Identification of a small set of plasma signalling proteins using neural network for prediction of Alzheimer's disease.

MOTIVATION: Alzheimer's disease (AD) is a dementia that gets worse with time resulting in loss of memory and cognitive functions. The life expectancy of AD patients following diagnosis is ∼7 years. In 2006, researchers estimated that 0.40% of the world population (range 0.17-0.89%) was afflicted by AD, and that the prevalence rate would be tripled by 2050. Usually, examination of brain tissues is required for definite diagnosis of AD. So, it is crucial to diagnose AD at an early stage via some alternative methods. As the brain controls many functions via releasing signalling proteins through blood, we analyse blood plasma proteins for diagnosis of AD. RESULTS: Here, we use a radial basis function (RBF) network for feature selection called feature selection RBF network for selection of plasma proteins that can help diagnosis of AD. We have identified a set of plasma proteins, smaller in size than previous study, with comparable prediction accuracy. We have also analysed mild cognitive impairment (MCI) samples with our selected proteins. We have used neural networks and support vector machines as classifiers. The principle component analysis, Sammmon projection and heat-map of the selected proteins have been used to demonstrate the proteins' discriminating power for diagnosis of AD. We have also found a set of plasma signalling proteins that can distinguish incipient AD from MCI at an early stage. Literature survey strongly supports the AD diagnosis capability of the selected plasma proteins.

Bi-Level Spectral Feature Selection.

Unsupervised feature selection (UFS) aims to learn an indicator matrix relying on some characteristics of the high-dimensional data to identify the features to be selected. However, traditional unsupervised methods perform only at the feature level, i.e., they directly select useful features by feature ranking. Such methods do not pay any attention to the interaction information with other tasks such as classification, which severely degrades their feature selection performance. In this article, we propose an UFS method which also takes into account the classification level, and selects features that perform well both in clustering and classification. To achieve this, we design a bi-level spectral feature selection (BLSFS) method, which combines classification level and feature level. More concretely, at the classification level, we first apply the spectral clustering to generate pseudolabels, and then train a linear classifier to obtain the optimal regression matrix. At the feature level, we select useful features via maintaining the intrinsic structure of data in the embedding space with the learned regression matrix from the classification level, which in turn guides classifier training. We utilize a balancing parameter to seamlessly bridge the classification and feature levels together to construct a unified framework. A series of experiments on 12 benchmark datasets are carried out to demonstrate the superiority of BLSFS in both clustering and classification performance.

Multimodal fusion for anticipating human decision performance.

Anticipating human decisions while performing complex tasks remains a formidable challenge. This study proposes a multimodal machine-learning approach that leverages image features and electroencephalography (EEG) data to predict human response correctness in a demanding visual searching task. Notably, we extract a novel set of image features pertaining to object relationships using the Segment Anything Model (SAM), which enhances prediction accuracy compared to traditional features. Additionally, our approach effectively utilizes a combination of EEG signals and image features to streamline the feature set required for the Random Forest Classifier (RFC) while maintaining high accuracy. The findings of this research hold substantial potential for developing advanced fault alert systems, particularly in critical decision-making environments such as the medical and defence sectors.

Universal Approximation Abilities of a Modular Differentiable Neural Network.

Approximation ability is one of the most important topics in the field of neural networks (NNs). Feedforward NNs, activated by rectified linear units and some of their specific smoothed versions, provide universal approximators to convex as well as continuous functions. However, most of these networks are investigated empirically, or their characteristics are analyzed based on specific operation rules. Moreover, an adequate level of interpretability of the networks is missing as well. In this work, we propose a class of new network architecture, built with reusable neural modules (functional blocks), to supply differentiable and interpretable approximators for convex and continuous target functions. Specifically, first, we introduce a concrete model construction mechanism with particular blocks based on differentiable programming and the composition essence of the max operator, extending the scope of existing activation functions. Moreover, explicit block diagrams are provided for a clear understanding of the external architecture and the internal processing mechanism. Subsequently, the approximation behavior of the proposed network to convex functions and continuous functions is rigorously proved as well, by virtue of mathematical induction. Finally, plenty of numerical experiments are conducted on a wide variety of problems, which exhibit the effectiveness and the superiority of the proposed model over some existing ones.

Supervised Feature Selection via Collaborative Neurodynamic Optimization.

As a crucial part of machine learning and pattern recognition, feature selection aims at selecting a subset of the most informative features from the set of all available features. In this article, supervised feature selection is at first formulated as a mixed-integer optimization problem with an objective function of weighted feature redundancy and relevancy subject to a cardinality constraint on the number of selected features. It is equivalently reformulated as a bound-constrained mixed-integer optimization problem by augmenting the objective function with a penalty function for realizing the cardinality constraint. With additional bilinear and linear equality constraints for realizing the integrality constraints, it is further reformulated as a bound-constrained biconvex optimization problem with two more penalty terms. Two collaborative neurodynamic optimization (CNO) approaches are proposed for solving the formulated and reformulated feature selection problems. One of the proposed CNO approaches uses a population of discrete-time recurrent neural networks (RNNs), and the other use a pair of continuous-time projection networks operating concurrently on two timescales. Experimental results on 13 benchmark datasets are elaborated to substantiate the superiority of the CNO approaches to several mainstream methods in terms of average classification accuracy with three commonly used classifiers.

Fractional Approximation of Broad Learning System.

Approximation ability is of much importance for neural networks. The broad learning system (BLS) (Chen and Liu, 2018), widely used in the industry with good performance, has been proved to be a universal approximator from the aspect of density. This kind of approximation property is very important, which proves the existence of the desired network but does not provide a means of construction that is commonly implemented through complexity aspect. Thus, such an approach lacks the advantage of determining constructively the network architecture and its weights. To the best of our knowledge, for a BLS, there is a few theory providing a constructive approach to obtain the network structure along with weights ensuring the approximation properties. By virtue of the long-term memory and nonlocality properties, fractional calculus has observed many distinctive applications. The purpose of this article is to study the BLS approximation ability constructively, which is valid for fractional case as well. Specifically, first we introduce two simplified BLSs by means of extending functions. For each of the simplified BLSs, an upper bound of error is derived through the modulus of continuity of Caputo fractional derivatives. As a result, two types of fractional convergent behaviors of BLS, that is: 1) pointwise and 2) uniform convergence, have been rigorously proved as well. Finally, some numerical experiments are conducted to demonstrate the approximation capabilities of BLSs.

Unsupervised feature selection via adaptive autoencoder with redundancy control.

Unsupervised feature selection is one of the efficient approaches to reduce the dimension of unlabeled high-dimensional data. We present a novel adaptive autoencoder with redundancy control (AARC) as an unsupervised feature selector. By adding two Group Lasso penalties to the objective function, AARC integrates unsupervised feature selection and determination of a compact network structure into a single framework. Besides, a penalty based on a measure of dependency between features (such as Pearson correlation, mutual information) is added to the objective function for controlling the level of redundancy in the selected features. To realize the desired effects of different regularizers in different phases of the training, we introduce adaptive parameters which change with iterations. In addition, a smoothing function is utilized to approximate the three penalties since they are not differentiable at the origin. An ablation study is carried out to validate the capabilities of redundancy control and structure optimization of AARC. Subsequently, comparisons with nine state-of-the-art methods illustrate the efficiency of AARC for unsupervised feature selection.

Feature Selection Using a Neural Network With Group Lasso Regularization and Controlled Redundancy.

We propose a neural network-based feature selection (FS) scheme that can control the level of redundancy in the selected features by integrating two penalties into a single objective function. The Group Lasso penalty aims to produce sparsity in features in a grouped manner. The redundancy-control penalty, which is defined based on a measure of dependence among features, is utilized to control the level of redundancy among the selected features. Both the penalty terms involve the L2,1 -norm of weight matrix between the input and hidden layers. These penalty terms are nonsmooth at the origin, and hence, one simple but efficient smoothing technique is employed to overcome this issue. The monotonicity and convergence of the proposed algorithm are specified and proved under suitable assumptions. Then, extensive experiments are conducted on both artificial and real data sets. Empirical results explicitly demonstrate the ability of the proposed FS scheme and its effectiveness in controlling redundancy. The empirical simulations are observed to be consistent with the theoretical results.

Exploring Covert States of Brain Dynamics via Fuzzy Inference Encoding.

Human brain inherently exhibits latent mental processes which are likely to change rapidly over time. A framework that adopts a fuzzy inference system is proposed to model the dynamics of the human brain. The fuzzy inference system is used to encode real-world data to represent the salient features of the EEG signals. Then, an unsupervised clustering is conducted on the extracted feature space to identify the brain (external and covert) states that respond to different cognitive demands. To understand the human state change, a state transition diagram is introduced, allowing visualization of connectivity patterns between every pair of states. We compute the transition probability between every pair of states to represent the relationships between the states. This state transition diagram is named as the Fuzzy Covert State Transition Diagram (FCOSTD), which helps the understanding of human states and human performance. We then apply FCOSTD on distracted driving experiments. FCOSTD successfully discovers the external and covert states, faithfully reveals the transition of the brain between states, and the route of the state change when humans are distracted during a driving task. The experimental results demonstrate that different subjects have similar states and inter-state transition behaviour (establishing the consistency of the system) but different ways to allocate brain resources as different actions are being taken.

In Search of Trustworthy and Transparent Intelligent Systems With Human-Like Cognitive and Reasoning Capabilities.

At present we are witnessing a tremendous interest in Artificial Intelligence (AI), particularly in Deep Learning (DL)/Deep Neural Networks (DNNs). One of the reasons appears to be the unmatched performance achieved by such systems. This has resulted in an enormous hope on such techniques and often these are viewed as all-cure solutions. But most of these systems cannot explain why a particular decision is made (black box) and sometimes miserably fail in cases where other systems would not. Consequently, in critical applications such as healthcare and defense practitioners do not like to trust such systems. Although an AI system is often designed taking inspiration from the brain, there is not much attempt to exploit cues from the brain in true sense. In our opinion, to realize intelligent systems with human like reasoning ability, we need to exploit knowledge from the brain science. Here we discuss a few findings in brain science that may help designing intelligent systems. We explain the relevance of transparency, explainability, learning from a few examples, and the trustworthiness of an AI system. We also discuss a few ways that may help to achieve these attributes in a learning system.

Learning Optimized Structure of Neural Networks by Hidden Node Pruning With L1 Regularization.

We propose three different methods to determine the optimal number of hidden nodes based on L1 regularization for a multilayer perceptron network. The first two methods, respectively, use a set of multiplier functions and multipliers for the hidden-layer nodes and implement the L1 regularization on those, while the third method equipped with the same multipliers uses a smoothing approximation of the L1 regularization. Each of these methods begins with a given number of hidden nodes, then the network is trained to obtain an optimal architecture discarding redundant hidden nodes using the multiplier functions or multipliers. A simple and generic method, namely, the matrix-based convergence proving method (MCPM), is introduced to prove the weak and strong convergence of the presented smoothing algorithms. The performance of the three pruning methods has been tested on 11 different classification datasets. The results demonstrate the efficient pruning abilities and competitive generalization by the proposed methods. The theoretical results are also validated by the results.

Distributed Adaptive Tracking Synchronization for Coupled Reaction-Diffusion Neural Network.

This paper considers the tracking synchronization problem for a class of coupled reaction-diffusion neural networks (CRDNNs) with undirected topology. For the case where the tracking trajectory has identical individual dynamic as that of the network nodes, the edge-based and vertex-based adaptive strategies on coupling strengths as well as adaptive controllers, which demand merely the local neighbor information, are proposed to synchronize the CRDNNs to the tracking trajectory. To reduce the control costs, an adaptive pinning control technique is employed. For the case where the tracking trajectory has different individual dynamic from that of the network nodes, the vertex-based adaptive strategy is proposed to drive the synchronization error to a relatively small area, which is adjustable according to the parameters of the adaptive strategy. This kind of adaptive design can enhance the robustness of the network against the external disturbance posed on the tracking trajectory. The obtained theoretical results are verified by two representative examples.

Weight Noise Injection-Based MLPs With Group Lasso Penalty: Asymptotic Convergence and Application to Node Pruning.

The application and theoretical analysis of fault tolerant learning are very important for neural networks. Our objective here is to realize fault tolerant sparse multilayer perceptron (MLP) networks. The stochastic gradient descent method has been employed to perform online learning for MLPs. For weight noise injection-based network models, it is a common strategy to add a weight decay regularizer while constructing the objective function for learning. However, this l2 -norm penalty does not generate sparse optimal solutions. In this paper, a group lasso penalty term is used as a regularizer, where a group is defined by the set of weights connected to a node from nodes in the preceding layer. Group lasso penalty enables us to prune redundant hidden nodes. Due to its nondifferentiability at the origin, a smooth approximation of the group lasso penalty is developed. Then, a rigorous proof for the asymptotic convergence of the learning algorithm is provided. Finally, some simulations have been performed to verify the sparseness of the network and the theoretical results.

Selecting useful groups of features in a connectionist framework.

Suppose for a given classification or function approximation (FA) problem data are collected using l sensors. From the output of the ith sensor, ni features are extracted, thereby generating p = sigma li = 1 ni features, so for the task we have X subset Rp as input data along with their corresponding outputs or class labels Y subset Rc. Here, we propose two connectionist schemes that can simultaneously select the useful sensors and learn the relation between X and Y. One scheme is based on the radial basis function (RBF) network and the other uses the multilayered perceptron (MLP) network. Both schemes are shown to possess the universal approximation property. Simulations show that the methods can detect the bad/derogatory groups of features online and can eliminate the effect of these bad features while doing the FA or classification task.

Discovering biomarkers from gene expression data for predicting cancer subgroups using neural networks and relational fuzzy clustering.

BACKGROUND: The four heterogeneous childhood cancers, neuroblastoma, non-Hodgkin lymphoma, rhabdomyosarcoma, and Ewing sarcoma present a similar histology of small round blue cell tumor (SRBCT) and thus often leads to misdiagnosis. Identification of biomarkers for distinguishing these cancers is a well studied problem. Existing methods typically evaluate each gene separately and do not take into account the nonlinear interaction between genes and the tools that are used to design the diagnostic prediction system. Consequently, more genes are usually identified as necessary for prediction. We propose a general scheme for finding a small set of biomarkers to design a diagnostic system for accurate classification of the cancer subgroups. We use multilayer networks with online gene selection ability and relational fuzzy clustering to identify a small set of biomarkers for accurate classification of the training and blind test cases of a well studied data set. RESULTS: Our method discerned just seven biomarkers that precisely categorized the four subgroups of cancer both in training and blind samples. For the same problem, others suggested 19-94 genes. These seven biomarkers include three novel genes (NAB2, LSP1 and EHD1 - not identified by others) with distinct class-specific signatures and important role in cancer biology, including cellular proliferation, transendothelial migration and trafficking of MHC class antigens. Interestingly, NAB2 is downregulated in other tumors including Non-Hodgkin lymphoma and Neuroblastoma but we observed moderate to high upregulation in a few cases of Ewing sarcoma and Rabhdomyosarcoma, suggesting that NAB2 might be mutated in these tumors. These genes can discover the subgroups correctly with unsupervised learning, can differentiate non-SRBCT samples and they perform equally well with other machine learning tools including support vector machines. These biomarkers lead to four simple human interpretable rules for the diagnostic task. CONCLUSION: Although the proposed method is tested on a SRBCT data set, it is quite general and can be applied to other cancer data sets. Our scheme takes into account the interaction between genes as well as that between genes and the tool and thus is able find a very small set and can discover novel genes. Our findings suggest the possibility of developing specialized microarray chips or use of real-time qPCR assays or antibody based methods such as ELISA and western blot analysis for an easy and low cost diagnosis of the subgroups.

Fuzzy Decision-Making Fuser (FDMF) for Integrating Human-Machine Autonomous (HMA) Systems with Adaptive Evidence Sources.

A brain-computer interface (BCI) creates a direct communication pathway between the human brain and an external device or system. In contrast to patient-oriented BCIs, which are intended to restore inoperative or malfunctioning aspects of the nervous system, a growing number of BCI studies focus on designing auxiliary systems that are intended for everyday use. The goal of building these BCIs is to provide capabilities that augment existing intact physical and mental capabilities. However, a key challenge to BCI research is human variability; factors such as fatigue, inattention, and stress vary both across different individuals and for the same individual over time. If these issues are addressed, autonomous systems may provide additional benefits that enhance system performance and prevent problems introduced by individual human variability. This study proposes a human-machine autonomous (HMA) system that simultaneously aggregates human and machine knowledge to recognize targets in a rapid serial visual presentation (RSVP) task. The HMA focuses on integrating an RSVP BCI with computer vision techniques in an image-labeling domain. A fuzzy decision-making fuser (FDMF) is then applied in the HMA system to provide a natural adaptive framework for evidence-based inference by incorporating an integrated summary of the available evidence (i.e., human and machine decisions) and associated uncertainty. Consequently, the HMA system dynamically aggregates decisions involving uncertainties from both human and autonomous agents. The collaborative decisions made by an HMA system can achieve and maintain superior performance more efficiently than either the human or autonomous agents can achieve independently. The experimental results shown in this study suggest that the proposed HMA system with the FDMF can effectively fuse decisions from human brain activities and the computer vision techniques to improve overall performance on the RSVP recognition task. This conclusion demonstrates the potential benefits of integrating autonomous systems with BCI systems.

Genetic programming for simultaneous feature selection and classifier design.

This paper presents an online feature selection algorithm using genetic programming (GP). The proposed GP methodology simultaneously selects a good subset of features and constructs a classifier using the selected features. For a c-class problem, it provides a classifier having c trees. In this context, we introduce two new crossover operations to suit the feature selection process. As a byproduct, our algorithm produces a feature ranking scheme. We tested our method on several data sets having dimensions varying from 4 to 7129. We compared the performance of our method with results available in the literature and found that the proposed method produces consistently good results. To demonstrate the robustness of the scheme, we studied its effectiveness on data sets with known (synthetically added) redundant/bad features.

A novel connectionist framework for computation of an approximate convex-hull of a set of planar points, circles and ellipses.

We propose a two layer neural network for computation of an approximate convex-hull of a set of points or a set of circles/ellipses of different sizes. The algorithm is based on a very elegant concept - shrinking of a rubber band surrounding the set of planar objects. Logically, a set of neurons is placed on a circle (rubber band) surrounding the objects. Each neuron has a parameter vector associated with it. This may be viewed as the current position of the neuron. The given set of points/objects exerts a force of attraction on every neuron, which determines how its current position will be updated (as if, the force determines the direction of movement of the neuron lying on the rubber band). As the network evolves, the neurons (parameter vectors) approximate the convex-hull more and more accurately. The scheme can be applied to find the convex-hull of a planar set of circles or ellipses or a mixture of the two. Some properties related to the evolution of the algorithm are also presented.

A Multiobjective Genetic Programming-Based Ensemble for Simultaneous Feature Selection and Classification.

We present an integrated algorithm for simultaneous feature selection (FS) and designing of diverse classifiers using a steady state multiobjective genetic programming (GP), which minimizes three objectives: 1) false positives (FPs); 2) false negatives (FNs); and 3) the number of leaf nodes in the tree. Our method divides a c -class problem into c binary classification problems. It evolves c sets of genetic programs to create c ensembles. During mutation operation, our method exploits the fitness as well as unfitness of features, which dynamically change with generations with a view to using a set of highly relevant features with low redundancy. The classifiers of i th class determine the net belongingness of an unknown data point to the i th class using a weighted voting scheme, which makes use of the FP and FN mistakes made on the training data. We test our method on eight microarray and 11 text data sets with diverse number of classes (from 2 to 44), large number of features (from 2000 to 49 151), and high feature-to-sample ratio (from 1.03 to 273.1). We compare our method with a bi-objective GP scheme that does not use any FS and rule size reduction strategy. It depicts the effectiveness of the proposed FS and rule size reduction schemes. Furthermore, we compare our method with four classification methods in conjunction with six features selection algorithms and full feature set. Our scheme performs the best for 380 out of 474 combinations of data sets, algorithm and FS method.

Feature selection using a neural framework with controlled redundancy.

We first present a feature selection method based on a multilayer perceptron (MLP) neural network, called feature selection MLP (FSMLP). We explain how FSMLP can select essential features and discard derogatory and indifferent features. Such a method may pick up some useful but dependent (say correlated) features, all of which may not be needed. We then propose a general scheme for dealing with feature selection with "controlled redundancy" (CoR). The proposed scheme, named as FSMLP-CoR, can select features with a controlled redundancy both for classification and function approximation/prediction type problems. We have also proposed a new more effective training scheme named mFSMLP-CoR. The idea is general in nature and can be used with other learning schemes also. We demonstrate the effectiveness of the algorithms using several data sets including a synthetic data set. We also show that the selected features are adequate to solve the problem at hand. Here, we have considered a measure of linear dependency to control the redundancy. The use of nonlinear measures of dependency, such as mutual information, is straightforward. Here, there are some advantages of the proposed schemes. They do not require explicit evaluation of the feature subsets. Here, feature selection is integrated into designing of the decision-making system. Hence, it can look at all features together and pick up whatever is necessary. Our methods can account for possible nonlinear subtle interactions between features, as well as that between features, tools, and the problem being solved. They can also control the level of redundancy in the selected features. Of the two learning schemes, mFSMLP-CoR, not only improves the performance of the system, but also significantly reduces the dependency of the network's behavior on the initialization of connection weights.