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PubMed2005

Modularized learning of genetic interaction networks from biological annotations and mRNA expression data.

MOTIVATION: Inferring the genetic interaction mechanism using Bayesian networks has recently drawn increasing attention due to its well-established theoretical foundation and statistical robustness. However, the relative insufficiency of experiments with respect to the number of genes leads to many false positive inferences. RESULTS: We propose a novel method to infer genetic networks by alleviating the shortage of available mRNA expression data with prior knowledge. We call the proposed method 'modularized network learning' (MONET). Firstly, the proposed method divides a whole gene set to overlapped modules considering biological annotations and expression data together. Secondly, it infers a Bayesian network for each module, and integrates the learned subnetworks to a global network. An algorithm that measures a similarity between genes based on hierarchy, specificity and multiplicity of biological annotations is presented. The proposed method draws a global picture of inter-module relationships as well as a detailed look of intra-module interactions. We applied the proposed method to analyze Saccharomyces cerevisiae stress data, and found several hypotheses to suggest putative functions of unclassified genes. We also compared the proposed method with a whole-set-based approach and two expression-based clustering approaches.

Algorithms↗

PubMed2006

Comparative evaluation of reverse engineering gene regulatory networks with relevance networks, graphical gaussian models and bayesian networks.

MOTIVATION: An important problem in systems biology is the inference of biochemical pathways and regulatory networks from postgenomic data. Various reverse engineering methods have been proposed in the literature, and it is important to understand their relative merits and shortcomings. In the present paper, we compare the accuracy of reconstructing gene regulatory networks with three different modelling and inference paradigms: (1) Relevance networks (RNs): pairwise association scores independent of the remaining network; (2) graphical Gaussian models (GGMs): undirected graphical models with constraint-based inference, and (3) Bayesian networks (BNs): directed graphical models with score-based inference. The evaluation is carried out on the Raf pathway, a cellular signalling network describing the interaction of 11 phosphorylated proteins and phospholipids in human immune system cells. We use both laboratory data from cytometry experiments as well as data simulated from the gold-standard network. We also compare passive observations with active interventions. RESULTS: On Gaussian observational data, BNs and GGMs were found to outperform RNs. The difference in performance was not significant for the non-linear simulated data and the cytoflow data, though. Also, we did not observe a significant difference between BNs and GGMs on observational data in general. However, for interventional data, BNs outperform GGMs and RNs, especially when taking the edge directions rather than just the skeletons of the graphs into account. This suggests that the higher computational costs of inference with BNs over GGMs and RNs are not justified when using only passive observations, but that active interventions in the form of gene knockouts and over-expressions are required to exploit the full potential of BNs. AVAILABILITY: Data, software and supplementary material are available from http://www.bioss.sari.ac.uk/staff/adriano/research.html

Algorithms↗

PubMed2006

Monitoring metal-fill in a lost foam casting process.

The lost foam casting (LFC) process is emerging as a reliable casting method. The metal-fill profile in LFC plays an important role among several factors that affect casting quality. The metal-fill profile is in turn affected by several factors. Several casting defects may result due to an improper metal-fill process. Hence, it becomes essential to characterize and control, if possible, the metal-fill process in LFC. This research presents instrumentation and a technique to monitor and characterize the metal-fill process. The characterization included the determination of the position of the metal front and the profile in which the metal fills up the foam pattern. The instrumentation included capacitive sensors. Each sensor is comprised of two electrodes whose capacitive coupling changes as the metal fills the foam pattern. Foundry tests were conducted to obtain the sensors' responses to the metal fill. Two such sensors were used in the foundry tests. Data representing the responses of these sensors during the metal-fill process were collected using a data acquisition system. A number of finite element electrostatic simulations were carried out to study the metal-fill process under conditions similar to those experienced in foundry tests. An artificial neural network was trained using the simulation data as inputs and the corresponding metal-fill profiles as outputs. The neural network was then used to infer the profile of the metal-fill during foundry tests. The results were verified by comparing the metal-fill profile inferred from the neural network to the actual metal-fill profile captured by an infrared camera used during the foundry tests. The match up between the inferred profiles and the infrared camera measurements was satisfactory, indicating that the developed technique provides a reliable and cost effective method to monitor the metal-fill profile in LFC.

Journal Article↗

PubMed2004

Likelihood-based inference for stochastic models of sexual network formation.

Sexually-transmitted diseases (STDs) constitute a major public health concern. Mathematical models for the transmission dynamics of STDs indicate that heterogeneity in sexual activity level allow them to persist even when the typical behavior of the population would not support endemicity. This insight focuses attention on the distribution of sexual activity level in a population. In this paper, we develop several stochastic process models for the formation of sexual partnership networks. Using likelihood-based model selection procedures, we assess the fit of the different models to three large distributions of sexual partner counts: (1) Rakai, Uganda, (2) Sweden, and (3) the USA. Five of the six single-sex networks were fit best by the negative binomial model. The American women's network was best fit by a power-law model, the Yule. For most networks, several competing models fit approximately equally well. These results suggest three conclusions: (1) no single unitary process clearly underlies the formation of these sexual networks, (2) behavioral heterogeneity plays an essential role in network structure, (3) substantial model uncertainty exists for sexual network degree distributions. Behavioral research focused on the mechanisms of partnership formation will play an essential role in specifying the best model for empirical degree distributions. We discuss the limitations of inferences from such data, and the utility of degree-based epidemiological models more generally.

Databases as Topic↗

PubMed1992

Inferring articulation and recognizing gestures from acoustics with a neural network trained on x-ray microbeam data.

This paper describes a method for inferring articulatory parameters from acoustics with a neural network trained on paired acoustic and articulatory data. An x-ray microbeam recorded the vertical movements of the lower lip, tongue tip, and tongue dorsum of three speakers saying the English stop consonants in repeated Ce syllables. A neural network was then trained to map from simultaneously recorded acoustic data to the articulatory data. To evaluate learning, acoustics from the training set were passed through the neural network. To evaluate generalization, acoustics from speakers or consonants excluded from the training set were passed through the network. The articulatory trajectories thus inferred were a good fit to the actual movements in both the learning and generalization conditions, as judged by root-mean-square error and correlation. Inferred trajectories were also matched to templates of lower lip, tongue tip, and tongue dorsum release gestures extracted from the original data. This technique correctly recognized from 94.4% to 98.9% of all gestures in the learning and cross-speaker generalization conditions, and 75% of gestures underlying consonants excluded from the training set. In addition, greater regularity was observed for movements of articulators that were critical in the formation of each consonant.

Adult↗

PubMed2005

Inferring meaningful pathways in weighted metabolic networks.

An approach is presented for computing meaningful pathways in the network of small molecule metabolism comprising the chemical reactions characterized in all organisms. The metabolic network is described as a weighted graph in which all the compounds are included, but each compound is assigned a weight equal to the number of reactions in which it participates. Path finding is performed in this graph by searching for one or more paths with lowest weight. Performance is evaluated systematically by computing paths between the first and last reactions in annotated metabolic pathways, and comparing the intermediate reactions in the computed pathways to those in the annotated ones. For the sake of comparison, paths are computed also in the un-weighted raw (all compounds and reactions) and filtered (highly connected pool metabolites removed) metabolic graphs, respectively. The correspondence between the computed and annotated pathways is very poor (<30%) in the raw graph; increasing to approximately 65% in the filtered graph; reaching approximately 85% in the weighted graph. Considering the best-matching path among the five lightest paths increases the correspondence to 92%, on average. We then show that the average distance between pairs of metabolites is significantly larger in the weighted graph than in the raw unfiltered graph, suggesting that the small-world properties previously reported for metabolic networks probably result from irrelevant shortcuts through pool metabolites. In addition, we provide evidence that the length of the shortest path in the weighted graph represents a valid measure of the "metabolic distance" between enzymes. We suggest that the success of our simplistic approach is rooted in the high degree of specificity of the reactions in metabolic pathways, presumably reflecting thermodynamic constraints operating in these pathways. We expect our approach to find useful applications in inferring metabolic pathways in newly sequenced genomes.

Amino Acids↗

PubMed2005

Functional annotation from predicted protein interaction networks.

MOTIVATION: Progress in large-scale experimental determination of protein-protein interaction networks for several organisms has resulted in innovative methods of functional inference based on network connectivity. However, the amount of effort and resources required for the elucidation of experimental protein interaction networks is prohibitive. Previously we, and others, have developed techniques to predict protein interactions for novel genomes using computational methods and data generated from other genomes. RESULTS: We evaluated the performance of a network-based functional annotation method that makes use of our predicted protein interaction networks. We show that this approach performs equally well on experimentally derived and predicted interaction networks, for both manually and computationally assigned annotations. We applied the method to predicted protein interaction networks for over 50 organisms from all domains of life, providing annotations for many previously unannotated proteins and verifying existing low-confidence annotations. AVAILABILITY: Functional predictions for over 50 organisms are available at http://bioverse.compbio.washington.edu and datasets used for analysis at http://data.compbio.washington.edu/misc/downloads/nannotation_data/. SUPPLEMENTARY INFORMATION: A supplemental appendix gives additional details not in the main text. (http://data.compbio.washington.edu/misc/downloads/nannotation_data/supplement.pdf).

Chromosome Mapping↗

PubMed2004

Predicting protein complex membership using probabilistic network reliability.

Evidence for specific protein-protein interactions is increasingly available from both small- and large-scale studies, and can be viewed as a network. It has previously been noted that errors are frequent among large-scale studies, and that error frequency depends on the large-scale method used. Despite knowledge of the error-prone nature of interaction evidence, edges (connections) in this network are typically viewed as either present or absent. However, use of a probabilistic network that considers quantity and quality of supporting evidence should improve inference derived from protein networks. Here we demonstrate inference of membership in a partially known protein complex by using a probabilistic network model and an algorithm previously used to evaluate reliability in communication networks.

Fungal Proteins↗

PubMed2004

From molecular noise to behavioural variability in a single bacterium.

The chemotaxis network that governs the motion of Escherichia coli has long been studied to gain a general understanding of signal transduction. Although this pathway is composed of just a few components, it exhibits some essential characteristics of biological complexity, such as adaptation and response to environmental signals. In studying intracellular networks, most experiments and mathematical models have assumed that network properties can be inferred from population measurements. However, this approach masks underlying temporal fluctuations of intracellular signalling events. We have inferred fundamental properties of the chemotaxis network from a noise analysis of behavioural variations in individual bacteria. Here we show that certain properties established by population measurements, such as adapted states, are not conserved at the single-cell level: for timescales ranging from seconds to several minutes, the behaviour of non-stimulated cells exhibit temporal variations much larger than the expected statistical fluctuations. We find that the signalling network itself causes this noise and identify the molecular events that produce it. Small changes in the concentration of one key network component suppress temporal behavioural variability, suggesting that such variability is a selected property of this adaptive system.

Adaptation, Physiological↗

PubMed2003

The phylogeography of dusky dolphins (Lagenorhynchus obscurus): a critical examination of network methods and rooting procedures.

We investigated the phylogeography and evolutionary history of dusky dolphins (Lagenorhynchus obscurus) using DNA sequences of the full mitochondrial cytochrome b gene in 124 individuals from the putative stocks off Peru, Argentina and Southwest Africa. While genetic differentiation within oceans is surprisingly low, there is no evidence for recent female gene flow between Atlantic and Pacific waters. Highest genetic variability in terms of sequence divergence and number of haplotypes is found in the Atlantic. Our analyses also indicate that the eastern South Pacific dusky dolphins stock should be considered a separate management unit. Given the high level of mortality experienced by the Peruvian dusky dolphin in local fishery activities, these findings have important implications for an objective management of the species. Furthermore, we analysed our mitochondrial sequence data with several widely used network estimation and rooting methods. The resulting intraspecific gene genealogies and rooting inferences exhibited substantial differences, underlying the limitations of some algorithms. Given that scientific hypotheses and management decisions depend strongly on inferred tree or network topologies, there is a clear need for a systematic comparative analysis of available methods. Finally, the present study indicates that (i) the dusky and the Pacific white-sided dolphins are sister species and (ii) not only the Westwind Drift hypothesis but also other models of dispersion are compatible with the current geographical distribution of dusky dolphins.

Animals↗

PubMed2005

Inferring the connectivity of a regulatory network from mRNA quantification in Synechocystis PCC6803.

A major task of contemporary biology is to understand and predict the functioning of regulatory networks. We use expression data to deduce the regulation network connecting the sigma factors of Synechocystis PCC6803, the most global regulators in bacteria. Synechocystis contains one group 1 (SigA) and four group 2 (SigB, SigC, SigD and SigE) sigma factors. From the relative abundance of the sig mRNA measured in the wild-type and the four group 2 sigma mutants, we derive a network of the influences of each sigma factor on the transcription of all other sigma factors. Internal or external stimuli acting on only one of the sigma factors will thus indirectly modify the expression of most of the others. From this model, we predict the control points through which the circadian time modulates the expression of the sigma factors. Our results show that the cross regulation between the group 1 and group 2 sigma factors is very important for the adaptation of the bacterium to different environmental and physiological conditions.

Bacterial Proteins↗

PubMed2004

Dynamic algorithm for inferring qualitative models of gene regulatory networks.

It is still an open problem to identify functional relations with o(N . n(k)) time for any domain[2], where N is the number of learning instances, n is the number of genes (or variables) in the Gene Regulatory Network (GRN) models and k is the indegree of the genes. To solve the problem, we introduce a novel algorithm, DFL (Discrete Function Learning), for reconstructing qualitative models of GRNs from gene expression data in this paper. We analyze its complexity of O(k . N . n(2)) on the average and its data requirements. We also perform experiments on both synthetic and Cho et al. [7] yeast cell cycle gene expression data to validate the efficiency and prediction performance of the DFL algorithm. The experiments of synthetic Boolean networks show that the DFL algorithm is more efficient than current algorithms without loss of prediction performances. The results of yeast cell cycle gene expression data show that the DFL algorithm can identify biologically significant models with reasonable accuracy, sensitivity and high precision with respect to the literature evidences. We further introduce a method called epsilon function to deal with noises in data sets. The experimental results show that the epsilon function method is a good supplement to the DFL algorithm.

Algorithms↗

PubMed2004

Sparse graphical Gaussian modeling of the isoprenoid gene network in Arabidopsis thaliana.

We present a novel graphical Gaussian modeling approach for reverse engineering of genetic regulatory networks with many genes and few observations. When applying our approach to infer a gene network for isoprenoid biosynthesis in Arabidopsis thaliana, we detect modules of closely connected genes and candidate genes for possible cross-talk between the isoprenoid pathways. Genes of downstream pathways also fit well into the network. We evaluate our approach in a simulation study and using the yeast galactose network.

Arabidopsis↗

PubMed2004

Inferring dynamic properties of biochemical reaction networks from structural knowledge.

Functional properties of biochemical networks depend on both the network structure and the kinetic parameters. Extensive data on metabolic network topologies have been collected in databases, but much less information is available about the kinetic constants or metabolite concentrations. Depending on the values of these parameters, metabolic fluxes and control coefficients may vary within a wide range. Nevertheless, some of the parameters may have little influence on the observables of interest. We address the question whether, despite uncertainty about kinetic parameters, probabilistic statements can be made about dynamic network features. To this end, we perform a variability analysis of the parameters: assuming that the parameters follow statistical distributions, we compute the resulting distributions of the network properties like metabolic fluxes, concentrations, or control coefficients by Monte Carlo simulation. In this manner, we study systematically the possible distributions arising from typical topologies of biochemical networks such as linear chains, branched networks, and signaling and gene expression cascades. This analysis reveals how much information about dynamic behavior can be drawn from structural knowledge.

Biochemistry↗

PubMed1995

The circum-Chryse region as a possible example of a hydrologic cycle on Mars: geologic observations and theoretical evaluation.

The transection and superposition relationships among channels, chaos, surface materials units, and other features in the circum-Chryse region of Mars were used to evaluate relative age relationships and evolution of flood events. Channels and chaos in contact (with one another) were treated as single discrete flood-carved systems. Some outflow channel systems form networks and are inferred to have been created by multiple flood events. Within some outflow channel networks, several separate individual channel systems can be traced to a specific chaos which acted as flood-source area to that specific flood channel. Individual flood-carved systems were related to widespread materials units or other surface features that served as stratigraphic horizons. Chryse outflow channels are inferred to have formed over most of the perceivable history of Mars. Outflow channels are inferred to become younger with increasing proximity to the Chryse basin. In addition, outflow channels closer to the basin show a greater diversity in age. The relationship of subsequent outflow channel sources to the sources of earlier floods is inferred to disfavor episodic flooding due to the progressive tapping of a juvenile near-surface water supply. Instead, we propose the circum-Chryse region as a candidate site of past hydrological recycling. The discharge rates necessary to carve the circum-Chryse outflow channels would have inevitably formed temporary standing bodies of H2O on the Martian surface where the flood-waters stagnated and pooled (the Chryse basin is topographically enclosed). These observations and inferences have led us to formulate and evaluate two hypotheses: (1) large amounts of the sublimated H2O off the Chryse basin flood lakes precipitated (snowed) onto the flood-source highlands and this H2O was incorporated into the near surface, recharging the H2O sources, making possible subsequent deluges; and (2) ponded flood-water in Chryse basin drained back down an anti basinward dipping subsurface layer accessed long the southern edge of the lake, recharging the flood-source aquifers. H2O not redeposited in the flood-source region was largely lost to the hydrologic cycle. This loss progressively lowered the vitality of the cycle, probably by now killing it. Our numerical evaluations indicate that of the two hypotheses we formulated, the groundwater seep cycle seems by far the more viable. Optimally, approximately 3/4 of the original mass of an ice-covered cylindrical lake (albedo 0.5, 1 km deep, 100-km radius, draining along its rim for one quarter of its circumference into substrata with a permeability of 3000 darcies) can be modeled to have moved underground (on timescales of the order of 10(3) years) before the competing mechanisms of sublimation and freeze down choked off further water removal. Once underground, this water can travel distances equal to the separation between Chryse basin and flood-source sites in geologically short (approximately 10(6) year-scale) times. Conversely, we calculate that optimally only approximately 40% of the H2O carried from Chryse can condense at the highlands, and most of the precipitate would either collect at the base of the highlands/lowlands scarp or sublimate at rates greater than it would accumulate over the flood-source sites. Further observations from forthcoming missions may permit the determination of which mechanisms may have operated to recycle the Chryse flood-waters.

Disasters↗

PubMed1991

GAMEES: a probabilistic environment for expert systems.

This paper describes GAMEES (Graphical Modelling Environment for Expert Systems), an interactive graphical environment for building and processing Belief Networks and Influence Diagrams. We review the existing systems designed for analogous purposes, and, after a brief introduction to Belief Networks and Influence Diagrams, we describe the graphical interface, discuss algorithms for probabilistic inference on these networks and illustrate the current implementation of GAMEES. The system has been designed for being integrated within wider expert systems and actually it is part of the Therapy Advisor module within an expert system for the management of anemic patients.

Algorithms↗

PubMed2003

Alike performance during nonverbal episodic learning from diversely imprinted neural networks.

Performance on neuropsychological testing permits inferences to be made regarding neural networks required to solve the task. In healthy young human subjects it is common sense that differential performance in cognitive tasks results from recruitment of different neural networks and that alike performance results from recruitment of alike neural networks. It was the goal of the present study to investigate whether these assumptions are also valid in cross-cultural studies. To address this, we used functional MRI during a nonverbal episodic memory task with repeated learning of abstract geometric patterns. Behavioural performance in this task was alike over repeated trials in native Chinese and Caucasian subjects. Given this equivalent performance, the distinct pattern of neuronal activation observed is interpreted as the outcome of different culturally imprinted processing routines. In the 'what' and 'where' framework of visuo-spatial processing initial learning in Chinese subjects activated the dorsal stream for analysis of spatial features whereas Caucasians recruited the ventral stream for object identification. With repeated learning Chinese subjects integrated visuo-spatial processing to object coding and vice versa. Thus, imprints of culture result in activation of distinct neural networks and mandate monitoring of both behavioural performance and neural recruitment in cross-cultural studies of cognition.

Adult↗

PubMed2005

Inference of combinatorial regulation in yeast transcriptional networks: a case study of sporulation.

Decomposing transcriptional regulatory networks into functional modules and determining logical relations between them is the first step toward understanding transcriptional regulation at the system level. Modules based on analysis of genome-scale data can serve as the basis for inferring combinatorial regulation and for building mathematical models to quantitatively describe the behavior of the networks. We present here an algorithm called modem to identify target genes of a transcription factor (TF) from a single expression experiment, based on a joint probabilistic model for promoter sequence and gene expression data. We show how this method can facilitate the discovery of specific instances of combinatorial regulation and illustrate this for a specific case of transcriptional networks that regulate sporulation in the yeast Saccharomyces cerevisiae. Applying this method to analyze two crucial TFs in sporulation, Ndt80p and Sum1p, we were able to delineate their overlapping binding sites. We proposed a mechanistic model for the competitive regulation by the two TFs on a defined subset of sporulation genes. We show that this model accounts for the temporal control of the "middle" sporulation genes and suggest a similar regulatory arrangement can be found in developmental programs in higher organisms.

Algorithms↗