Memristive Circuit Implementation of Biological Nonassociative Learning Mechanism and Its Applications

A memristor-based circuit design of avoidance learning with time delay and its application

Currently, the research in memristor-based associative memory neural networks pays more attention to positive stimuli and lays less attention to negative stimuli. Negative stimuli are superior to positive stimuli in some ways, but lack the associated circuit implementation. In this paper, a memristor-based circuit design of avoidance learning with time delay is designed. The circuit can respond to a negative stimulus after initial avoidance learning and the effect of delay time between stimuli is considered. The realization of avoidance learning is confirmed in the PSPICE simulation results. In addition, an extended application circuit based on the memristor-based circuit design of avoidance learning with time delay is proposed. The application circuit is based on the advantage of negative stimuli is more difficult to forget than positive stimuli in associative memory. Based on the features of objects as input, the output of the circuit is used to achieve the function of avoidance learning. The application circuit provides more references for neural networks of automatic driving with further development.

Operant Conditioning Neuromorphic Circuit With Addictiveness and Time Memory for Automatic Learning

Most operant conditioning circuits predominantly focus on simple feedback process, few studies consider the intricacies of feedback outcomes and the uncertainty of feedback time. This paper proposes a neuromorphic circuit based on operant conditioning with addictiveness and time memory for automatic learning. The circuit is mainly composed of hunger output module, neuron module, excitement output module, memristor-based decision module, and memory and feedback generation module. In the circuit, the process of output excitement and addiction in stochastic feedback is achieved. The memory of interval between the two rewards is formed. The circuit can adapt to complex scenarios with these functions. In addition, hunger and satiety are introduced to realize the interaction between biological behavior and exploration desire, which enables the circuit to continuously reshape its memories and actions. The process of operant conditioning theory for automatic learning is accomplished. The study of operant conditioning can serve as a reference for more intelligent brain-inspired neural systems.

Behavioral Modeling of Memristors under Harmonic Excitation

Memristors are devices built on the basis of fourth passive electrical elements in nanosystems. Because of the multitude of technologies used for memristor implementation, it is not always possible to obtain analytical models of memristors. This difficulty can be overcome using behavioral modeling, which is when mathematical models are constructed according to the input-output relationships on the input and output signals. For memristor modeling, piecewise neural and polynomial models with split signals are proposed. At harmonic input signals of memristors, this study suggests that split signals should be formed using a delay line. This method produces the minimum number of split signals and, as a result, simplifies behavioral models. Simplicity helps reduce the dimension of the nonlinear approximation problem solved in behavioral modeling. Based on the proposed method, the piecewise neural and polynomial models with harmonic input signals were constructed to approximate the transfer characteristic of the memristor, in which the current dynamics are described using the Bernoulli differential equation. It is shown that the piecewise neural model based on the feedforward network ensures higher modeling accuracy at almost the same complexity as the piecewise polynomial model.

The Framework and Memristive Circuit Design for Multisensory Mutual Associative Memory Networks

In this work, we propose a multisensory mutual associative memory networks framework and memristive circuit to mimic the ability of the biological brain to make associations of information received simultaneously. The circuit inspired by neural mechanisms of associative memory cells mainly consists of three modules: 1) the storage neurons module, which encodes external multimodal information into the firing rate of spikes; 2) the synapse module, which uses the nonvolatility memristor to achieve weight adjustment and associative learning; and 3) the retrieval neuron module, which feeds the retrieval signal output from each sensory pathway to other sensory pathways, so that achieve mutual association and retrieval between multiple modalities. Different from other one-to-one or many-to-one unidirectional associative memory work, this circuit achieves bidirectional association from multiple modalities to multiple modalities. In addition, we simulate the acquisition, extinction, recovery, transmission, and consolidation properties of associative memory. The circuit is applied to cross-modal association of image and audio recognition results, and episodic memory is simulated, where multiple images in a scene are intramodal associated. With power and area analysis, the circuit is validated as hardware-friendly. Further research to extend this work into large-scale associative memory networks, combined with visual-auditory-tactile-gustatory sensory sensors, is promising for application in intelligent robotic platforms to facilitate the development of neuromorphic systems and brain-like intelligence.

A Memristor-Based Learning Engine for Synaptic Trace-Based Online Learning

The memristor has been extensively used to facilitate the synaptic online learning of brain-inspired spiking neural networks (SNNs). However, the current memristor-based work can not support the widely used yet sophisticated trace-based learning rules, including the trace-based Spike-Timing-Dependent Plasticity (STDP) and the Bayesian Confidence Propagation Neural Network (BCPNN) learning rules. This paper proposes a learning engine to implement trace-based online learning, consisting of memristor-based blocks and analog computing blocks. The memristor is used to mimic the synaptic trace dynamics by exploiting the nonlinear physical property of the device. The analog computing blocks are used for the addition, multiplication, logarithmic and integral operations. By organizing these building blocks, a reconfigurable learning engine is architected and realized to simulate the STDP and BCPNN online learning rules, using memristors and 180 nm analog CMOS technology. The results show that the proposed learning engine can achieve energy consumption of 10.61 pJ and 51.49 pJ per synaptic update for the STDP and BCPNN learning rules, respectively, with a 147.03× and 93.61× reduction compared to the 180 nm ASIC counterparts, and also a 9.39× and 5.63× reduction compared to the 40 nm ASIC counterparts. Compared with the state-of-the-art work of Loihi and eBrainII, the learning engine can reduce the energy per synaptic update by 11.31× and 13.13× for trace-based STDP and BCPNN learning rules, respectively.

Memristive neural network circuit implementation of associative learning with overshadowing and blocking

In the field of second language acquisition, overshadowing and blocking by cue competition effects in classical conditioning affect the learning and expression of human cognitive associations. In this work, a memristive neural network circuit based on neurobiological mechanisms is proposed, which consists of synapse module, neuron module, and control module. In particular, the designed network introduces an inhibitory interneuron to divide memristive synapses into excitatory and inhibitory memristive synapses, so as to mimic synaptic plasticity better. In addition, the proposed circuit can implement six functions of second language acquisition conditioning, including learning, overshadowing, blocking, recovery from overshadowing, recovery from blocking, and long-term effect of overshadowing over time leading to blocking. Overshadowing, which denotes that the more salient stimulus overshadows the learning of the less salient stimulus when two stimuli differ in salience, reduces the associative strength acquired by the less salient stimulus. Blocking, which indicates that pretraining on one stimulus blocks learning about a second stimulus, inhibits the associative strength acquired by a second stimulus. Finally, the correctness and effectiveness of implementing functions mentioned above are verified by the simulation results in PSPICE. Through further research, the proposed circuit is applied to bionic devices such as social robots or educational robots, which can address language and cognitive disorders via assisted learning and training.

Memristor-Based Neural Network Circuit With Multimode Generalization and Differentiation on Pavlov Associative Memory

Most of the classical conditioning laws implemented by existing circuits are involved in learning and forgetting between only three neurons, and the problems between multiple neurons are not considered. In this article, a multimode generalization and differentiation circuit for the Pavlov associative memory is proposed based on memristors. The designed circuit is mainly composed of voltage control modules, synaptic neuron modules, and inhibition modules. The secondary differentiation is accomplished through the process of associative learning and forgetting among multiple neurons. The process of multiple generalization and differentiation is realized based on the nonvolatility and thresholding properties of memristors. The extinction inhibition and differentiation inhibition in forgetting is considered through the inhibition modules. The Pavlov associative memory neural network with multimodal generalization and differentiation may provide a reference for the further development of brain-like intelligence.

Memristor Neural Network Circuit Based on Operant Conditioning With Immediacy and Satiety

Most of the operant conditioning only consider the basic theory, but the influencing factors such as immediacy and satiety are ignored. In this paper, a memristor neural network circuit based on operant conditioning with immediacy and satiety is proposed. The designed circuit is mainly composed of voltage control modules, synapse modules and promotion-suppression modules. The various processes of operant conditioning theory are realized. The relationship between positive reward and negative punishment is implemented through promotion-suppression modules and synapse modules. The influence of immediacy on operant conditioning is achieved through voltage control module. The effect of satiety on operant conditioning is discussed using memristive non-volatility. The study of operant conditioning may provide a reference for smarter brain-like nerves.

Memristive Cluster Based Compact High-Density Nonvolatile Memory Design and Application for Image Storage

As a new type of nonvolatile device, the memristor has become one of the most promising technologies for designing a new generation of high-density memory. In this paper, a 4-bit high-density nonvolatile memory based on a memristor is designed and applied to image storage. Firstly, a memristor cluster structure consisting of a transistor and four memristors is designed. Furthermore, the memristor cluster is used as a memory cell in the crossbar array structure to realize the memory design. In addition, when the designed non-volatile memory is applied to gray scale image storage, only two memory cells are needed for the storage of one pixel. Through the Pspice circuit simulation, the results show that compared with the state-of-the-art technology, the memory designed in this paper has better storage density and read–write speed. When it is applied to image storage, it achieves the effect of no distortion and fast storage.

Memristive Circuit Implementation of a Self-Repairing Network Based on Biological Astrocytes in Robot Application

A large number of studies have shown that astrocytes can be combined with the presynaptic terminals and postsynaptic spines of neurons to constitute a triple synapse via an endocannabinoid retrograde messenger to achieve a self-repair ability in the human brain. Inspired by the biological self-repair mechanism of astrocytes, this work proposes a self-repairing neuron network circuit that utilizes a memristor to simulate changes in neurotransmitters when a set threshold is reached. The proposed circuit simulates an astrocyte-neuron network and comprises the following: 1) a single-astrocyte-neuron circuit module; 2) an astrocyte-neuron network circuit; 3) a module to detect malfunctions; and 4) a neuron PR (release probability of synaptic transmission) enhancement module. When faults occur in a synapse, the neuron module becomes silent or near silent because of the low PR of the synapses. The circuit can detect faults automatically. The damaged neuron can be repaired by enhancing the PR of other healthy neurons, analogous to the biological repair mechanism of astrocytes. This mechanism helps to repair the damaged circuit. A simulation of the circuit revealed the following: 1) as the number of neurons in the circuit increases, the self-repair ability strengthens and 2) as the number of damaged neurons in the astrocyte-neuron network increases, the self-repair ability weakens, and there is a significant degradation in the performance of the circuit. The self-repairing circuit was used for a robot, and it effectively improved the robots' performance and reliability.

TMPpred: A support vector machine-based thermophilic protein identifier

MOTIVATION

The thermostability of proteins will cause them to break the temperature binding and play more functions. Using machine learning, we explored the mechanism of and reasons for protein thermostability characteristics.

RESULTS

Different from other methods that only pursue the performance of models, we aim to find important features so as to provide a powerful reference for in vitro experiments. We transformed this problem into a binary classification problem, that is, the distinction between thermophilic proteins and nonthermophilic proteins. Using support vector machine-based model construction and analysis, we inferred that Gly, Ala, Ser and Thr may be the most important components at the residue level that determine the thermal stability of proteins. It is also noteworthy that our proposed model obtains an Sn of 0.892, an Sp of 0.857, an ACC of 0.87566 and an AUC of 0.874. To facilitate other researchers, we wrapped our model and deployed it as a web server, which is accessible at http://112.124.26.17:7000/TMPpred/index.html.

Application of Sparse Representation in Bioinformatics

Inspired by L1-norm minimization methods, such as basis pursuit, compressed sensing, and Lasso feature selection, in recent years, sparse representation shows up as a novel and potent data processing method and displays powerful superiority. Researchers have not only extended the sparse representation of a signal to image presentation, but also applied the sparsity of vectors to that of matrices. Moreover, sparse representation has been applied to pattern recognition with good results. Because of its multiple advantages, such as insensitivity to noise, strong robustness, less sensitivity to selected features, and no “overfitting” phenomenon, the application of sparse representation in bioinformatics should be studied further. This article reviews the development of sparse representation, and explains its applications in bioinformatics, namely the use of low-rank representation matrices to identify and study cancer molecules, low-rank sparse representations to analyze and process gene expression profiles, and an introduction to related cancers and gene expression profile database.

A Multi-functional Memristive Pavlov Associative Memory Circuit Based on Neural Mechanisms

Pavlov conditioning is a typical associative memory, which involves associative learning between the gustatory and auditory cortex, known as Pavlov associative memory. Inspired by neural mechanisms and biological phenomena of Pavlov associative memory, this paper proposes a multi-functional memristive Pavlov associative memory circuit. In addition to learning and forgetting, whose rates change with the number of associative learning times, the circuit also achieves other innovative functions. First, consolidation learning, which refers to the continued learning process after acquiring associative memory, changes the rates of learning and forgetting. Secondly, the natural forgetting rate tends to zero when the associative memory has been acquired several times, which means the formation of long-term memory. Thirdly, the generalization and differentiation of associative memory caused by similar stimuli are realized through a simplified memristive feedforward neural network. Besides, this circuit implements the associative learning function of interval stimuli through a simpler structure, which refers to "the longer the stimuli interval, the slower the learning rate". The above functions are realized by the time interval module, variable rates module, and generalization and differentiation module. It has been shown that the proposed circuit has good robustness, and can reduce the influence of parasitic capacitance, memristive conductance drift, and input noise on circuit functions. Through further research, this circuit is expected to be used in robot platforms to realize human-like perception and associative cognitive functions.

Recent development of machine learning methods in sumoylation sites prediction

Sumoylation of proteins is an important reversible post-translational modification of proteins and mediates a variety of cellular processes. Sumo-modified proteins can change their subcellular localization, activity and stability. In addition, it also plays an important role in various cellular processes such as transcriptional regulation and signal transduction. The abnormal sumoylation is involved in many diseases, including neurodegeneration and immune-related diseases, as well as the development of cancer. Therefore, identification of the sumoylation site (SUMO site) is fundamental to understanding their molecular mechanisms and regulatory roles. In contrast to labor-intensive and costly experimental approaches, computational prediction of sumoylation sites in silico also attracted much attention for its accuracy, convenience and speed. At present, many computational prediction models have been used to identify SUMO sites, but these contents have not been comprehensively summarized and reviewed. Therefore, the research progress of relevant models is summarized and discussed in this paper. We will briefly summarize the development of bioinformatics methods on sumoylation site prediction. We will mainly focus on the benchmark dataset construction, feature extraction, machine learning method, published results and online tools. We hope the review will provide more help for wet-experimental scholars.

Memristor-Based Neural Network Circuit of Emotion Congruent Memory With Mental Fatigue and Emotion Inhibition

Most memristor-based neural networks only consider a single mode of memory or emotion, but ignore the relationship between emotion and memory. In this paper, a memristor-based neural network circuit of emotion congruent memory is proposed and verified by the simulation results. The designed circuit consists of a memory module, an emotion module and an association neuron module. Varieties of memory and emotion functions are considered. The functions such as learning, forgetting, variable rate and emotion generation are implemented by the circuit. Furthermore, mental fatigue and emotion inhibition which are two important self-protective measures of the brain are realized in this paper on the basis of emotion congruent memory. Finally, the paper also considers the congruence between emotion and memory materials and the regulation of emotion on memory. The neural network circuit of emotion congruent memory can provide more references for the application of memristor.

A prognosis-related based method for miRNA selection on liver hepatocellular carcinoma prediction

Hepatocellular carcinoma (HCC) is considered as the sixth most common cancer in the world, and it is also considered as one of the causes of death. Moreover, the poor prognosis of recurrence of HCC after surgery and metastasis is also a big problem for human health. If the disease can be diagnosed earlier, the survival rate of the patients will be improved significantly. In the early stage of hepatocellular carcinoma, the expression of miRNAs is likely to become abnormal. In our work, the expression profile of miRNAs of human HCC in cancer tissue is compared with their adjacent tissue samples collected from tumor cancer genomic Atlas (TCGA) platform, then the genes with significant difference are selected by Limma test. Selected genes are referred to predict miRNAs related to the prognosis of HCC patients. Finally, miRNAs regulated by target genes are selected by our method, and the experimental results demonstrated that our method is more efficient than biology wet experimental method with lower cost.

RA-UNet: A Hybrid Deep Attention-Aware Network to Extract Liver and Tumor in CT Scans

Automatic extraction of liver and tumor from CT volumes is a challenging task due to their heterogeneous and diffusive shapes. Recently, 2D deep convolutional neural networks have become popular in medical image segmentation tasks because of the utilization of large labeled datasets to learn hierarchical features. However, few studies investigate 3D networks for liver tumor segmentation. In this paper, we propose a 3D hybrid residual attention-aware segmentation method, i.e., RA-UNet, to precisely extract the liver region and segment tumors from the liver. The proposed network has a basic architecture as U-Net which extracts contextual information combining low-level feature maps with high-level ones. Attention residual modules are integrated so that the attention-aware features change adaptively. This is the first work that an attention residual mechanism is used to segment tumors from 3D medical volumetric images. We evaluated our framework on the public MICCAI 2017 Liver Tumor Segmentation dataset and tested the generalization on the 3DIRCADb dataset. The experiments show that our architecture obtains competitive results.

Predicting the Disease Risk of Protein Mutation Sequences With Pre-training Model

Accurately identifying the missense mutations is of great help to alleviate the loss of protein function and structural changes, which might greatly reduce the risk of disease for tumor suppressor genes (e.g., BRCA1 and PTEN). In this paper, we propose a hybrid framework, called BertVS, that predicts the disease risk for the missense mutation of proteins. Our framework is able to learn sequence representations from the protein domain through pre-training BERT models, and also integrates with the hydrophilic properties of amino acids to obtain the sequence representations of biochemical characteristics. The concatenation of two learned representations are then sent to the classifier to predict the missense mutations of protein sequences. Specifically, we use the protein family database (Pfam) as a corpus to train the BERT model to learn the contextual information of protein sequences, and our pre-training BERT model achieves a value of 0.984 on accuracy in the masked language model prediction task. We conduct extensive experiments on BRCA1 and PTEN datasets. With comparison to the baselines, results show that BertVS achieves higher performance of 0.920 on AUROC and 0.915 on AUPR in the functionally critical domain of the BRCA1 gene. Additionally, the extended experiment on the ClinVar dataset can illustrate that gene variants with known clinical significance can also be efficiently classified by our method. Therefore, BertVS can learn the functional information of the protein sequences and effectively predict the disease risk of variants with an uncertain clinical significance.

PredAmyl-MLP: Prediction of Amyloid Proteins Using Multilayer Perceptron

Amyloid is generally an aggregate of insoluble fibrin; its abnormal deposition is the pathogenic mechanism of various diseases, such as Alzheimer's disease and type II diabetes. Therefore, accurately identifying amyloid is necessary to understand its role in pathology. We proposed a machine learning-based prediction model called PredAmyl-MLP, which consists of the following three steps: feature extraction, feature selection, and classification. In the step of feature extraction, seven feature extraction algorithms and different combinations of them are investigated, and the combination of SVMProt-188D and tripeptide composition (TPC) is selected according to the experimental results. In the step of feature selection, maximum relevant maximum distance (MRMD) and binomial distribution (BD) are, respectively, used to remove the redundant or noise features, and the appropriate features are selected according to the experimental results. In the step of classification, we employed multilayer perceptron (MLP) to train the prediction model. The 10-fold cross-validation results show that the overall accuracy of PredAmyl-MLP reached 91.59%, and the performance was better than the existing methods.