An adaptive stereo basis method for convolutive blind audio source separation

NOTICE: this is the author’s version of a work that was accepted for publication in Neurocomputing. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. A definitive version was subsequently published in PUBLICATION, [71, 10-12, June 2008] DOI:neucom.2007.08.02

The Escherichia coli transcriptome mostly consists of independently regulated modules

Underlying cellular responses is a transcriptional regulatory network (TRN) that modulates gene expression. A useful description of the TRN would decompose the transcriptome into targeted effects of individual transcriptional regulators. Here, we apply unsupervised machine learning to a diverse compendium of over 250 high-quality Escherichia coli RNA-seq datasets to identify 92 statistically independent signals that modulate the expression of specific gene sets. We show that 61 of these transcriptomic signals represent the effects of currently characterized transcriptional regulators. Condition-specific activation of signals is validated by exposure of E. coli to new environmental conditions. The resulting decomposition of the transcriptome provides: a mechanistic, systems-level, network-based explanation of responses to environmental and genetic perturbations; a guide to gene and regulator function discovery; and a basis for characterizing transcriptomic differences in multiple strains. Taken together, our results show that signal summation describes the composition of a model prokaryotic transcriptome

Flexible methods for blind separation of complex signals

One of the main matter in Blind Source Separation (BSS) performed with a neural network approach is the choice of the nonlinear activation function (AF). In fact if the shape of the activation function is chosen as the cumulative density function (c.d.f.) of the original source the problem is solved. For this scope in this thesis a flexible approach is introduced and the shape of the activation functions is changed during the learning process using the so-called “spline functions”. The problem is complicated in the case of separation of complex sources where there is the problem of the dichotomy between analyticity and boundedness of the complex activation functions. The problem is solved introducing the “splitting function” model as activation function. The “splitting function” is a couple of “spline function” which wind off the real and the imaginary part of the complex activation function, each of one depending from the real and imaginary variable. A more realistic model is the “generalized splitting function”, which is formed by a couple of two bi-dimensional functions (surfaces), one for the real and one for the imaginary part of the complex function, each depending by both the real and imaginary part of the complex variable. Unfortunately the linear environment is unrealistic in many practical applications. In this way there is the need of extending BSS problem in the nonlinear environment: in this case both the activation function than the nonlinear distorting function are realized by the “splitting function” made of “spline function”. The complex and instantaneous separation in linear and nonlinear environment allow us to perform a complex-valued extension of the well-known INFOMAX algorithm in several practical situations, such as convolutive mixtures, fMRI signal analysis and bandpass signal transmission. In addition advanced characteristics on the proposed approach are introduced and deeply described. First of all it is shows as splines are universal nonlinear functions for BSS problem: they are able to perform separation in anyway. Then it is analyzed as the “splitting solution” allows the algorithm to obtain a phase recovery: usually there is a phase ambiguity. Finally a Cramér-Rao lower bound for ICA is discussed. Several experimental results, tested by different objective indexes, show the effectiveness of the proposed approaches

Flexible methods for blind separation of complex signals

One of the main matter in Blind Source Separation (BSS) performed with a neural network approach is the choice of the nonlinear activation function (AF). In fact if the shape of the activation function is chosen as the cumulative density function (c.d.f.) of the original source the problem is solved. For this scope in this thesis a flexible approach is introduced and the shape of the activation functions is changed during the learning process using the so-called “spline functions”. The problem is complicated in the case of separation of complex sources where there is the problem of the dichotomy between analyticity and boundedness of the complex activation functions. The problem is solved introducing the “splitting function” model as activation function. The “splitting function” is a couple of “spline function” which wind off the real and the imaginary part of the complex activation function, each of one depending from the real and imaginary variable. A more realistic model is the “generalized splitting function”, which is formed by a couple of two bi-dimensional functions (surfaces), one for the real and one for the imaginary part of the complex function, each depending by both the real and imaginary part of the complex variable. Unfortunately the linear environment is unrealistic in many practical applications. In this way there is the need of extending BSS problem in the nonlinear environment: in this case both the activation function than the nonlinear distorting function are realized by the “splitting function” made of “spline function”. The complex and instantaneous separation in linear and nonlinear environment allow us to perform a complex-valued extension of the well-known INFOMAX algorithm in several practical situations, such as convolutive mixtures, fMRI signal analysis and bandpass signal transmission. In addition advanced characteristics on the proposed approach are introduced and deeply described. First of all it is shows as splines are universal nonlinear functions for BSS problem: they are able to perform separation in anyway. Then it is analyzed as the “splitting solution” allows the algorithm to obtain a phase recovery: usually there is a phase ambiguity. Finally a Cramér-Rao lower bound for ICA is discussed. Several experimental results, tested by different objective indexes, show the effectiveness of the proposed approaches

Fetal electrocardiogram extraction by sequential source separation in the wavelet domain

This work addresses the problem of fetal electrocardiogram extraction using blind source separation (BSS) in the wavelet domain. A new approach is proposed, which is particularly advantageous when the mixing environment is noisy and time-varying, and that is shown, analytically and in simulation, to improve the convergence rate of the natural gradient algorithm. The distribution of the wavelet coefficients of the source signals is then modeled by a generalized Gaussian probability density, whereby in the time-scale domain the problem of selecting appropriate nonlinearities when separating mixtures of both sub- and super-Gaussian signals is mitigated, as shown by experimental results

Anxiety and depression: a model for assessment and therapy in primary care

Patients who feel anxious and depressed often turn to primary care for initial professional help. However, systematic service evaluations allege poor standards of diagnosis and treatment, resulting in disappointing clinical outcomes. All the same, special educational and quality improvement initiatives have not raised standards significantly. Why this should be so and possible remedies are suggested by this article, on the basis that the empirical evidence base for criticising primary care standards is weaker than commonly acknowledged. Systematic clinical trials are often premised by assumptions that are not relevant to primary care, they tend to select subject populations unrepresentative of those typically seen by general practitioners and results are often compromised by a series of methodological flaws. This article proposes an alternative conceptualisation of anxiety and depression apposite to primary care assessment and therapy. It draws on an emergent evidence base within psychobiology that recognises that these reactions have two adaptive functions. Firstly, they are responses evoked by actual personal adversity, secondly they have the function of prompting communication to self and to others of the need for practical remedial action to be taken independently, or with assistance, to improve the quality of the recovery environment. A table summarises the phased stages of anxiety and depression and lists their adaptive and communicative functions along with some phase-appropriate primary care interventions. This new model of assessment and therapy is offered to stimulate discussion and inspire future research that is appropriate for primary care service improvement

Hierarchical coexistence of universality and diversity controls robustness and multi-functionality in intermediate filament protein networks

Proteins constitute the elementary building blocks of a vast variety of biological materials such as cellular protein networks, spider silk or bone, where they create extremely robust, multi-functional materials by self-organization of structures over many length- and time scales, from nano to macro. Some of the structural features are commonly found in a many different tissues, that is, they are highly conserved. Examples of such universal building blocks include alpha-helices, beta-sheets or tropocollagen molecules. In contrast, other features are highly specific to tissue types, such as particular filament assemblies, beta-sheet nanocrystals in spider silk or tendon fascicles. These examples illustrate that the coexistence of universality and diversity – in the following referred to as the universality-diversity paradigm (UDP) – is an overarching feature in protein materials. This paradigm is a paradox: How can a structure be universal and diverse at the same time? In protein materials, the coexistence of universality and diversity is enabled by utilizing hierarchies, which serve as an additional dimension beyond the 3D or 4D physical space. This may be crucial to understand how their structure and properties are linked, and how these materials are capable of combining seemingly disparate properties such as strength and robustness. Here we illustrate how the UDP enables to unify universal building blocks and highly diversified patterns through formation of hierarchical structures that lead to multi-functional, robust yet highly adapted structures. We illustrate these concepts in an analysis of three types of intermediate filament proteins, including vimentin, lamin and keratin

From source to target and back: symmetric bi-directional adaptive GAN

The effectiveness of generative adversarial approaches in producing images according to a specific style or visual domain has recently opened new directions to solve the unsupervised domain adaptation problem. It has been shown that source labeled images can be modified to mimic target samples making it possible to train directly a classifier in the target domain, despite the original lack of annotated data. Inverse mappings from the target to the source domain have also been evaluated but only passing through adapted feature spaces, thus without new image generation. In this paper we propose to better exploit the potential of generative adversarial networks for adaptation by introducing a novel symmetric mapping among domains. We jointly optimize bi-directional image transformations combining them with target self-labeling. Moreover we define a new class consistency loss that aligns the generators in the two directions imposing to conserve the class identity of an image passing through both domain mappings. A detailed qualitative and quantitative analysis of the reconstructed images confirm the power of our approach. By integrating the two domain specific classifiers obtained with our bi-directional network we exceed previous state-of-the-art unsupervised adaptation results on four different benchmark datasets