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1.
Entropy (Basel) ; 25(1)2022 Dec 24.
Artículo en Inglés | MEDLINE | ID: mdl-36673174

RESUMEN

Domain adaptation is a popular paradigm in modern machine learning which aims at tackling the problem of divergence (or shift) between the labeled training and validation datasets (source domain) and a potentially large unlabeled dataset (target domain). The task is to embed both datasets into a common space in which the source dataset is informative for training while the divergence between source and target is minimized. The most popular domain adaptation solutions are based on training neural networks that combine classification and adversarial learning modules, frequently making them both data-hungry and difficult to train. We present a method called Domain Adaptation Principal Component Analysis (DAPCA) that identifies a linear reduced data representation useful for solving the domain adaptation task. DAPCA algorithm introduces positive and negative weights between pairs of data points, and generalizes the supervised extension of principal component analysis. DAPCA is an iterative algorithm that solves a simple quadratic optimization problem at each iteration. The convergence of the algorithm is guaranteed, and the number of iterations is small in practice. We validate the suggested algorithm on previously proposed benchmarks for solving the domain adaptation task. We also show the benefit of using DAPCA in analyzing single-cell omics datasets in biomedical applications. Overall, DAPCA can serve as a practical preprocessing step in many machine learning applications leading to reduced dataset representations, taking into account possible divergence between source and target domains.

2.
Sensors (Basel) ; 21(22)2021 Nov 18.
Artículo en Inglés | MEDLINE | ID: mdl-34833738

RESUMEN

Data on artificial night-time light (NTL), emitted from the areas, and captured by satellites, are available at a global scale in panchromatic format. In the meantime, data on spectral properties of NTL give more information for further analysis. Such data, however, are available locally or on a commercial basis only. In our recent work, we examined several machine learning techniques, such as linear regression, kernel regression, random forest, and elastic map models, to convert the panchromatic NTL images into colored ones. We compared red, green, and blue light levels for eight geographical areas all over the world with panchromatic light intensities and characteristics of built-up extent from spatially corresponding pixels and their nearest neighbors. In the meantime, information from more distant neighboring pixels might improve the predictive power of models. In the present study, we explore this neighborhood effect using convolutional neural networks (CNN). The main outcome of our analysis is that the neighborhood effect goes in line with the geographical extent of metropolitan areas under analysis: For smaller areas, optimal input image size is smaller than for bigger ones. At that, for relatively large cities, the optimal input image size tends to differ for different colors, being on average higher for red and lower for blue lights. Compared to other machine learning techniques, CNN models emerged comparable in terms of Pearson's correlation but showed performed better in terms of WMSE, especially for testing datasets.


Asunto(s)
Aprendizaje Automático , Redes Neurales de la Computación , Ciudades , Luz
3.
Entropy (Basel) ; 23(10)2021 Oct 19.
Artículo en Inglés | MEDLINE | ID: mdl-34682092

RESUMEN

Dealing with uncertainty in applications of machine learning to real-life data critically depends on the knowledge of intrinsic dimensionality (ID). A number of methods have been suggested for the purpose of estimating ID, but no standard package to easily apply them one by one or all at once has been implemented in Python. This technical note introduces scikit-dimension, an open-source Python package for intrinsic dimension estimation. The scikit-dimension package provides a uniform implementation of most of the known ID estimators based on the scikit-learn application programming interface to evaluate the global and local intrinsic dimension, as well as generators of synthetic toy and benchmark datasets widespread in the literature. The package is developed with tools assessing the code quality, coverage, unit testing and continuous integration. We briefly describe the package and demonstrate its use in a large-scale (more than 500 datasets) benchmarking of methods for ID estimation for real-life and synthetic data.

4.
Entropy (Basel) ; 23(8)2021 Aug 22.
Artículo en Inglés | MEDLINE | ID: mdl-34441230

RESUMEN

This work is driven by a practical question: corrections of Artificial Intelligence (AI) errors. These corrections should be quick and non-iterative. To solve this problem without modification of a legacy AI system, we propose special 'external' devices, correctors. Elementary correctors consist of two parts, a classifier that separates the situations with high risk of error from the situations in which the legacy AI system works well and a new decision that should be recommended for situations with potential errors. Input signals for the correctors can be the inputs of the legacy AI system, its internal signals, and outputs. If the intrinsic dimensionality of data is high enough then the classifiers for correction of small number of errors can be very simple. According to the blessing of dimensionality effects, even simple and robust Fisher's discriminants can be used for one-shot learning of AI correctors. Stochastic separation theorems provide the mathematical basis for this one-short learning. However, as the number of correctors needed grows, the cluster structure of data becomes important and a new family of stochastic separation theorems is required. We refuse the classical hypothesis of the regularity of the data distribution and assume that the data can have a rich fine-grained structure with many clusters and corresponding peaks in the probability density. New stochastic separation theorems for data with fine-grained structure are formulated and proved. On the basis of these theorems, the multi-correctors for granular data are proposed. The advantages of the multi-corrector technology were demonstrated by examples of correcting errors and learning new classes of objects by a deep convolutional neural network on the CIFAR-10 dataset. The key problems of the non-classical high-dimensional data analysis are reviewed together with the basic preprocessing steps including the correlation transformation, supervised Principal Component Analysis (PCA), semi-supervised PCA, transfer component analysis, and new domain adaptation PCA.

5.
J Allergy Clin Immunol ; 144(1): 83-93, 2019 07.
Artículo en Inglés | MEDLINE | ID: mdl-30682455

RESUMEN

BACKGROUND: Asthma is a disease characterized by ventilation heterogeneity (VH). A number of studies have demonstrated that VH markers derived by using impulse oscillometry (IOS) or multiple-breath washout (MBW) are associated with key asthmatic patient-related outcome measures and airways hyperresponsiveness. However, the topographical mechanisms of VH in the lung remain poorly understood. OBJECTIVES: We hypothesized that specific regionalization of topographical small-airway disease would best account for IOS- and MBW-measured indices in patients. METHODS: We evaluated the results of paired expiratory/inspiratory computed tomography in a cohort of asthmatic (n = 41) and healthy (n = 11) volunteers to understand the determinants of clinical VH indices commonly reported by using IOS and MBW. Parametric response mapping (PRM) was used to calculate the functional small-airways disease marker PRMfSAD and Hounsfield unit (HU)-based density changes from total lung capacity to functional residual capacity (ΔHU); gradients of ΔHU in gravitationally perpendicular (parallel) inferior-superior (anterior-posterior) axes were quantified. RESULTS: The ΔHU gradient in the inferior-superior axis provided the highest level of discrimination of both acinar VH (measured by using phase 3 slope analysis of multiple-breath washout data) and resistance at 5 Hz minus resistance at 20 Hz measured by using impulse oscillometry (R5-R20) values. Patients with a high inferior-superior ΔHU gradient demonstrated evidence of reduced specific ventilation in the lower lobes of the lungs and high levels of PRMfSAD. A computational small-airway tree model confirmed that constriction of gravitationally dependent, lower-zone, small-airway branches would promote the largest increases in R5-R20 values. Ventilation gradients correlated with asthma control and quality of life but not with exacerbation frequency. CONCLUSIONS: Lower lobe-predominant small-airways disease is a major driver of clinically measured VH in adults with asthma.


Asunto(s)
Asma/diagnóstico por imagen , Pulmón/diagnóstico por imagen , Adulto , Anciano , Asma/tratamiento farmacológico , Asma/fisiopatología , Broncodilatadores/uso terapéutico , Volumen Espiratorio Forzado , Humanos , Pulmón/fisiopatología , Masculino , Persona de Mediana Edad , Tomografía Computarizada por Rayos X , Capacidad Vital
6.
Entropy (Basel) ; 22(1)2020 Jan 09.
Artículo en Inglés | MEDLINE | ID: mdl-33285855

RESUMEN

High-dimensional data and high-dimensional representations of reality are inherent features of modern Artificial Intelligence systems and applications of machine learning. The well-known phenomenon of the "curse of dimensionality" states: many problems become exponentially difficult in high dimensions. Recently, the other side of the coin, the "blessing of dimensionality", has attracted much attention. It turns out that generic high-dimensional datasets exhibit fairly simple geometric properties. Thus, there is a fundamental tradeoff between complexity and simplicity in high dimensional spaces. Here we present a brief explanatory review of recent ideas, results and hypotheses about the blessing of dimensionality and related simplifying effects relevant to machine learning and neuroscience.

7.
Bull Math Biol ; 81(11): 4856-4888, 2019 11.
Artículo en Inglés | MEDLINE | ID: mdl-29556797

RESUMEN

Codifying memories is one of the fundamental problems of modern Neuroscience. The functional mechanisms behind this phenomenon remain largely unknown. Experimental evidence suggests that some of the memory functions are performed by stratified brain structures such as the hippocampus. In this particular case, single neurons in the CA1 region receive a highly multidimensional input from the CA3 area, which is a hub for information processing. We thus assess the implication of the abundance of neuronal signalling routes converging onto single cells on the information processing. We show that single neurons can selectively detect and learn arbitrary information items, given that they operate in high dimensions. The argument is based on stochastic separation theorems and the concentration of measure phenomena. We demonstrate that a simple enough functional neuronal model is capable of explaining: (i) the extreme selectivity of single neurons to the information content, (ii) simultaneous separation of several uncorrelated stimuli or informational items from a large set, and (iii) dynamic learning of new items by associating them with already "known" ones. These results constitute a basis for organization of complex memories in ensembles of single neurons. Moreover, they show that no a priori assumptions on the structural organization of neuronal ensembles are necessary for explaining basic concepts of static and dynamic memories.


Asunto(s)
Encéfalo/citología , Encéfalo/fisiología , Aprendizaje/fisiología , Memoria/fisiología , Modelos Neurológicos , Neuronas/fisiología , Animales , Aprendizaje por Asociación/fisiología , Región CA1 Hipocampal/citología , Región CA1 Hipocampal/fisiología , Región CA3 Hipocampal/citología , Región CA3 Hipocampal/fisiología , Simulación por Computador , Humanos , Aprendizaje Automático , Conceptos Matemáticos , Redes Neurales de la Computación , Plasticidad Neuronal/fisiología , Estimulación Luminosa , Células Piramidales/citología , Células Piramidales/fisiología , Procesos Estocásticos
9.
J Theor Biol ; 405: 127-39, 2016 09 21.
Artículo en Inglés | MEDLINE | ID: mdl-26801872

RESUMEN

In 1938, Selye proposed the notion of adaptation energy and published 'Experimental evidence supporting the conception of adaptation energy.' Adaptation of an animal to different factors appears as the spending of one resource. Adaptation energy is a hypothetical extensive quantity spent for adaptation. This term causes much debate when one takes it literally, as a physical quantity, i.e. a sort of energy. The controversial points of view impede the systematic use of the notion of adaptation energy despite experimental evidence. Nevertheless, the response to many harmful factors often has general non-specific form and we suggest that the mechanisms of physiological adaptation admit a very general and nonspecific description. We aim to demonstrate that Selye׳s adaptation energy is the cornerstone of the top-down approach to modelling of non-specific adaptation processes. We analyze Selye׳s axioms of adaptation energy together with Goldstone׳s modifications and propose a series of models for interpretation of these axioms. Adaptation energy is considered as an internal coordinate on the 'dominant path' in the model of adaptation. The phenomena of 'oscillating death' and 'oscillating remission' are predicted on the base of the dynamical models of adaptation. Natural selection plays a key role in the evolution of mechanisms of physiological adaptation. We use the fitness optimization approach to study of the distribution of resources for neutralization of harmful factors, during adaptation to a multifactor environment, and analyze the optimal strategies for different systems of factors.


Asunto(s)
Adaptación Fisiológica , Evolución Biológica , Estrés Fisiológico , Animales , Aptitud Genética , Genotipo , Modelos Biológicos
10.
RNA ; 18(9): 1635-55, 2012 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-22850425

RESUMEN

MicroRNAs (miRNAs) are key regulators of all important biological processes, including development, differentiation, and cancer. Although remarkable progress has been made in deciphering the mechanisms used by miRNAs to regulate translation, many contradictory findings have been published that stimulate active debate in this field. Here we contribute to this discussion in three ways. First, based on a comprehensive analysis of the existing literature, we hypothesize a model in which all proposed mechanisms of microRNA action coexist, and where the apparent mechanism that is detected in a given experiment is determined by the relative values of the intrinsic characteristics of the target mRNAs and associated biological processes. Among several coexisting miRNA mechanisms, the one that will effectively be measurable is that which acts on or changes the sensitive parameters of the translation process. Second, we have created a mathematical model that combines nine known mechanisms of miRNA action and estimated the model parameters from the literature. Third, based on the mathematical modeling, we have developed a computational tool for discriminating among different possible individual mechanisms of miRNA action based on translation kinetics data that can be experimentally measured (kinetic signatures). To confirm the discriminatory power of these kinetic signatures and to test our hypothesis, we have performed several computational experiments with the model in which we simulated the coexistence of several miRNA action mechanisms in the context of variable parameter values of the translation.


Asunto(s)
MicroARNs/metabolismo , Modelos Biológicos , Cinética , Biosíntesis de Proteínas/fisiología
11.
Adv Exp Med Biol ; 774: 189-224, 2013.
Artículo en Inglés | MEDLINE | ID: mdl-23377975

RESUMEN

MicroRNAs can affect the protein translation using nine mechanistically different mechanisms, including repression of initiation and degradation of the transcript. There is a hot debate in the current literature about which mechanism and in which situations has a dominant role in living cells. The worst, same experimental systems dealing with the same pairs of mRNA and miRNA can provide ambiguous evidences about which is the actual mechanism of translation repression observed in the experiment. We start with reviewing the current knowledge of various mechanisms of miRNA action and suggest that mathematical modeling can help resolving some of the controversial interpretations. We describe three simple mathematical models of miRNA translation that can be used as tools in interpreting the experimental data on the dynamics of protein synthesis. The most complex model developed by us includes all known mechanisms of miRNA action. It allowed us to study possible dynamical patterns corresponding to different miRNA-mediated mechanisms of translation repression and to suggest concrete recipes on determining the dominant mechanism of miRNA action in the form of kinetic signatures. Using computational experiments and systematizing existing evidences from the literature, we justify a hypothesis about co-existence of distinct miRNA-mediated mechanisms of translation repression. The actually observed mechanism will be that acting on or changing the sensitive parameters of the translation process. The limiting place can vary from one experimental setting to another. This model explains the majority of existing controversies reported.


Asunto(s)
Regulación de la Expresión Génica , MicroARNs/metabolismo , Modelos Biológicos , Biosíntesis de Proteínas/genética , Animales , Humanos , Cinética , MicroARNs/genética , ARN Mensajero/genética , ARN Mensajero/metabolismo
12.
Artículo en Inglés | MEDLINE | ID: mdl-38048242

RESUMEN

Mammalian brains operate in very special surroundings: to survive they have to react quickly and effectively to the pool of stimuli patterns previously recognized as danger. Many learning tasks often encountered by living organisms involve a specific set-up centered around a relatively small set of patterns presented in a particular environment. For example, at a party, people recognize friends immediately, without deep analysis, just by seeing a fragment of their clothes. This set-up with reduced "ontology" is referred to as a "situation." Situations are usually local in space and time. In this work, we propose that neuron-astrocyte networks provide a network topology that is effectively adapted to accommodate situation-based memory. In order to illustrate this, we numerically simulate and analyze a well-established model of a neuron-astrocyte network, which is subjected to stimuli conforming to the situation-driven environment. Three pools of stimuli patterns are considered: external patterns, patterns from the situation associative pool regularly presented to the network and learned by the network, and patterns already learned and remembered by astrocytes. Patterns from the external world are added to and removed from the associative pool. Then, we show that astrocytes are structurally necessary for an effective function in such a learning and testing set-up. To demonstrate this we present a novel neuromorphic computational model for short-term memory implemented by a two-net spiking neural-astrocytic network. Our results show that such a system tested on synthesized data with selective astrocyte-induced modulation of neuronal activity provides an enhancement of retrieval quality in comparison to standard spiking neural networks trained via Hebbian plasticity only. We argue that the proposed set-up may offer a new way to analyze, model, and understand neuromorphic artificial intelligence systems.

13.
Bull Math Biol ; 73(9): 2013-44, 2011 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-21088995

RESUMEN

The "Law of the Minimum" states that growth is controlled by the scarcest resource (limiting factor). This concept was originally applied to plant or crop growth (Justus von Liebig, 1840, Salisbury, Plant physiology, 4th edn., Wadsworth, Belmont, 1992) and quantitatively supported by many experiments. Some generalizations based on more complicated "dose-response" curves were proposed. Violations of this law in natural and experimental ecosystems were also reported. We study models of adaptation in ensembles of similar organisms under load of environmental factors and prove that violation of Liebig's law follows from adaptation effects. If the fitness of an organism in a fixed environment satisfies the Law of the Minimum then adaptation equalizes the pressure of essential factors and, therefore, acts against the Liebig's law. This is the the Law of the Minimum paradox: if for a randomly chosen pair "organism-environment" the Law of the Minimum typically holds, then in a well-adapted system, we have to expect violations of this law.For the opposite interaction of factors (a synergistic system of factors which amplify each other), adaptation leads from factor equivalence to limitations by a smaller number of factors.For analysis of adaptation, we develop a system of models based on Selye's idea of the universal adaptation resource (adaptation energy). These models predict that under the load of an environmental factor a population separates into two groups (phases): a less correlated, well adapted group and a highly correlated group with a larger variance of attributes, which experiences problems with adaptation. Some empirical data are presented and evidences of interdisciplinary applications to econometrics are discussed.


Asunto(s)
Adaptación Fisiológica , Ecosistema , Modelos Biológicos , Dinámica Poblacional
14.
Neural Netw ; 138: 33-56, 2021 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-33621897

RESUMEN

Phenomenon of stochastic separability was revealed and used in machine learning to correct errors of Artificial Intelligence (AI) systems and analyze AI instabilities. In high-dimensional datasets under broad assumptions each point can be separated from the rest of the set by simple and robust Fisher's discriminant (is Fisher separable). Errors or clusters of errors can be separated from the rest of the data. The ability to correct an AI system also opens up the possibility of an attack on it, and the high dimensionality induces vulnerabilities caused by the same stochastic separability that holds the keys to understanding the fundamentals of robustness and adaptivity in high-dimensional data-driven AI. To manage errors and analyze vulnerabilities, the stochastic separation theorems should evaluate the probability that the dataset will be Fisher separable in given dimensionality and for a given class of distributions. Explicit and optimal estimates of these separation probabilities are required, and this problem is solved in the present work. The general stochastic separation theorems with optimal probability estimates are obtained for important classes of distributions: log-concave distribution, their convex combinations and product distributions. The standard i.i.d. assumption was significantly relaxed. These theorems and estimates can be used both for correction of high-dimensional data driven AI systems and for analysis of their vulnerabilities. The third area of application is the emergence of memories in ensembles of neurons, the phenomena of grandmother's cells and sparse coding in the brain, and explanation of unexpected effectiveness of small neural ensembles in high-dimensional brain.


Asunto(s)
Aprendizaje Automático , Procesos Estocásticos
15.
Sci Rep ; 11(1): 22497, 2021 11 18.
Artículo en Inglés | MEDLINE | ID: mdl-34795311

RESUMEN

The dynamics of epidemics depend on how people's behavior changes during an outbreak. At the beginning of the epidemic, people do not know about the virus, then, after the outbreak of epidemics and alarm, they begin to comply with the restrictions and the spreading of epidemics may decline. Over time, some people get tired/frustrated by the restrictions and stop following them (exhaustion), especially if the number of new cases drops down. After resting for a while, they can follow the restrictions again. But during this pause the second wave can come and become even stronger then the first one. Studies based on SIR models do not predict the observed quick exit from the first wave of epidemics. Social dynamics should be considered. The appearance of the second wave also depends on social factors. Many generalizations of the SIR model have been developed that take into account the weakening of immunity over time, the evolution of the virus, vaccination and other medical and biological details. However, these more sophisticated models do not explain the apparent differences in outbreak profiles between countries with different intrinsic socio-cultural features. In our work, a system of models of the COVID-19 pandemic is proposed, combining the dynamics of social stress with classical epidemic models. Social stress is described by the tools of sociophysics. The combination of a dynamic SIR-type model with the classical triad of stages of the general adaptation syndrome, alarm-resistance-exhaustion, makes it possible to describe with high accuracy the available statistical data for 13 countries. The sets of kinetic constants corresponding to optimal fit of model to data were found. These constants characterize the ability of society to mobilize efforts against epidemics and maintain this concentration over time and can further help in the development of management strategies specific to a particular society.


Asunto(s)
COVID-19 , Modelos Biológicos , Pandemias , SARS-CoV-2 , COVID-19/epidemiología , COVID-19/prevención & control , COVID-19/transmisión , Humanos
16.
Front Mol Biosci ; 8: 793912, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-35178429

RESUMEN

Cell cycle is a biological process underlying the existence and propagation of life in time and space. It has been an object for mathematical modeling for long, with several alternative mechanistic modeling principles suggested, describing in more or less details the known molecular mechanisms. Recently, cell cycle has been investigated at single cell level in snapshots of unsynchronized cell populations, exploiting the new methods for transcriptomic and proteomic molecular profiling. This raises a need for simplified semi-phenomenological cell cycle models, in order to formalize the processes underlying the cell cycle, at a higher abstracted level. Here we suggest a modeling framework, recapitulating the most important properties of the cell cycle as a limit trajectory of a dynamical process characterized by several internal states with switches between them. In the simplest form, this leads to a limit cycle trajectory, composed by linear segments in logarithmic coordinates describing some extensive (depending on system size) cell properties. We prove a theorem connecting the effective embedding dimensionality of the cell cycle trajectory with the number of its linear segments. We also develop a simplified kinetic model with piecewise-constant kinetic rates describing the dynamics of lumps of genes involved in S-phase and G2/M phases. We show how the developed cell cycle models can be applied to analyze the available single cell datasets and simulate certain properties of the observed cell cycle trajectories. Based on our model, we can predict with good accuracy the cell line doubling time from the length of cell cycle trajectory.

17.
Front Cell Neurosci ; 15: 631485, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-33867939

RESUMEN

We propose a novel biologically plausible computational model of working memory (WM) implemented by a spiking neuron network (SNN) interacting with a network of astrocytes. The SNN is modeled by synaptically coupled Izhikevich neurons with a non-specific architecture connection topology. Astrocytes generating calcium signals are connected by local gap junction diffusive couplings and interact with neurons via chemicals diffused in the extracellular space. Calcium elevations occur in response to the increased concentration of the neurotransmitter released by spiking neurons when a group of them fire coherently. In turn, gliotransmitters are released by activated astrocytes modulating the strength of the synaptic connections in the corresponding neuronal group. Input information is encoded as two-dimensional patterns of short applied current pulses stimulating neurons. The output is taken from frequencies of transient discharges of corresponding neurons. We show how a set of information patterns with quite significant overlapping areas can be uploaded into the neuron-astrocyte network and stored for several seconds. Information retrieval is organized by the application of a cue pattern representing one from the memory set distorted by noise. We found that successful retrieval with the level of the correlation between the recalled pattern and ideal pattern exceeding 90% is possible for the multi-item WM task. Having analyzed the dynamical mechanism of WM formation, we discovered that astrocytes operating at a time scale of a dozen of seconds can successfully store traces of neuronal activations corresponding to information patterns. In the retrieval stage, the astrocytic network selectively modulates synaptic connections in the SNN leading to successful recall. Information and dynamical characteristics of the proposed WM model agrees with classical concepts and other WM models.

18.
Gigascience ; 9(11)2020 11 25.
Artículo en Inglés | MEDLINE | ID: mdl-33241287

RESUMEN

BACKGROUND: Large observational clinical datasets are becoming increasingly available for mining associations between various disease traits and administered therapy. These datasets can be considered as representations of the landscape of all possible disease conditions, in which a concrete disease state develops through stereotypical routes, characterized by "points of no return" and "final states" (such as lethal or recovery states). Extracting this information directly from the data remains challenging, especially in the case of synchronic (with a short-term follow-up) observations. RESULTS: Here we suggest a semi-supervised methodology for the analysis of large clinical datasets, characterized by mixed data types and missing values, through modeling the geometrical data structure as a bouquet of bifurcating clinical trajectories. The methodology is based on application of elastic principal graphs, which can address simultaneously the tasks of dimensionality reduction, data visualization, clustering, feature selection, and quantifying the geodesic distances (pseudo-time) in partially ordered sequences of observations. The methodology allows a patient to be positioned on a particular clinical trajectory (pathological scenario) and the degree of progression along it to be characterized with a qualitative estimate of the uncertainty of the prognosis. We developed a tool ClinTrajan for clinical trajectory analysis implemented in the Python programming language. We test the methodology in 2 large publicly available datasets: myocardial infarction complications and readmission of diabetic patients data. CONCLUSIONS: Our pseudo-time quantification-based approach makes it possible to apply the methods developed for dynamical disease phenotyping and illness trajectory analysis (diachronic data analysis) to synchronic observational data.


Asunto(s)
Diabetes Mellitus , Infarto del Miocardio , Análisis por Conglomerados , Humanos
19.
Math Biosci Eng ; 16(6): 6602-6622, 2019 07 17.
Artículo en Inglés | MEDLINE | ID: mdl-31698578

RESUMEN

Protein synthesis is one of the most fundamental biological processes. Despite existence of multiple mathematical models of translation, surprisingly, there is no basic and simple chemical kinetic model of this process, derived directly from the detailed kinetic scheme. One of the reasons for this is that the translation process is characterized by indefinite number of states, because of the structure of the polysome. We bypass this difficulty by applying lumping of multiple states of translated mRNA into few dynamical variables and by introducing a variable describing the pool of translating ribosomes. The simplest model can be solved analytically. The simplest model can be extended, if necessary, to take into account various phenomena such as the limited amount of ribosomal units or regulation of translation by microRNA. The introduced model is more suitable to describe the protein synthesis in eukaryotes but it can be extended to prokaryotes. The model can be used as a building block for more complex models of cellular processes. We demonstrate the utility of the model in two examples. First, we determine the critical parameters of the synthesis of a single protein for the case when the ribosomal units are abundant. Second, we demonstrate intrinsic bi-stability in the dynamics of the ribosomal protein turnover and predict that a minimal number of ribosomes should pre-exists in a living cell to sustain its protein synthesis machinery, even in the absence of proliferation.


Asunto(s)
Modelos Biológicos , Biosíntesis de Proteínas , Proliferación Celular , Humanos , Cinética , MicroARNs/metabolismo , Polirribosomas/metabolismo , ARN Mensajero/metabolismo , Proteínas Ribosómicas/metabolismo , Ribosomas/metabolismo , Levaduras/metabolismo
20.
Phys Life Rev ; 29: 55-88, 2019 07.
Artículo en Inglés | MEDLINE | ID: mdl-30366739

RESUMEN

Complexity is an indisputable, well-known, and broadly accepted feature of the brain. Despite the apparently obvious and widely-spread consensus on the brain complexity, sprouts of the single neuron revolution emerged in neuroscience in the 1970s. They brought many unexpected discoveries, including grandmother or concept cells and sparse coding of information in the brain. In machine learning for a long time, the famous curse of dimensionality seemed to be an unsolvable problem. Nevertheless, the idea of the blessing of dimensionality becomes gradually more and more popular. Ensembles of non-interacting or weakly interacting simple units prove to be an effective tool for solving essentially multidimensional and apparently incomprehensible problems. This approach is especially useful for one-shot (non-iterative) correction of errors in large legacy artificial intelligence systems and when the complete re-training is impossible or too expensive. These simplicity revolutions in the era of complexity have deep fundamental reasons grounded in geometry of multidimensional data spaces. To explore and understand these reasons we revisit the background ideas of statistical physics. In the course of the 20th century they were developed into the concentration of measure theory. The Gibbs equivalence of ensembles with further generalizations shows that the data in high-dimensional spaces are concentrated near shells of smaller dimension. New stochastic separation theorems reveal the fine structure of the data clouds. We review and analyse biological, physical, and mathematical problems at the core of the fundamental question: how can high-dimensional brain organise reliable and fast learning in high-dimensional world of data by simple tools? To meet this challenge, we outline and setup a framework based on statistical physics of data. Two critical applications are reviewed to exemplify the approach: one-shot correction of errors in intellectual systems and emergence of static and associative memories in ensembles of single neurons. Error correctors should be simple; not damage the existing skills of the system; allow fast non-iterative learning and correction of new mistakes without destroying the previous fixes. All these demands can be satisfied by new tools based on the concentration of measure phenomena and stochastic separation theory. We show how a simple enough functional neuronal model is capable of explaining: i) the extreme selectivity of single neurons to the information content of high-dimensional data, ii) simultaneous separation of several uncorrelated informational items from a large set of stimuli, and iii) dynamic learning of new items by associating them with already "known" ones. These results constitute a basis for organisation of complex memories in ensembles of single neurons.


Asunto(s)
Encéfalo/fisiología , Modelos Biológicos , Neuronas/fisiología , Algoritmos , Inteligencia Artificial , Simulación por Computador , Humanos , Aprendizaje Automático , Memoria
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