Flexible nonlinear blind signal separation in the complex domain

This paper introduces an Independent Component Analysis (ICA) approach to the separation of nonlinear mixtures in the complex domain. Source separation is performed by a complex INFOMAX approach. The neural network which realizes the separation employs the so called "Mirror Model" and is based on adaptive activation functions, whose shape is properly modified during learning. Nonlinear functions involved in the processing of complex signals are realized by pairs of spline neurons called "splitting functions", working on the real and the imaginary part of the signal respectively. Theoretical proof of existence and uniqueness of the solution under proper assumptions is also provided. In particular a simple adaptation algorithm is derived and some experimental results that demonstrate the effectiveness of the proposed solution are shown.     

A bootstrap-aggregated hybrid semi-parametric modeling framework for bioprocess development

Bioprocess and Biosystems Engineering - Hybrid semi-parametric modeling, combining mechanistic and machine-learning methods, has proven to be a powerful method for process development. This paper...     

Least-squares methods for blind source separation based on nonlinear PCA

In standard blind source separation, one tries to extract unknown source signals from their instantaneous linear mixtures by using a minimum of a priori information. We have recently shown that certain nonlinear extensions of principal component type neural algorithms can be successfully applied to this problem. In this paper, we show that a nonlinear PCA criterion can be minimized using least-squares approaches, leading to computationally efficient and fast converging algorithms. Several versions of this approach are developed and studied, some of which can be regarded as neural learning algorithms. A connection to the nonlinear PCA subspace rule is also shown. Experimental results are given, showing that the least-squares methods usually converge clearly faster than stochastic gradient algorithms in blind separation problems.     

A semi-parametric Bayesian model for unsupervised differential co-expression analysis

Background  

Differential co-expression analysis is an emerging strategy for characterizing disease related dysregulation of gene expression regulatory networks. Given pre-defined sets of biological samples, such analysis aims at identifying genes that are co-expressed in one, but not in the other set of samples.     

A semi-parametric statistical model for integrating gene expression profiles across different platforms

Determining differentially expressed genes (DEGs) between biological samples is the key to understand how genotype gives rise to phenotype. RNA-seq and microarray are two main technologies for profiling gene expression levels. However, considerable discrepancy has been found between DEGs detected using the two technologies. Integration data across these two platforms has the potential to improve the power and reliability of DEG detection. We propose a rank-based semi-parametric model to determine DEGs using information across different sources and apply it to the integration of RNA-seq and microarray data. By incorporating both the significance of differential expression and the consistency across platforms, our method effectively detects DEGs with moderate but consistent signals. We demonstrate the effectiveness of our method using simulation studies, MAQC/SEQC data and a synthetic microRNA dataset. Our integration method is not only robust to noise and heterogeneity in the data, but also adaptive to the structure of data. In our simulations and real data studies, our approach shows a higher discriminate power and identifies more biologically relevant DEGs than eBayes, DEseq and some commonly used meta-analysis methods.     

A semi-parametric shared parameter model to handle nonmonotone nonignorable missingness

Summary .  Longitudinal studies often generate incomplete response patterns according to a missing not at random mechanism. Shared parameter models provide an appealing framework for the joint modelling of the measurement and missingness processes, especially in the nonmonotone missingness case, and assume a set of random effects to induce the interdependence. Parametric assumptions are typically made for the random effects distribution, violation of which leads to model misspecification with a potential effect on the parameter estimates and standard errors. In this article we avoid any parametric assumption for the random effects distribution and leave it completely unspecified. The estimation of the model is then made using a semi-parametric maximum likelihood method. Our proposal is illustrated on a randomized longitudinal study on patients with rheumatoid arthritis exhibiting nonmonotone missingness.     

Novel two-stage hybrid neural discriminant model for predicting proteins structural classes

In order to establish novel hybrid neural discriminant model, linear discriminant analysis (LDA) was used at the first stage to evaluate the contribution of sequence parameters in determining the protein structural class. An in-house program generated parameters including single amino acid and all dipeptide composition frequencies for 498 proteins came from Zhou [An intriguing controversy over protein structural class prediction, J. Protein Chem. 17(8) (1998) 729-738]. Then, 127 statistically effective parameters were selected by stepwise LDA and were used as inputs of the artificial neural networks (ANNs) to build a two-stage hybrid predictor. In this study, self-consistency and jackknife tests were used to verify the performance of this hybrid model, and were compared with some of prior works. The results showed that our two-stage hybrid neural discriminant model approach is very promising and may play a complementary role to the existing powerful approaches.     

A hybrid model for the neural representation of complex mental processing in the human brain

In the present conceptual review several theoretical and empirical sources of information were integrated, and a hybrid model of the neural representation of complex mental processing in the human brain was proposed. Based on empirical evidence for strategy-related and inter-individually different task-related brain activation networks, and further based on empirical evidence for a remarkable overlap of fronto-parietal activation networks across different complex mental processes, it was concluded by the author that there might be innate and modular organized neuro-developmental starting regions, for example, in intra-parietal, and both medial and middle frontal brain regions, from which the neural organization of different kinds of complex mental processes emerge differently during individually shaped learning histories. Thus, the here proposed model provides a hybrid of both massive modular and holistic concepts of idiosyncratic brain physiological elaboration of complex mental processing. It is further concluded that 3-D information, obtained by respective methodological approaches, are not appropriate to identify the non-linear spatio-temporal dynamics of complex mental process-related brain activity in a sufficient way. How different participating network parts communicate with each other seems to be an indispensable aspect, which has to be considered in particular to improve our understanding of the neural organization of complex cognition.     

Advances in blind source separation (BSS) and independent component analysis (ICA) for nonlinear mixtures

In this paper, we review recent advances in blind source separation (BSS) and independent component analysis (ICA) for nonlinear mixing models. After a general introduction to BSS and ICA, we discuss in more detail uniqueness and separability issues, presenting some new results. A fundamental difficulty in the nonlinear BSS problem and even more so in the nonlinear ICA problem is that they provide non-unique solutions without extra constraints, which are often implemented by using a suitable regularization. In this paper, we explore two possible approaches. The first one is based on structural constraints. Especially, post-nonlinear mixtures are an important special case, where a nonlinearity is applied to linear mixtures. For such mixtures, the ambiguities are essentially the same as for the linear ICA or BSS problems. The second approach uses Bayesian inference methods for estimating the best statistical parameters, under almost unconstrained models in which priors can be easily added. In the later part of this paper, various separation techniques proposed for post-nonlinear mixtures and general nonlinear mixtures are reviewed.     

A neural network dynamic model reproducing the output signal of the ganglion cell

A functional model of a neural network reproducing the output signal of the ganglion cell is proposed. The model assumes that receptive fields with antagonistic center and periphery are formed.     

A linear framework for time-scale separation in nonlinear biochemical systems

Cellular physiology is implemented by formidably complex biochemical systems with highly nonlinear dynamics, presenting a challenge for both experiment and theory. Time-scale separation has been one of the few theoretical methods for distilling general principles from such complexity. It has provided essential insights in areas such as enzyme kinetics, allosteric enzymes, G-protein coupled receptors, ion channels, gene regulation and post-translational modification. In each case, internal molecular complexity has been eliminated, leading to rational algebraic expressions among the remaining components. This has yielded familiar formulas such as those of Michaelis-Menten in enzyme kinetics, Monod-Wyman-Changeux in allostery and Ackers-Johnson-Shea in gene regulation. Here we show that these calculations are all instances of a single graph-theoretic framework. Despite the biochemical nonlinearity to which it is applied, this framework is entirely linear, yet requires no approximation. We show that elimination of internal complexity is feasible when the relevant graph is strongly connected. The framework provides a new methodology with the potential to subdue combinatorial explosion at the molecular level.     

A neural net model for epilepsy

A neural net model based in our previous studies with randomly interconnected neural nets is presented here capable of exhibiting epileptic features. These features can be explained in terms of the structural and dynamical properties of the model. In addition, apart from the fact that this model can imitate epileptic phenomena, it might also help to explain some poorly understood clinical phenomena from which general disturbances can produce focal seizures in the brain.     

A neural model for category learning

We present a general neural model for supervised learning of pattern categories which can resolve pattern classes separated by nonlinear, essentially arbitrary boundaries. The concept of a pattern class develops from storing in memory a limited number of class elements (prototypes). Associated with each prototype is a modifiable scalar weighting factor () which effectively defines the threshold for categorization of an input with the class of the given prototype. Learning involves (1) commitment of prototypes to memory and (2) adjustment of the various factors to eliminate classification errors. In tests, the model ably defined classification boundaries that largely separated complicated pattern regions. We discuss the role which divisive inhibition might play in a possible implementation of the model by a network of neurons.This work was supported in part by the Alfred P. Sloan Foundation and the Ittleson Foundation, Inc.     

A hybrid model for reducing ecological bias

A major drawback of epidemiological ecological studies, in which the association between area-level summaries of risk and exposure is used to make inference about individual risk, is the difficulty in characterizing within-area variability in exposure and confounder variables. To avoid ecological bias, samples of individual exposure/confounder data within each area are required. Unfortunately, these may be difficult or expensive to obtain, particularly if large samples are required. In this paper, we propose a new approach suitable for use with small samples. We combine a Bayesian nonparametric Dirichlet process prior with an estimating functions' approach and show that this model gives a compromise between 2 previously described methods. The method is investigated using simulated data, and a practical illustration is provided through an analysis of lung cancer mortality and residential radon exposure in counties of Minnesota. We conclude that we require good quality prior information about the exposure/confounder distributions and a large between- to within-area variability ratio for an ecological study to be feasible using only small samples of individual data.     

A signal process method for DNA segments separation in micro-channel electrophoresis

This paper presents a signal process method for DNA segments separation in micro-channel electrophoresis. It is developed and optimized by using a laser induced fluorescence (LIF) based detection system. In this detection system, signal is sampled and processed through a novel signal process module. The results show that this signal process method provides good signal-to-noise ratios and lower limit of detection (LOD).     

Simulation of biomass gasification with a hybrid neural network model

Gasification of several types of biomass has been conducted in a fluidized bed gasifier at atmospheric pressure with steam as the fluidizing medium. In order to obtain the gasification profiles for each type of biomass, an artificial neural network model has been developed to simulate this gasification processes. Model-predicted gas production rates in this biomass gasification processes were consistent with the experimental data. Therefore, the gasification profiles generated by neural networks are considered to have properly reflected the real gasification process of a biomass. Gasification profiles identified by neural network suggest that gasification behavior of arboreal types of biomass is significantly different from that of herbaceous ones.     

A neural network model for cognitive activity

A consideration of the storage of information as an energized neuronal state leads to the development of a new type of neural network model which is capable of pattern recognition, concept formation and recognition of patterns of events in time. The network consists of several layers of cells, each cell representing by connections from the lower levels some combination of features or concepts. Information travels toward higher layers by such connections during an association phase, and then reverses during a recognition phase, where higher-order concepts can redirect the flow to more appropriate elements, revising the perception of the environment. This permits a more efficient method of distinguishing closely-related patterns and also permits the formation of negative associations, which is a likely requirement for formation of "abstract" concepts.     

A neural model for conditioned avoidance learning

A mathematical model for learning of a conditioned avoidance behavior is presented. An identification of the net excitation of a neural model (Rashevsky, N., 1960.Mathematical Biophysics. Vol. II. New York: Dover Publications, Inc.) with the instantaneous probability of response is introduced and its usefulness in discussing block-trial learning performances in the conditioned avoidance situation is outlined for normal and brain-operated animals, using experimental data collected by the author. Later, the model is applied to consecutive trial learning and connection is made with the approach of H. D. Landahl (1964. “An Avoidance Learning Situation. A Neural Net Model.”Bull. Math. Biophysics,26, 83–89; and 1965, “A Neural Net Model for Escape Learning.”Bull. Math. Biophysics,27, Special Edition, 317–328) wherein lie further data with which the model can be compared.     

A neural network model for trace conditioning

We studied the dynamics of a neural network that has both recurrent excitatory and random inhibitory connections. Neurons started to become active when a relatively weak transient excitatory signal was presented and the activity was sustained due to the recurrent excitatory connections. The sustained activity stopped when a strong transient signal was presented or when neurons were disinhibited. The random inhibitory connections modulated the activity patterns of neurons so that the patterns evolved without recurrence with time. Hence, a time passage between the onsets of the two transient signals was represented by the sequence of activity patterns. We then applied this model to represent the trace eye blink conditioning, which is mediated by the hippocampus. We assumed this model as CA3 of the hippocampus and considered an output neuron corresponding to a neuron in CA1. The activity pattern of the output neuron was similar to that of CA1 neurons during trace eye blink conditioning, which was experimentally observed.     

A neural net model for masking phenomena

Some aspects of masking phenomena are considered in terms of the simplest possible model of two-factor neural elements. The effect of a number of variables can be accounted for, but the introduction of an internuncial element results in a masking function which need not be symmetric about zero delay interval. As an illustration, the results for a special case are compared with available data. In general, such a model results in a masking function which depends on the intensity, area, and duration of the stimuli, as well as on the temporal and spatial separation between them.