Elucidation of molecular kinetic schemes from macroscopic traces using system identification

Overall cellular responses to biologically-relevant stimuli are mediated by networks of simpler lower-level processes. Although information about some of these processes can now be obtained by visualizing and recording events at the molecular level, this is still possible only in especially favorable cases. Therefore the development of methods to extract the dynamics and relationships between the different lower-level (microscopic) processes from the overall (macroscopic) response remains a crucial challenge in the understanding of many aspects of physiology. Here we have devised a hybrid computational-analytical method to accomplish this task, the SYStems-based MOLecular kinetic scheme Extractor (SYSMOLE). SYSMOLE utilizes system-identification input-output analysis to obtain a transfer function between the stimulus and the overall cellular response in the Laplace-transformed domain. It then derives a Markov-chain state molecular kinetic scheme uniquely associated with the transfer function by means of a classification procedure and an analytical step that imposes general biological constraints. We first tested SYSMOLE with synthetic data and evaluated its performance in terms of its rate of convergence to the correct molecular kinetic scheme and its robustness to noise. We then examined its performance on real experimental traces by analyzing macroscopic calcium-current traces elicited by membrane depolarization. SYSMOLE derived the correct, previously known molecular kinetic scheme describing the activation and inactivation of the underlying calcium channels and correctly identified the accepted mechanism of action of nifedipine, a calcium-channel blocker clinically used in patients with cardiovascular disease. Finally, we applied SYSMOLE to study the pharmacology of a new class of glutamate antipsychotic drugs and their crosstalk mechanism through a heteromeric complex of G protein-coupled receptors. Our results indicate that our methodology can be successfully applied to accurately derive molecular kinetic schemes from experimental macroscopic traces, and we anticipate that it may be useful in the study of a wide variety of biological systems

Class-Based Feature Matching Across Unrestricted Transformations

We develop a novel method for class-based feature matching across large changes in viewing conditions. The method is based on the property that when objects share a similar part, the similarity is preserved across viewing conditions. Given a feature and a training set of object images, we first identify the subset of objects that share this feature. The transformation of the feature's appearance across viewing conditions is determined mainly by properties of the feature, rather than of the object in which it is embedded. Therefore, the transformed feature will be shared by approximately the same set of objects. Based on this consistency requirement, corresponding features can be reliably identified from a set of candidate matches. Unlike previous approaches, the proposed scheme compares feature appearances only in similar viewing conditions, rather than across different viewing conditions. As a result, the scheme is not restricted to locally planar objects or affine transformations. The approach also does not require examples of correct matches. We show that by using the proposed method, a dense set of accurate correspondences can be obtained. Experimental comparisons demonstrate that matching accuracy is significantly improved over previous schemes. Finally, we show that the scheme can be successfully used for invariant object recognition

A Cognitive Science Based Machine Learning Architecture

In an attempt to illustrate the application of cognitive science principles to hard AI problems in machine learning we propose the LIDA technology, a cognitive science based architecture capable of more human-like learning. A LIDA based software agent or cognitive robot will be capable of three fundamental, continuously active, humanlike learning mechanisms:\ud 1) perceptual learning, the learning of new objects, categories, relations, etc.,\ud 2) episodic learning of events, the what, where, and when,\ud 3) procedural learning, the learning of new actions and action sequences with which to accomplish new tasks. The paper argues for the use of modular components, each specializing in implementing individual facets of human and animal cognition, as a viable approach towards achieving general intelligence

Connectionist Inference Models

The performance of symbolic inference tasks has long been a challenge to connectionists. In this paper, we present an extended survey of this area. Existing connectionist inference systems are reviewed, with particular reference to how they perform variable binding and rule-based reasoning, and whether they involve distributed or localist representations. The benefits and disadvantages of different representations and systems are outlined, and conclusions drawn regarding the capabilities of connectionist inference systems when compared with symbolic inference systems or when used for cognitive modeling

Modelling the Developing Mind: From Structure to Change

This paper presents a theory of cognitive change. The theory assumes that the fundamental causes of cognitive change reside in the architecture of mind. Thus, the architecture of mind as specified by the theory is described first. It is assumed that the mind is a three-level universe involving (1) a processing system that constrains processing potentials, (2) a set of specialized capacity systems that guide understanding of different reality and knowledge domains, and (3) a hypecognitive system that monitors and controls the functioning of all other systems. The paper then specifies the types of change that may occur in cognitive development (changes within the levels of mind, changes in the relations between structures across levels, changes in the efficiency of a structure) and a series of general (e.g., metarepresentation) and more specific mechanisms (e.g., bridging, interweaving, and fusion) that bring the changes about. It is argued that different types of change require different mechanisms. Finally, a general model of the nature of cognitive development is offered. The relations between the theory proposed in the paper and other theories and research in cognitive development and cognitive neuroscience is discussed throughout the paper

Neural coding strategies and mechanisms of competition

A long running debate has concerned the question of whether neural representations are encoded using a distributed or a local coding scheme. In both schemes individual neurons respond to certain specific patterns of pre-synaptic activity. Hence, rather than being dichotomous, both coding schemes are based on the same representational mechanism. We argue that a population of neurons needs to be capable of learning both local and distributed representations, as appropriate to the task, and should be capable of generating both local and distributed codes in response to different stimuli. Many neural network algorithms, which are often employed as models of cognitive processes, fail to meet all these requirements. In contrast, we present a neural network architecture which enables a single algorithm to efficiently learn, and respond using, both types of coding scheme

Emotion Recognition from Acted and Spontaneous Speech

Dizertační práce se zabývá rozpoznáním emočního stavu mluvčích z řečového signálu. Práce je rozdělena do dvou hlavních častí, první část popisuju navržené metody pro rozpoznání emočního stavu z hraných databází. V rámci této části jsou představeny výsledky rozpoznání použitím dvou různých databází s různými jazyky. Hlavními přínosy této části je detailní analýza rozsáhlé škály různých příznaků získaných z řečového signálu, návrh nových klasifikačních architektur jako je například „emoční párování“ a návrh nové metody pro mapování diskrétních emočních stavů do dvou dimenzionálního prostoru. Druhá část se zabývá rozpoznáním emočních stavů z databáze spontánní řeči, která byla získána ze záznamů hovorů z reálných call center. Poznatky z analýzy a návrhu metod rozpoznání z hrané řeči byly využity pro návrh nového systému pro rozpoznání sedmi spontánních emočních stavů. Jádrem navrženého přístupu je komplexní klasifikační architektura založena na fúzi různých systémů. Práce se dále zabývá vlivem emočního stavu mluvčího na úspěšnosti rozpoznání pohlaví a návrhem systému pro automatickou detekci úspěšných hovorů v call centrech na základě analýzy parametrů dialogu mezi účastníky telefonních hovorů.Doctoral thesis deals with emotion recognition from speech signals. The thesis is divided into two main parts; the first part describes proposed approaches for emotion recognition using two different multilingual databases of acted emotional speech. The main contributions of this part are detailed analysis of a big set of acoustic features, new classification schemes for vocal emotion recognition such as “emotion coupling” and new method for mapping discrete emotions into two-dimensional space. The second part of this thesis is devoted to emotion recognition using multilingual databases of spontaneous emotional speech, which is based on telephone records obtained from real call centers. The knowledge gained from experiments with emotion recognition from acted speech was exploited to design a new approach for classifying seven emotional states. The core of the proposed approach is a complex classification architecture based on the fusion of different systems. The thesis also examines the influence of speaker’s emotional state on gender recognition performance and proposes system for automatic identification of successful phone calls in call center by means of dialogue features.

Hybrid Building/Floor Classification and Location Coordinates Regression Using A Single-Input and Multi-Output Deep Neural Network for Large-Scale Indoor Localization Based on Wi-Fi Fingerprinting

In this paper, we propose hybrid building/floor classification and floor-level two-dimensional location coordinates regression using a single-input and multi-output (SIMO) deep neural network (DNN) for large-scale indoor localization based on Wi-Fi fingerprinting. The proposed scheme exploits the different nature of the estimation of building/floor and floor-level location coordinates and uses a different estimation framework for each task with a dedicated output and hidden layers enabled by SIMO DNN architecture. We carry out preliminary evaluation of the performance of the hybrid floor classification and floor-level two-dimensional location coordinates regression using new Wi-Fi crowdsourced fingerprinting datasets provided by Tampere University of Technology (TUT), Finland, covering a single building with five floors. Experimental results demonstrate that the proposed SIMO-DNN-based hybrid classification/regression scheme outperforms existing schemes in terms of both floor detection rate and mean positioning errors.Comment: 6 pages, 4 figures, 3rd International Workshop on GPU Computing and AI (GCA'18