85 research outputs found
The IBMAP approach for Markov networks structure learning
In this work we consider the problem of learning the structure of Markov
networks from data. We present an approach for tackling this problem called
IBMAP, together with an efficient instantiation of the approach: the IBMAP-HC
algorithm, designed for avoiding important limitations of existing
independence-based algorithms. These algorithms proceed by performing
statistical independence tests on data, trusting completely the outcome of each
test. In practice tests may be incorrect, resulting in potential cascading
errors and the consequent reduction in the quality of the structures learned.
IBMAP contemplates this uncertainty in the outcome of the tests through a
probabilistic maximum-a-posteriori approach. The approach is instantiated in
the IBMAP-HC algorithm, a structure selection strategy that performs a
polynomial heuristic local search in the space of possible structures. We
present an extensive empirical evaluation on synthetic and real data, showing
that our algorithm outperforms significantly the current independence-based
algorithms, in terms of data efficiency and quality of learned structures, with
equivalent computational complexities. We also show the performance of IBMAP-HC
in a real-world application of knowledge discovery: EDAs, which are
evolutionary algorithms that use structure learning on each generation for
modeling the distribution of populations. The experiments show that when
IBMAP-HC is used to learn the structure, EDAs improve the convergence to the
optimum
Corrected score methods for estimating Bayesian networks with error-prone nodes
Motivated by inferring cellular signaling networks using noisy flow cytometry
data, we develop procedures to draw inference for Bayesian networks based on
error-prone data. Two methods for inferring causal relationships between nodes
in a network are proposed based on penalized estimation methods that account
for measurement error and encourage sparsity. We discuss consistency of the
proposed network estimators and develop an approach for selecting the tuning
parameter in the penalized estimation methods. Empirical studies are carried
out to compare the proposed methods and a naive method that ignores measurement
error with applications to synthetic data and to single cell flow cytometry
data
Seeded Bayesian Networks: Constructing genetic networks from microarray data
<p>Abstract</p> <p>Background</p> <p>DNA microarrays and other genomics-inspired technologies provide large datasets that often include hidden patterns of correlation between genes reflecting the complex processes that underlie cellular metabolism and physiology. The challenge in analyzing large-scale expression data has been to extract biologically meaningful inferences regarding these processes – often represented as networks – in an environment where the datasets are often imperfect and biological noise can obscure the actual signal. Although many techniques have been developed in an attempt to address these issues, to date their ability to extract meaningful and predictive network relationships has been limited. Here we describe a method that draws on prior information about gene-gene interactions to infer biologically relevant pathways from microarray data. Our approach consists of using preliminary networks derived from the literature and/or protein-protein interaction data as seeds for a Bayesian network analysis of microarray results.</p> <p>Results</p> <p>Through a bootstrap analysis of gene expression data derived from a number of leukemia studies, we demonstrate that seeded Bayesian Networks have the ability to identify high-confidence gene-gene interactions which can then be validated by comparison to other sources of pathway data.</p> <p>Conclusion</p> <p>The use of network seeds greatly improves the ability of Bayesian Network analysis to learn gene interaction networks from gene expression data. We demonstrate that the use of seeds derived from the biomedical literature or high-throughput protein-protein interaction data, or the combination, provides improvement over a standard Bayesian Network analysis, allowing networks involving dynamic processes to be deduced from the static snapshots of biological systems that represent the most common source of microarray data. Software implementing these methods has been included in the widely used TM4 microarray analysis package.</p
The identification of informative genes from multiple datasets with increasing complexity
Background
In microarray data analysis, factors such as data quality, biological variation, and the increasingly multi-layered nature of more complex biological systems complicates the modelling of regulatory networks that can represent and capture the interactions among genes. We believe that the use of multiple datasets derived from related biological systems leads to more robust models. Therefore, we developed a novel framework for modelling regulatory networks that involves training and evaluation on independent datasets. Our approach includes the following steps: (1) ordering the datasets based on their level of noise and informativeness; (2) selection of a Bayesian classifier with an appropriate level of complexity by evaluation of predictive performance on independent data sets; (3) comparing the different gene selections and the influence of increasing the model complexity; (4) functional analysis of the informative genes.
Results
In this paper, we identify the most appropriate model complexity using cross-validation and independent test set validation for predicting gene expression in three published datasets related to myogenesis and muscle differentiation. Furthermore, we demonstrate that models trained on simpler datasets can be used to identify interactions among genes and select the most informative. We also show that these models can explain the myogenesis-related genes (genes of interest) significantly better than others (P < 0.004) since the improvement in their rankings is much more pronounced. Finally, after further evaluating our results on synthetic datasets, we show that our approach outperforms a concordance method by Lai et al. in identifying informative genes from multiple datasets with increasing complexity whilst additionally modelling the interaction between genes.
Conclusions
We show that Bayesian networks derived from simpler controlled systems have better performance than those trained on datasets from more complex biological systems. Further, we present that highly predictive and consistent genes, from the pool of differentially expressed genes, across independent datasets are more likely to be fundamentally involved in the biological process under study. We conclude that networks trained on simpler controlled systems, such as in vitro experiments, can be used to model and capture interactions among genes in more complex datasets, such as in vivo experiments, where these interactions would otherwise be concealed by a multitude of other ongoing events
Evolutionary approaches for the reverse-engineering of gene regulatory networks: A study on a biologically realistic dataset
<p>Abstract</p> <p>Background</p> <p>Inferring gene regulatory networks from data requires the development of algorithms devoted to structure extraction. When only static data are available, gene interactions may be modelled by a Bayesian Network (BN) that represents the presence of direct interactions from regulators to regulees by conditional probability distributions. We used enhanced evolutionary algorithms to stochastically evolve a set of candidate BN structures and found the model that best fits data without prior knowledge.</p> <p>Results</p> <p>We proposed various evolutionary strategies suitable for the task and tested our choices using simulated data drawn from a given bio-realistic network of 35 nodes, the so-called insulin network, which has been used in the literature for benchmarking. We assessed the inferred models against this reference to obtain statistical performance results. We then compared performances of evolutionary algorithms using two kinds of recombination operators that operate at different scales in the graphs. We introduced a niching strategy that reinforces diversity through the population and avoided trapping of the algorithm in one local minimum in the early steps of learning. We show the limited effect of the mutation operator when niching is applied. Finally, we compared our best evolutionary approach with various well known learning algorithms (MCMC, K2, greedy search, TPDA, MMHC) devoted to BN structure learning.</p> <p>Conclusion</p> <p>We studied the behaviour of an evolutionary approach enhanced by niching for the learning of gene regulatory networks with BN. We show that this approach outperforms classical structure learning methods in elucidating the original model. These results were obtained for the learning of a bio-realistic network and, more importantly, on various small datasets. This is a suitable approach for learning transcriptional regulatory networks from real datasets without prior knowledge.</p
Fault Trees from Data: Efficient Learning with an Evolutionary Algorithm
Cyber-physical systems come with increasingly complex architectures and
failure modes, which complicates the task of obtaining accurate system
reliability models. At the same time, with the emergence of the (industrial)
Internet-of-Things, systems are more and more often being monitored via
advanced sensor systems. These sensors produce large amounts of data about the
components' failure behaviour, and can, therefore, be fruitfully exploited to
learn reliability models automatically. This paper presents an effective
algorithm for learning a prominent class of reliability models, namely fault
trees, from observational data. Our algorithm is evolutionary in nature; i.e.,
is an iterative, population-based, randomized search method among fault-tree
structures that are increasingly more consistent with the observational data.
We have evaluated our method on a large number of case studies, both on
synthetic data, and industrial data. Our experiments show that our algorithm
outperforms other methods and provides near-optimal results.Comment: This paper is an extended version of the SETTA 2019 paper,
Springer-Verla
- …