arXiv subjects

Andrei Zinovyev

Publications and source records attributed to Andrei Zinovyev.

At least 19 recordsLinked to original sources

arXiv2024

Messenger size optimality in cellular communications

Living cells presumably employ optimized information transfer methods, enabling efficient communication even in noisy environments. As expected, the efficiency of chemical communications between cells depends on the properties of the molecular messenger. Evidence suggests that proteins from narrow ranges of molecular masses have been naturally selected to mediate cellular communications, yet the underlying communication design principles are not understood. Using a simple physical model that considers the cost of chemical synthesis, diffusion, molecular binding, and degradation, we show that optimal mass values exist that ensure efficient communication of various types of signals. Our findings provide insights into the design principles of biological communications and can be used to engineer chemically communicating biomimetic systems.

physics.bio-ph↗

arXiv2024

Multilayer network approaches to omics data integration in Digital Twins for cancer research

This review examines current and potential applications of DTs in healthcare, focusing on the integration of multi-omics data using multilayer network approaches in cancer research. We discuss methodologies, tools and platforms commonly used for this integration, while highlighting case studies, challenges, and research gaps. Finally, we advocate the need for incorporating diverse data types to produce more effective DTs for personalization of cancer treatments and in silico clinical trials.

q-bio.MN↗

arXiv2024

Exploring the impact of social stress on the adaptive dynamics of COVID-19: Typing the behavior of naïve populations faced with epidemics

In the context of natural disasters, human responses inevitably intertwine with natural factors. The COVID-19 pandemic, as a significant stress factor, has brought to light profound variations among different countries in terms of their adaptive dynamics in addressing the spread of infection outbreaks across different regions. This emphasizes the crucial role of cultural characteristics in natural disaster analysis. The theoretical understanding of large-scale epidemics primarily relies on mean-field kinetic models. However, conventional SIR-like models failed to fully explain the observed phenomena at the onset of the COVID-19 outbreak. These phenomena included the unexpected cessation of exponential growth, the reaching of plateaus, and the occurrence of multi-wave dynamics. In situations where an outbreak of a highly virulent and unfamiliar infection arises, it becomes crucial to respond swiftly at a non-medical level to mitigate the negative socio-economic impact. Here we present a theoretical examination of the first wave of the epidemic based on a simple SIRSS model (SIR with Social Stress). We conduct an analysis of the socio-cultural features of naïve population behaviors across various countries worldwide. The unique characteristics of each country/territory are encapsulated in only a few constants within our model, derived from the fitted COVID-19 statistics. These constants also reflect the societal response dynamics to the external stress factor, underscoring the importance of studying the mutual behavior of humanity and natural factors during global social disasters. Based on these distinctive characteristics of specific regions, local authorities can optimize their strategies to effectively combat epidemics until vaccines are developed.

physics.soc-ph↗

arXiv2022

Domain Adaptation Principal Component Analysis: base linear method for learning with out-of-distribution data

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 red 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 the 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.

cs.LG↗

arXiv2022

Computational challenges of cell cycle analysis using single cell transcriptomics

The cell cycle is one of the most fundamental biological processes important for understanding normal physiology and various pathologies such as cancer. Single cell RNA sequencing technologies give an opportunity to analyse the cell cycle transcriptome dynamics in an unprecedented range of conditions (cell types and perturbations), with thousands of publicly available datasets. Here we review the main computational tasks in such analysis: 1) identification of cell cycle phases, 2) pseudotime inference, 3) identification and profiling of cell cycle-related genes, 4) removing cell cycle effect, 5) identification and analysis of the G0 (quiescent) cells. We review seventeen software packages that are available today for the cell cycle analysis using scRNA-seq data. Despite huge progress achieved, none of the packages can produce complete and reliable results with respect to all aforementioned tasks. One of the major difficulties for existing packages is distinguishing between two patterns of cell cycle transcriptomic dynamics: normal and characteristic for embryonic stem cells (ESC), with the latter one shared by many cancer cell lines. Moreover, some cell lines are characterized by a mixture of two subpopulations, one following the standard and one ESC-like cell cycle, which makes the analysis even more challenging. In conclusion, we discuss the difficulties of the analysis of cell cycle-related single cell transcriptome and provide certain guidelines for the use of the existing methods.

q-bio.QM↗

arXiv2022

Quasi-orthogonality and intrinsic dimensions as measures of learning and generalisation

Finding best architectures of learning machines, such as deep neural networks, is a well-known technical and theoretical challenge. Recent work by Mellor et al (2021) showed that there may exist correlations between the accuracies of trained networks and the values of some easily computable measures defined on randomly initialised networks which may enable to search tens of thousands of neural architectures without training. Mellor et al used the Hamming distance evaluated over all ReLU neurons as such a measure. Motivated by these findings, in our work, we ask the question of the existence of other and perhaps more principled measures which could be used as determinants of success of a given neural architecture. In particular, we examine, if the dimensionality and quasi-orthogonality of neural networks' feature space could be correlated with the network's performance after training. We showed, using the setup as in Mellor et al, that dimensionality and quasi-orthogonality may jointly serve as network's performance discriminants. In addition to offering new opportunities to accelerate neural architecture search, our findings suggest important relationships between the networks' final performance and properties of their randomly initialised feature spaces: data dimension and quasi-orthogonality.

cs.LG↗

arXiv2021

Scikit-dimension: a Python package for intrinsic dimension estimation

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 \texttt{scikit-dimension}, an open-source Python package for intrinsic dimension estimation. \texttt{scikit-dimension} package provides a uniform implementation of most of the known ID estimators based on scikit-learn application programming interface to evaluate 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 in real-life and synthetic data. The source code is available from https://github.com/j-bac/scikit-dimension , the documentation is available from https://scikit-dimension.readthedocs.io .

cs.LG↗

arXiv2020

Trajectories, bifurcations and pseudotime in large clinical datasets: applications to myocardial infarction and diabetes data

Large observational clinical datasets become 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 pathology develops through a number of 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. 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 (pseudotime) in partially ordered sequences of observations. The methodology allows positioning a patient on a particular clinical trajectory (pathological scenario) and characterizing the degree of progression along it with a qualitative estimate of the uncertainty of the prognosis. Overall, our pseudo-time quantification-based approach gives a possibility to apply the methods developed for dynamical disease phenotyping and illness trajectory analysis (diachronic data analysis) to synchronic observational data. We developed a tool $ClinTrajan$ for clinical trajectory analysis implemented in Python programming language. We test the methodology in two large publicly available datasets: myocardial infarction complications and readmission of diabetic patients data.

stat.AP↗

arXiv2020

Local intrinsic dimensionality estimators based on concentration of measure

Intrinsic dimensionality (ID) is one of the most fundamental characteristics of multi-dimensional data point clouds. Knowing ID is crucial to choose the appropriate machine learning approach as well as to understand its behavior and validate it. ID can be computed globally for the whole data point distribution, or computed locally in different regions of the data space. In this paper, we introduce new local estimators of ID based on linear separability of multi-dimensional data point clouds, which is one of the manifestations of concentration of measure. We empirically study the properties of these estimators and compare them with other recently introduced ID estimators exploiting various effects of measure concentration. Observed differences between estimators can be used to anticipate their behaviour in practical applications.

cs.LG↗

arXiv2020

Synthesis of Boolean Networks from Biological Dynamical Constraints using Answer-Set Programming

Boolean networks model finite discrete dynamical systems with complex behaviours. The state of each component is determined by a Boolean function of the state of (a subset of) the components of the network. This paper addresses the synthesis of these Boolean functions from constraints on their domain and emerging dynamical properties of the resulting network. The dynamical properties relate to the existence and absence of trajectories between partially observed configurations, and to the stable behaviours (fixpoints and cyclic attractors). The synthesis is expressed as a Boolean satisfiability problem relying on Answer-Set Programming with a parametrized complexity, and leads to a complete non-redundant characterization of the set of solutions. Considered constraints are particularly suited to address the synthesis of models of cellular differentiation processes, as illustrated on a case study. The scalability of the approach is demonstrated on random networks with scale-free structures up to 100 to 1,000 nodes depending on the type of constraints.

cs.AI↗

arXiv2019

Basic, simple and extendable kinetic model of protein synthesis

Protein synthesis is one of the most fundamental biological processes, which consumes a significant amount of cellular resources. Despite existence of multiple mathematical models of translation, varying in the level of mechanistical details, surprisingly, there is no basic and simple chemical kinetic model of this process, derived directly from the detailed kinetic model. One of the reasons for this is that the translation process is characterized by indefinite number of states, thanks to existence of polysomes. We bypass this difficulty by applying a trick consisting in lumping 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 under some assumptions. The basic and simple model can be extended, if necessary, to take into account various phenomena such as the interaction between translating ribosomes, limited amount of ribosomal units or regulation of translation by microRNA. The model can be used as a building block (translation module) 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 single protein synthesis 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.

q-bio.MN↗

arXiv2019

Estimating the effective dimension of large biological datasets using Fisher separability analysis

Modern large-scale datasets are frequently said to be high-dimensional. However, their data point clouds frequently possess structures, significantly decreasing their intrinsic dimensionality (ID) due to the presence of clusters, points being located close to low-dimensional varieties or fine-grained lumping. We test a recently introduced dimensionality estimator, based on analysing the separability properties of data points, on several benchmarks and real biological datasets. We show that the introduced measure of ID has performance competitive with state-of-the-art measures, being efficient across a wide range of dimensions and performing better in the case of noisy samples. Moreover, it allows estimating the intrinsic dimension in situations where the intrinsic manifold assumption is not valid.

cs.LG↗

arXiv2018

Robust And Scalable Learning Of Complex Dataset Topologies Via Elpigraph

Large datasets represented by multidimensional data point clouds often possess non-trivial distributions with branching trajectories and excluded regions, with the recent single-cell transcriptomic studies of developing embryo being notable examples. Reducing the complexity and producing compact and interpretable representations of such data remains a challenging task. Most of the existing computational methods are based on exploring the local data point neighbourhood relations, a step that can perform poorly in the case of multidimensional and noisy data. Here we present ElPiGraph, a scalable and robust method for approximation of datasets with complex structures which does not require computing the complete data distance matrix or the data point neighbourhood graph. This method is able to withstand high levels of noise and is capable of approximating complex topologies via principal graph ensembles that can be combined into a consensus principal graph. ElPiGraph deals efficiently with large and complex datasets in various fields from biology, where it can be used to infer gene dynamics from single-cell RNA-Seq, to astronomy, where it can be used to explore complex structures in the distribution of galaxies.

cs.LG↗

arXiv2018

Identification of microRNA clusters cooperatively acting on Epithelial to Mesenchymal Transition in Triple Negative Breast Cancer

MicroRNAs play important roles in many biological processes. Their aberrant expression can have oncogenic or tumor suppressor function directly participating to carcinogenesis, malignant transformation, invasiveness and metastasis. Indeed, miRNA profiles can distinguish not only between normal and cancerous tissue but they can also successfully classify different subtypes of a particular cancer. Here, we focus on a particular class of transcripts encoding polycistronic miRNA genes that yields multiple miRNA components. We describe clustered MiRNA Master Regulator Analysis (ClustMMRA), a fully redesigned release of the MMRA computational pipeline (MiRNA Master Regulator Analysis), developed to search for clustered miRNAs potentially driving cancer molecular subtyping. Genomically clustered miRNAs are frequently co-expressed to target different components of pro-tumorigenic signalling pathways. By applying ClustMMRA to breast cancer patient data, we identified key miRNA clusters driving the phenotype of different tumor subgroups. The pipeline was applied to two independent breast cancer datasets, providing statistically concordant results between the two analysis. We validated in cell lines the miR-199/miR-214 as a novel cluster of miRNAs promoting the triple negative subtype phenotype through its control of proliferation and EMT.

q-bio.MN↗

arXiv2018

Creation and analysis of biochemical constraint-based models: the COBRA Toolbox v3.0

COnstraint-Based Reconstruction and Analysis (COBRA) provides a molecular mechanistic framework for integrative analysis of experimental data and quantitative prediction of physicochemically and biochemically feasible phenotypic states. The COBRA Toolbox is a comprehensive software suite of interoperable COBRA methods. It has found widespread applications in biology, biomedicine, and biotechnology because its functions can be flexibly combined to implement tailored COBRA protocols for any biochemical network. Version 3.0 includes new methods for quality controlled reconstruction, modelling, topological analysis, strain and experimental design, network visualisation as well as network integration of chemoinformatic, metabolomic, transcriptomic, proteomic, and thermochemical data. New multi-lingual code integration also enables an expansion in COBRA application scope via high-precision, high-performance, and nonlinear numerical optimisation solvers for multi-scale, multi-cellular and reaction kinetic modelling, respectively. This protocol can be adapted for the generation and analysis of a constraint-based model in a wide variety of molecular systems biology scenarios. This protocol is an update to the COBRA Toolbox 1.0 and 2.0. The COBRA Toolbox 3.0 provides an unparalleled depth of constraint-based reconstruction and analysis methods.

q-bio.QM↗

arXiv2015

Predicting genetic interactions from Boolean models of biological networks

Genetic interaction can be defined as a deviation of the phenotypic quantitative effect of a double gene mutation from the effect predicted from single mutations using a simple (e.g., multiplicative or linear additive) statistical model. Experimentally characterized genetic interaction networks in model organisms provide important insights into relationships between different biological functions. We describe a computational methodology allowing to systematically and quantitatively characterize a Boolean mathematical model of a biological network in terms of genetic interactions between all loss of function and gain of function mutations with respect to all model phenotypes or outputs. We use the probabilistic framework defined in MaBoSS software, based on continuous time Markov chains and stochastic simulations. In addition, we suggest several computational tools for studying the distribution of double mutants in the space of model phenotype probabilities. We demonstrate this methodology on three published models for each of which we derive the genetic interaction networks and analyze their properties. We classify the obtained interactions according to their class of epistasis, dependence on the chosen initial conditions and phenotype. The use of this methodology for validating mathematical models from experimental data and designing new experiments is discussed.

q-bio.MN↗

arXiv2015

DeDaL: Cytoscape 3.0 app for producing and morphing data-driven and structure-driven network layouts

Visualization and analysis of molecular profiling data together with biological networks are able to provide new mechanistical insights into biological functions. Currently, high-throughput data are usually visualized on top of predefined network layouts which are not always adapted to a given data analysis task. We developed a Cytoscape app which allows to construct biological network layouts based on the data from molecular profiles imported as values of nodes attributes. DeDaL is a Cytoscape 3.0 app which uses linear and non-linear algorithms of dimension reduction to produce data-driven network layouts based on multidimensional data (typically gene expression). DeDaL implements several data pre-processing and layout post-processing steps such as continuous morphing between two arbitrary network layouts and aligning one network layout with respect to another one by rotating and mirroring. Combining these possibilities facilitates creating insightful network layouts representing both structural network features and the correlation patterns in multivariate data. DeDaL is the first method allowing to construct biological network layouts from high-throughput data. DeDaL is freely available for downloading together with step-by-step tutorial at http://bioinfo-out.curie.fr/projects/dedal/.

q-bio.QM↗

arXiv2014

ViDaExpert: user-friendly tool for nonlinear visualization and analysis of multidimensional vectorial data

ViDaExpert is a tool for visualization and analysis of multidimensional vectorial data. ViDaExpert is able to work with data tables of "object-feature" type that might contain numerical feature values as well as textual labels for rows (objects) and columns (features). ViDaExpert implements several statistical methods such as standard and weighted Principal Component Analysis (PCA) and the method of elastic maps (non-linear version of PCA), Linear Discriminant Analysis (LDA), multilinear regression, K-Means clustering, a variant of decision tree construction algorithm. Equipped with several user-friendly dialogs for configuring data point representations (size, shape, color) and fast 3D viewer, ViDaExpert is a handy tool allowing to construct an interactive 3D-scene representing a table of data in multidimensional space and perform its quick and insightfull statistical analysis, from basic to advanced methods.

cs.MS↗