Drug-target interaction prediction based on protein features, using wrapper feature selection.

Drug-target interaction prediction is a vital stage in drug development, involving lots of methods. Experimental methods that identify these relationships on the basis of clinical remedies are time-taking, costly, laborious, and complex introducing a lot of challenges. One group of new methods is called computational methods. The development of new computational methods which are more accurate can be preferable to experimental methods, in terms of total cost and time. In this paper, a new computational model to predict drug-target interaction (DTI), consisting of three phases, including feature extraction, feature selection, and classification is proposed. In feature extraction phase, different features such as EAAC, PSSM and etc. would be extracted from sequence of proteins and fingerprint features from drugs. These extracted features would then be combined. In the next step, one of the wrapper feature selection methods named IWSSR, due to the large amount of extracted data, is applied. The selected features are then given to rotation forest classification, to have a more efficient prediction. Actually, the innovation of our work is that we extract different features; and then select features by the use of IWSSR. The accuracy of the rotation forest classifier based on tenfold on the golden standard datasets (enzyme, ion channels, G-protein-coupled receptors, nuclear receptors) is as follows: 98.12, 98.07, 96.82, and 95.64. The results of experiments indicate that the proposed model has an acceptable rate in DTI prediction and is compatible with the proposed methods in other papers.

Class-Incremental Learning on Video-Based Action Recognition by Distillation of Various Knowledge.

Recognition of activities in the video is an important field in computer vision. Many successful works have been done on activity recognition and they achieved acceptable results in recent years. However, their training is completely static, meaning that all classes are taught to the system in one training step. The system is only able to recognize the equivalent classes. The main disadvantage of this type of training is that if new classes need to be taught to the system, the system must be retrained from scratch and all classes retaught to the system. This specification has many challenges, such as storing and retaining data and respending training costs. We propose an approach for training the action recognition system in video data which can teach new classes to the system without the need for previous data. We will provide an incremental learning algorithm for class recognition tasks in video data. Two different approaches are combined to prevent catastrophic forgetting in the proposed algorithm. In the proposed incremental learning algorithm, two approaches are introduced and used to maintain network information in combination. These two approaches are network sharing and network knowledge distillation. We introduce a neural network architecture for action recognition to understand and represent the video data. We propose the distillation of network knowledge at the classification and feature level, which can be divided into spatial and temporal parts at the feature level. We also suggest initializing new classifiers using previous classifiers. The proposed algorithm is evaluated on the USCF101, HMDB51, and Kinetics-400 datasets. We will consider various factors such as the amount of distillation knowledge, the number of new classes and the incremental learnings stages, and their impact on the final recognition system. Finally, we will show that the proposed algorithm can teach new classes to the recognition system without forgetting the previous classes and does not need the previous data or exemplar data.

Scaling Human-Object Interaction Recognition in the Video through Zero-Shot Learning.

Recognition of human activities is an essential field in computer vision. The most human activity consists of the interaction between humans and objects. Many successful works have been done on human-object interaction (HOI) recognition and achieved acceptable results in recent years. Still, they are fully supervised and need to train labeled data for all HOIs. Due to the enormous space of human-object interactions, listing and providing the training data for all possible categories is costly and impractical. We propose an approach for scaling human-object interaction recognition in video data through the zero-shot learning technique to solve this problem. Our method recognizes a verb and an object from the video and makes an HOI class. Recognition of the verbs and objects instead of HOIs allows identifying a new combination of verbs and objects. So, a new HOI class can be identified, which is not seen by the recognizer system. We introduce a neural network architecture that can understand and represent the video data. The proposed system learns verbs and objects from available training data at the training phase and can identify the verb-object pairs in a video at test time. So, the system can identify the HOI class with different combinations of objects and verbs. Also, we propose to use lateral information for combining the verbs and the objects to make valid verb-object pairs. It helps to prevent the detection of rare and probably wrong HOIs. The lateral information comes from word embedding techniques. Furthermore, we propose a new feature aggregation method for aggregating extracted high-level features from video frames before feeding them to the classifier. We illustrate that this feature aggregation method is more effective for actions that include multiple subactions. We evaluated our system by recently introduced Charades challengeable dataset, which has lots of HOI categories in videos. We show that our proposed system can detect unseen HOI classes in addition to the acceptable recognition of seen types. Therefore, the number of classes identifiable by the system is greater than the number of classes used for training.

Information Transmitted From Bioinspired Neuron-Astrocyte Network Improves Cortical Spiking Network's Pattern Recognition Performance.

We trained two spiking neural networks (SNNs), the cortical spiking network (CSN) and the cortical neuron-astrocyte network (CNAN), using a spike-based unsupervised method, on the MNIST and alpha-digit data sets and achieve an accuracy of 96.1% and 77.35%, respectively. We then connected CNAN to CSN by preserving maximum synchronization between them thanks to the concept of prolate spheroidal wave functions (PSWF). As a result, CSN receives additional information from CNAN without retraining. The important outcome is that CSN reaches 70.57% correct classification rate on capital letters without being trained on them. The overall contribution of transfer is 87.47%. We observed that for CSN the classifying neurons that relate to digits 0-9 of the alpha-digit data set are completely supported by the ones that relate to digits 0-9 of the MNIST data set. This means that CSN recognizes the similarity between the digits of the MNIST and alpha-digit data sets and classifies each digit of both data sets in the same class.

A new approach to detect the coding rule of the cortical spiking model in the information transmission.

Investigation of the role of the local field potential (LFP) fluctuations in encoding the received sensory information by the nervous system remains largely unknown. On the other hand, transmission of these translation rules in information transmission between the structure of sensory stimuli and the cortical oscillations to the bio-inspired artificial neural networks operating at the efficiency of the nervous system is still a vague puzzle. In order to move towards this important goal, computational neuroscience tools can be useful so, we simulated a large-scale network of excitatory and inhibitory spiking neurons with synaptic connections consisting of AMPA and GABA currents as a model of cortical populations. Spiking network was equipped with spike-based unsupervised weight optimization based on the dynamical behavior of the excitatory (AMPA) and inhibitory (GABA) synapses using Spike Timing Dependent Plasticity (STDP) on the MNIST benchmark and we specified how the generated LFP by the network contained information about input patterns. The main result of this article is that the calculated coefficients of Prolate spheroidal wave functions (PSWF) from the input pattern with mean square error (MSE) criterion and power spectrum of LFP with maximum correntropy criterion (MCC) are equal. The more important result is that 82.3% of PSWF coefficients are the same as the connecting weights of the cortical neurons to the classifying neurons after the completion of the training process. Higher compliance percentage of coefficients with synaptic weights (82.3%) gives the expectance us that this coding rule will be able to extend to biological systems. Eventually, we introduced the cortical spiking network as an information channel, which transmits the information of the input pattern in the form of PSWF coefficients to the power spectrum of the output generated LFP.

Entropy-Based Video Steganalysis of Motion Vectors.

In this paper, a new method is proposed for motion vector steganalysis using the entropy value and its combination with the features of the optimized motion vector. In this method, the entropy of blocks is calculated to determine their texture and the precision of their motion vectors. Then, by using a fuzzy cluster, the blocks are clustered into the blocks with high and low texture, while the membership function of each block to a high texture class indicates the texture of that block. These membership functions are used to weight the effective features that are extracted by reconstructing the motion estimation equations. Characteristics of the results indicate that the use of entropy and the irregularity of each block increases the precision of the final video classification into cover and stego classes.

Fast and Efficient Four­class Motor Imagery Electroencephalography Signal Analysis Using Common Spatial Pattern-Ridge Regression Algorithm for the Purpose of Brain-Computer Interface.

Brain-computer interfaces enable users to control devices with electroencephalographic (EEG) activity from the scalp or with single-neuron activity from within the brain. One of the most challenging issues in this regard is the balance between the accuracy of brain signals from patients and the speed of interpreting them into machine language. The main objective of this paper is to analyze different approaches to achieve the balance more quickly and in a better way. To reduce the ocular artifacts, the symmetric prewhitening independent component analysis (ICA) algorithm has been evaluated, which has the lowest runtime and lowest signal-to-interference (SIR) index, without destroying the original signal. After quick elimination of all undesirable signals, two successful feature extractors - the log-band power algorithm and common spatial patterns (CSPs) - are used to extract features. The emphasis is on identifying discriminative properties of the feature sets representing EEG trials recorded during the imagination of the tongue, feet, and left-right-hand movement. Finally, three well-known classifiers are evaluated, where the ridge regression classifier and CSPs as feature extractor have the highest accuracy classification rate about 83.06% with a standard deviation of 1.22%, counterposing the recent studies.

A new bio-inspired stimulator to suppress hyper-synchronized neural firing in a cortical network.

Hyper-synchronous neural oscillations are the character of several neurological diseases such as epilepsy. On the other hand, glial cells and particularly astrocytes can influence neural synchronization. Therefore, based on the recent researches, a new bio-inspired stimulator is proposed which basically is a dynamical model of the astrocyte biophysical model. The performance of the new stimulator is investigated on a large-scale, cortical network. Both excitatory and inhibitory synapses are also considered in the simulated spiking neural network. The simulation results show that the new stimulator has a good performance and is able to reduce recurrent abnormal excitability which in turn avoids the hyper-synchronous neural firing in the spiking neural network. In this way, the proposed stimulator has a demand controlled characteristic and is a good candidate for deep brain stimulation (DBS) technique to successfully suppress the neural hyper-synchronization.

A digital implementation of neuron-astrocyte interaction for neuromorphic applications.

Recent neurophysiologic findings have shown that astrocytes play important roles in information processing and modulation of neuronal activity. Motivated by these findings, in the present research, a digital neuromorphic circuit to study neuron-astrocyte interaction is proposed. In this digital circuit, the firing dynamics of the neuron is described by Izhikevich model and the calcium dynamics of a single astrocyte is explained by a functional model introduced by Postnov and colleagues. For digital implementation of the neuron-astrocyte signaling, Single Constant Multiply (SCM) technique and several linear approximations are used for efficient low-cost hardware implementation on digital platforms. Using the proposed neuron-astrocyte circuit and based on the results of MATLAB simulations, hardware synthesis and FPGA implementation, it is demonstrated that the proposed digital astrocyte is able to change the firing patterns of the neuron through bidirectional communication. Utilizing the proposed digital circuit, it will be illustrated that information processing in synaptic clefts is strongly regulated by astrocyte. Moreover, our results suggest that the digital circuit of neuron-astrocyte crosstalk produces diverse neural responses and therefore enhances the information processing capabilities of the neuromorphic circuits. This is suitable for applications in reconfigurable neuromorphic devices which implement biologically brain circuits.

A digital neurmorphic circuit for a simplified model of astrocyte dynamics.

Recent neurophysiologic findings have shown that astrocytes (the most abundant type of glial cells) are active partners in neural information processing and regulate the synaptic transmission dynamically. Motivated by these findings, in the present research, a digital neuromorphic circuit to implement the astrocyte dynamics is developed. To model the dynamics of the intracellular Ca(2+) waves produced by astrocytes, we utilize a simplified model which considers the main physiological pathways of neuron-astrocyte interactions. Next, a digital circuit for the astrocyte dynamic is proposed which is simulated using ModelSim and finally, it is implemented in hardware on the ZedBoard. The results of hardware synthesis, FPGA implementations are in agreement with MATLAB and ModelSim simulations and confirm that the proposed digital astrocyte is suitable for applications in reconfigurable neuromorphic devices which implement biologically brain circuits.

Phase wavefront aberration modeling using Zernike and pseudo-Zernike polynomials.

Orthogonal polynomials can be used for representing complex surfaces on a specific domain. In optics, Zernike polynomials have widespread applications in testing optical instruments, measuring wavefront distributions, and aberration theory. This orthogonal set on the unit circle has an appropriate matching with the shape of optical system components, such as entrance and exit pupils. The existence of noise in the process of representation estimation of optical surfaces causes a reduction of precision in the process of estimation. Different strategies are developed to manage unwanted noise effects and to preserve the quality of the estimation. This article studies the modeling of phase wavefront aberrations in third-order optics by using a combination of Zernike and pseudo-Zernike polynomials and shows how this combination may increase the robustness of the estimation process of phase wavefront aberration distribution.

Estimation of phase wave-front aberration distribution function using wavelet transform profilometry.

Reduction of image quality under the effects of wavefront aberration of the optical system has a direct impact on the vision system's performance. This paper tries to estimate the amount of aberration with the use of wavelet transform profilometry. The basic idea is based on the principle that under aberration effects, the position of the fringes' image on the image plane will change, and this change correlates with the amount of aberration. So the distribution of aberration function can directly be extracted through measuring the amount of changes in the fringes' image on the image plane. Experimental results and the empirical validity of this idea are evaluated.