynamics are not yet well understood, especially when they are driven by external stimuli. In this article, we study the response of stable and unstable networks to different harmonically oscillating stimuli by varying a parameter ρ, the ratio between the timescale of the network and the stimulus, and use the dimensionality of the network's attractor as an estimate of the complexity of this response...
2017: Cognitive Computation
https://www.readbyqxmd.com/read/28678718/multistability-of-recurrent-neural-networks-with-nonmonotonic-activation-functions-and-unbounded-time-varying-delays
#12
Peng Liu, Zhigang Zeng, Jun Wang
This paper is concerned with the coexistence of multiple equilibrium points and dynamical behaviors of recurrent neural networks with nonmonotonic activation functions and unbounded time-varying delays. Based on a state space partition by using the geometrical properties of the activation functions, it is revealed that an n-neuron neural network can exhibit ∏i=1n(2Ki+1) equilibrium points with Ki≥0. In particular, several sufficient criteria are proposed to ascertain the asymptotical stability of ∏i=1n(Ki+1) equilibrium points for recurrent neural networks...
June 27, 2017: IEEE Transactions on Neural Networks and Learning Systems
https://www.readbyqxmd.com/read/28672867/spatiotemporal-recurrent-convolutional-networks-for-traffic-prediction-in-transportation-networks
#13
Haiyang Yu, Zhihai Wu, Shuqin Wang, Yunpeng Wang, Xiaolei Ma
Predicting large-scale transportation network traffic has become an important and challenging topic in recent decades. Inspired by the domain knowledge of motion prediction, in which the future motion of an object can be predicted based on previous scenes, we propose a network grid representation method that can retain the fine-scale structure of a transportation network. Network-wide traffic speeds are converted into a series of static images and input into a novel deep architecture, namely, spatiotemporal recurrent convolutional networks (SRCNs), for traffic forecasting...
June 26, 2017: Sensors
https://www.readbyqxmd.com/read/28668365/recurrent-neural-networks-as-versatile-tools-of-neuroscience-research
#14
REVIEW
Omri Barak
Recurrent neural networks (RNNs) are a class of computational models that are often used as a tool to explain neurobiological phenomena, considering anatomical, electrophysiological and computational constraints. RNNs can either be designed to implement a certain dynamical principle, or they can be trained by input-output examples. Recently, there has been large progress in utilizing trained RNNs both for computational tasks, and as explanations of neural phenomena. I will review how combining trained RNNs with reverse engineering can provide an alternative framework for modeling in neuroscience, potentially serving as a powerful hypothesis generation tool...
June 29, 2017: Current Opinion in Neurobiology
https://www.readbyqxmd.com/read/28659000/recurrent-neural-network-based-modeling-of-gene-regulatory-network-using-elephant-swarm-water-search-algorithm
#15
Sudip Mandal, Goutam Saha, Rajat Kumar Pal
Correct inference of genetic regulations inside a cell from the biological database like time series microarray data is one of the greatest challenges in post genomic era for biologists and researchers. Recurrent Neural Network (RNN) is one of the most popular and simple approach to model the dynamics as well as to infer correct dependencies among genes. Inspired by the behavior of social elephants, we propose a new metaheuristic namely Elephant Swarm Water Search Algorithm (ESWSA) to infer Gene Regulatory Network (GRN)...
June 13, 2017: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/28644841/low-dimensional-spike-rate-models-derived-from-networks-of-adaptive-integrate-and-fire-neurons-comparison-and-implementation
#16
Moritz Augustin, Josef Ladenbauer, Fabian Baumann, Klaus Obermayer
The spiking activity of single neurons can be well described by a nonlinear integrate-and-fire model that includes somatic adaptation. When exposed to fluctuating inputs sparsely coupled populations of these model neurons exhibit stochastic collective dynamics that can be effectively characterized using the Fokker-Planck equation. This approach, however, leads to a model with an infinite-dimensional state space and non-standard boundary conditions. Here we derive from that description four simple models for the spike rate dynamics in terms of low-dimensional ordinary differential equations using two different reduction techniques: one uses the spectral decomposition of the Fokker-Planck operator, the other is based on a cascade of two linear filters and a nonlinearity, which are determined from the Fokker-Planck equation and semi-analytically approximated...
June 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28644840/linking-structure-and-activity-in-nonlinear-spiking-networks
#17
Gabriel Koch Ocker, Krešimir Josić, Eric Shea-Brown, Michael A Buice
Recent experimental advances are producing an avalanche of data on both neural connectivity and neural activity. To take full advantage of these two emerging datasets we need a framework that links them, revealing how collective neural activity arises from the structure of neural connectivity and intrinsic neural dynamics. This problem of structure-driven activity has drawn major interest in computational neuroscience. Existing methods for relating activity and architecture in spiking networks rely on linearizing activity around a central operating point and thus fail to capture the nonlinear responses of individual neurons that are the hallmark of neural information processing...
June 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28620339/the-stress-acceleration-hypothesis-of-nightmares
#18
Tore Nielsen
Adverse childhood experiences can deleteriously affect future physical and mental health, increasing risk for many illnesses, including psychiatric problems, sleep disorders, and, according to the present hypothesis, idiopathic nightmares. Much like post-traumatic nightmares, which are triggered by trauma and lead to recurrent emotional dreaming about the trauma, idiopathic nightmares are hypothesized to originate in early adverse experiences that lead in later life to the expression of early memories and emotions in dream content...
2017: Frontiers in Neurology
https://www.readbyqxmd.com/read/28613187/detection-of-nocturnal-scratching-movements-in-patients-with-atopic-dermatitis-using-accelerometers-and-recurrent-neural-networks
#19
Arnaud Moreau, Peter Anderer, Marco Ross, Andreas Cerny, Timothy Almazan, Barry Peterson
Atopic dermatitis is a chronic inflammatory skin condition affecting both children and adults and is associated with pruritus. A method for objectively quantifying nocturnal scratching events could aid in the development of therapies for atopic dermatitis and other pruritic disorders. High-resolution wrist actigraphy (3-D accelerometer sensors sampled at 20 Hz) is a non-invasive method to record movement. This work presents an algorithm to detect nocturnal scratching events based on actigraphy data. The twofold process consists of segmenting the data into "no motion", "single handed motion" and "both handed motion" followed by discriminating motion segments into scratching and other motion using a bi-directional recurrent neural network classifier...
June 8, 2017: IEEE Journal of Biomedical and Health Informatics
https://www.readbyqxmd.com/read/28606869/predicting-mental-conditions-based-on-history-of-present-illness-in-psychiatric-notes-with-deep-neural-networks
#20
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 10, 2017: Journal of Biomedical Informatics
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