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At least 19 records

Dynamic Medical Risk Assessment Supported by Inference Networks

The Human Research Program's next generation risk model, the Medical Extensible Dynamic Probabilistic Risk Assessment Tool (MEDPRAT), provides researchers with estimates of astronaut medical and health risk. MEDPRATs Susceptibility Inference Network (SIN) facilitates the dynamic component of this tool. The SIN provides MEDPRAT with a "memory" that allows the system to use knowledge of what simulation events have occurred to alter the representative probability that future simulation events will occur during a given trial. The SIN allows for the medical events being simulated to be related to, and influence the likelihood of one another, providing a more robust risk estimate. We present initial work of our efforts to mathematically quantify and represent these dependent relationships between medical events.

McIntyre, L.↗

Understanding the Scalability of Bayesian Network Inference using Clique Tree Growth Curves

Bayesian networks (BNs) are used to represent and efficiently compute with multi-variate probability distributions in a wide range of disciplines. One of the main approaches to perform computation in BNs is clique tree clustering and propagation. In this approach, BN computation consists of propagation in a clique tree compiled from a Bayesian network. There is a lack of understanding of how clique tree computation time, and BN computation time in more general, depends on variations in BN size and structure. On the one hand, complexity results tell us that many interesting BN queries are NP-hard or worse to answer, and it is not hard to find application BNs where the clique tree approach in practice cannot be used. On the other hand, it is well-known that tree-structured BNs can be used to answer probabilistic queries in polynomial time. In this article, we develop an approach to characterizing clique tree growth as a function of parameters that can be computed in polynomial time from BNs, specifically: (i) the ratio of the number of a BN's non-root nodes to the number of root nodes, or (ii) the expected number of moral edges in their moral graphs. Our approach is based on combining analytical and experimental results. Analytically, we partition the set of cliques in a clique tree into different sets, and introduce a growth curve for each set. For the special case of bipartite BNs, we consequently have two growth curves, a mixed clique growth curve and a root clique growth curve. In experiments, we systematically increase the degree of the root nodes in bipartite Bayesian networks, and find that root clique growth is well-approximated by Gompertz growth curves. It is believed that this research improves the understanding of the scaling behavior of clique tree clustering, provides a foundation for benchmarking and developing improved BN inference and machine learning algorithms, and presents an aid for analytical trade-off studies of clique tree clustering using growth curves.

Mengshoel, Ole Jakob↗

Understanding the Scalability of Bayesian Network Inference Using Clique Tree Growth Curves

One of the main approaches to performing computation in Bayesian networks (BNs) is clique tree clustering and propagation. The clique tree approach consists of propagation in a clique tree compiled from a Bayesian network, and while it was introduced in the 1980s, there is still a lack of understanding of how clique tree computation time depends on variations in BN size and structure. In this article, we improve this understanding by developing an approach to characterizing clique tree growth as a function of parameters that can be computed in polynomial time from BNs, specifically: (i) the ratio of the number of a BN s non-root nodes to the number of root nodes, and (ii) the expected number of moral edges in their moral graphs. Analytically, we partition the set of cliques in a clique tree into different sets, and introduce a growth curve for the total size of each set. For the special case of bipartite BNs, there are two sets and two growth curves, a mixed clique growth curve and a root clique growth curve. In experiments, where random bipartite BNs generated using the BPART algorithm are studied, we systematically increase the out-degree of the root nodes in bipartite Bayesian networks, by increasing the number of leaf nodes. Surprisingly, root clique growth is well-approximated by Gompertz growth curves, an S-shaped family of curves that has previously been used to describe growth processes in biology, medicine, and neuroscience. We believe that this research improves the understanding of the scaling behavior of clique tree clustering for a certain class of Bayesian networks; presents an aid for trade-off studies of clique tree clustering using growth curves; and ultimately provides a foundation for benchmarking and developing improved BN inference and machine learning algorithms.

Mengshoel, Ole J.↗

Genetic Network Inference: From Co-Expression Clustering to Reverse Engineering

Advances in molecular biological, analytical, and computational technologies are enabling us to systematically investigate the complex molecular processes underlying biological systems. In particular, using high-throughput gene expression assays, we are able to measure the output of the gene regulatory network. We aim here to review datamining and modeling approaches for conceptualizing and unraveling the functional relationships implicit in these datasets. Clustering of co-expression profiles allows us to infer shared regulatory inputs and functional pathways. We discuss various aspects of clustering, ranging from distance measures to clustering algorithms and multiple-duster memberships. More advanced analysis aims to infer causal connections between genes directly, i.e., who is regulating whom and how. We discuss several approaches to the problem of reverse engineering of genetic networks, from discrete Boolean networks, to continuous linear and non-linear models. We conclude that the combination of predictive modeling with systematic experimental verification will be required to gain a deeper insight into living organisms, therapeutic targeting, and bioengineering.

Dhaeseleer, Patrik↗

An Artificial Neural Network for Inferring Solar Wind Proxies at Mars

We present a novel method to determine solar wind proxies from sheath measurements at Mars. Specifically, we develop an artificial neural network (ANN) to simultaneously infer seven solar wind proxies: ion density, ion speed, ion temperature, and interplanetary magnetic field magnitude and its vector components, using spacecraft measurements of ion moments, magnetic field magnitude, magnetic field components in the sheath, and the solar extreme ultraviolet flux. The ANN was trained and tested using3 years of data from the Mars Atmosphere and Volatile EvolutioN (MAVEN) spacecraft. When compared with MAVEN spacecraft's in situ measured values of the solar wind parameters, we find that the ANN proxies for the solar wind ion density, ion speed, ion temperature, and interplanetary magnetic field magnitude havepercentage differences of 50% or less for 84.4%, 99.9%, 86.8%, and 79.8% of the instances, respectively. Forthe cone angle and clock angle proxies, 69.1% and 53.3% of instances, respectively, have angle differences of 30* or less.

Neural Network↗

On the adequacy of the fixed locations of the surface-based international network for inferring interannual ozone variability

The influence of the geographical distribution and the number of the surface stations in the ozone detecting network on changes in global ozone inferred from the surface measurements is investigated by comparison with information obtained from satellite backscattered UV observations on the Nimbus 4 with nearly complete global coverage for the period 1970-1972. Results show that the geographical distribution of the stations does not properly represent different latitudes. While the number of stations in the north temperate zone appears adequate to represent monthly ozone averages to within 0.5% except during the early phase of the Northern Hemisphere spring maximum, the resultant error in the derived change in north temperature zone ozone between 1970-1972 is 0.5%. In the tropical and south temperate zones the smaller number of stations reduces precision, and the ozone averages for use in deriving seasonal variability and trends are uncertain by about 1%. However, in the south temperature zone, the average from the sample may differ as much as 5% in some months from the averages derived from the full set. It is concluded that the resulting uncertainty in the global averages is comparable in size to typical yearly changes.

Heath, D. F.↗

Discrete Recurrent Neural Networks for Grammatical Inference

Recurrent neural networks have recently been shown to have the ability to learn regular and context-free grammars from examples. We show that while conventional analog recurrent networks try to form clusters in activation space to represent discrete states of the grammars during learning, and can be successful in doing so, the clusters so formed tend to become unstable as longer and longer test input strings are presented to the network.

Neural↗

Methods for Determining Subsets of High Impact, Probabilistically Dependent Medical Conditions Represented in a Directed Graph

One of the longest standing questions in network theory is how a component influences other parts in the system, and how that role is affected when restricting the navigation through the network. The Katz score, one of many centrality measures created for this purpose, takes into account all possible walks through the network, penalizing each additional step in a walk by a scalar called the Katz parameter. This centrality measure often covers an infinite number of walks with infinite length. In this paper we identify the maximum path length which has influence on the Katz score. We ultimately provide guidance when deciding which Katz parameter to use as it depends on the path length of interest. We show how changing the Katz parameter affects the ranking of the vertices in some synthetic graphs as well as NASA's expert informed network of medical dependencies called the Susceptibility Inference Network (SIN).

Hunter Rehm↗

Precipitation and Aridity Constraints on Early Mars from Globally-Distributed Paleolakes

The widespread occurrence of fluvio-lacustrine features on Mars support long-lived flow and accumulation of water in a warmer, wetter past. However, martian climate models have been unable to recreate the necessary conditions required to support a persistent wet climate. Orbital and in-situ data sets have revealed the existence of > 400 paleolakes on Mars, which can be subdivided into open- and closed-basin lakes. Open-basin lakes require that sufficient water accumulated to fill and overtop the basin-confining topography, providing a minimum constraint on required water volumes. Conversely, closed-basin lakes provide maximum water volumes since the absence of an outlet breach generally implies they did not overflow. Importantly, a subset of both open- and closed-basin lakes are fed by valley networks inferred to have been sourced by precipitation during the era of valley network formation > 3.7 Ga and may be used to quantitatively constrain precipitation and aridity during early Mars.

Stucky De Quay, G.↗

Using Bayesian Networks for Candidate Generation in Consistency-based Diagnosis

Consistency-based diagnosis relies heavily on the assumption that discrepancies between model predictions and sensor observations can be detected accurately. When sources of uncertainty like sensor noise and model abstraction exist robust schemes have to be designed to make a binary decision on whether predictions are consistent with observations. This risks the occurrence of false alarms and missed alarms when an erroneous decision is made. Moreover when multiple sensors (with differing sensing properties) are available the degree of match between predictions and observations can be used to guide the search for fault candidates. In this paper we propose a novel approach to handle this problem using Bayesian networks. In the consistency- based diagnosis formulation, automatically generated Bayesian networks are used to encode a probabilistic measure of fit between predictions and observations. A Bayesian network inference algorithm is used to compute most probable fault candidates.

Narasimhan, Sriram↗

Efficient Probabilistic Diagnostics for Electrical Power Systems

We consider in this work the probabilistic approach to model-based diagnosis when applied to electrical power systems (EPSs). Our probabilistic approach is formally well-founded, as it based on Bayesian networks and arithmetic circuits. We investigate the diagnostic task known as fault isolation, and pay special attention to meeting two of the main challenges . model development and real-time reasoning . often associated with real-world application of model-based diagnosis technologies. To address the challenge of model development, we develop a systematic approach to representing electrical power systems as Bayesian networks, supported by an easy-to-use speci.cation language. To address the real-time reasoning challenge, we compile Bayesian networks into arithmetic circuits. Arithmetic circuit evaluation supports real-time diagnosis by being predictable and fast. In essence, we introduce a high-level EPS speci.cation language from which Bayesian networks that can diagnose multiple simultaneous failures are auto-generated, and we illustrate the feasibility of using arithmetic circuits, compiled from Bayesian networks, for real-time diagnosis on real-world EPSs of interest to NASA. The experimental system is a real-world EPS, namely the Advanced Diagnostic and Prognostic Testbed (ADAPT) located at the NASA Ames Research Center. In experiments with the ADAPT Bayesian network, which currently contains 503 discrete nodes and 579 edges, we .nd high diagnostic accuracy in scenarios where one to three faults, both in components and sensors, were inserted. The time taken to compute the most probable explanation using arithmetic circuits has a small mean of 0.2625 milliseconds and standard deviation of 0.2028 milliseconds. In experiments with data from ADAPT we also show that arithmetic circuit evaluation substantially outperforms joint tree propagation and variable elimination, two alternative algorithms for diagnosis using Bayesian network inference.

Mengshoel, Ole J.↗

Determining the Most Influencing Medical Conditions in MEDPRAT’s SIN Directed Graph

INTRODUCTION: The Susceptibility Inference Network (SIN) is a network of medical conditions, part of the Medical Extensible Probabilistic Risk Assessment Tool (MEDPRAT) developed by NASA to assess human health and medical risk to space exploration missions. The SIN is subject matter expert informed and acts as a prototype that provides relationships and dependencies between events modeled by MEDPRAT. Each vertex in the SIN has a weight which evaluates the severity of having the condition regardless of the progression from or to that condition. In this presentation, we consider two statistics to measure that stand alone risk: Quality Time Lost (QTL) and Loss of Crew Life (LOCL). Our goal is to identify the medical conditions that contribute the most to crew members QTL and LOCL risks due to progression of conditions in the network. We investigate how different computation parameters result in different condition rankings and address the choice of parameters that allows appropriate interventions to ensure space mission success. METHODS: The Katz score, one of many centrality measures created for ranking purposes in network analysis, takes into account all possible walks through the network, penalizing each additional step in a walk by a factor α called the Katz parameter. The literature does not provide specific values for the choice of α. We derive an analytical relationship between α and the maximum path length which has influence on the Katz score and ranking. Based on the probability of progression of each condition in the SIN, we identify that maximum path length of interest and calculate α that is then used in the Katz formula to rank the conditions in the SIN. RESULTS AND CONCLUSION: The effective probabilities of the SIN matrix generally fall below 10−6, which is below the level of the least influencing condition in the set. This corresponds to the probability of at most six consecutive progressions of a condition. Consequently, we calculate the Katz Parameter α and get 0.32. We rank the medical conditions and find that Acute Radiation Symptom is the condition the most prone to contribute to quality time loss due to progression.

risk analysis↗

Reveal, A General Reverse Engineering Algorithm for Inference of Genetic Network Architectures

Given the immanent gene expression mapping covering whole genomes during development, health and disease, we seek computational methods to maximize functional inference from such large data sets. Is it possible, in principle, to completely infer a complex regulatory network architecture from input/output patterns of its variables? We investigated this possibility using binary models of genetic networks. Trajectories, or state transition tables of Boolean nets, resemble time series of gene expression. By systematically analyzing the mutual information between input states and output states, one is able to infer the sets of input elements controlling each element or gene in the network. This process is unequivocal and exact for complete state transition tables. We implemented this REVerse Engineering ALgorithm (REVEAL) in a C program, and found the problem to be tractable within the conditions tested so far. For n = 50 (elements) and k = 3 (inputs per element), the analysis of incomplete state transition tables (100 state transition pairs out of a possible 10(exp 15)) reliably produced the original rule and wiring sets. While this study is limited to synchronous Boolean networks, the algorithm is generalizable to include multi-state models, essentially allowing direct application to realistic biological data sets. The ability to adequately solve the inverse problem may enable in-depth analysis of complex dynamic systems in biology and other fields.

Liang, Shoudan↗

Genetic Algorithm for Optimization of Neural Networks for Bayesian Inference of Model Uncertainty

The objective of this work was to develop a genetic optimization algorithm that can design a neural network capable of producing uncertainty estimates along with predictions. This algorithm is necessary because the inclusion of uncertainty modeling in a neural network greatly complicates the network’s design space, making the development of a converging model extremely difficult and time consuming. The genetic algorithm presented in this work uses a number of value ranges for various configurable neural network parameters to create a randomly generated population of network architectures. The initially generated population is then evolved over the course of several generations, with the best performing models breeding to produce novel network configurations. Mutations are randomly applied to the network designs to facilitate the development of adaptations beneficial to the task being performed. An experiment was conducted to validate the proposed algorithm, in which the genetic optimizer was tasked with producing a neural network capable of predicting the sound pressure level (SPL) resulting from jet-surface interaction (JSI) noise. The data used for this task was generated at the NASA Glenn Research Center in the Aero-Acoustic Propulsion Laboratory. Starting with an initial population size of 35 randomly generated networks, and evolved over the course of 10 generations, the genetic algorithm produced a design able to predict SPL as a result of JSI noise within 0.272 dB, on average.

Genetic algorithm↗

A Neural Network Approach to Infer Optical Depth of Thick Ice Clouds at Night

One of the roadblocks to continuously monitoring cloud properties is the tendency of clouds to become optically black at cloud optical depths (COD) of 6 or less. This constraint dramatically reduces the quantitative information content at night. A recent study found that because of their diffuse nature, ice clouds remain optically gray, to some extent, up to COD of 100 at certain wavelengths. Taking advantage of this weak dependency and the availability of COD retrievals from CloudSat, an artificial neural network algorithm was developed to estimate COD values up to 70 from common satellite imager infrared channels. The method was trained using matched 2007 CloudSat and Aqua MODIS data and is tested using similar data from 2008. The results show a significant improvement over the use of default values at night with high correlation. This paper summarizes the results and suggests paths for future improvement.

Minnis, P.↗

Use of Design of Experiments and Rule-Based Inference in Determining Neural Network Architectures for Loss of Control Detection

In this work, we describe methods for selecting the neural network architectures and input spaces to implement belief state inference on generic commercial transport aircraft. First, we highlight a case study on the planning, execution, and analysis of a set of experiments to determine the configurations of a conditional variational autoencoder (CVAE). We present a structured method that can be used in a number of aerospace applications, to optimize the structure and training parameters of the CVAE for belief state inference, using Design of Experiments (DOE) statistical methodologies. The motivation for this specific DOE was to identify the appropriate hyperparameters for measuring the CVAE reconstruction probability and latent space, such that the measurements can be used to infer qualitative state changes for the aircraft. We demonstrate that this process yields information about a trained neural network’s utility for this specific application, along with a quantifiable range of certainty. We execute 84 experiments using loss-of-control flight maneuver data from a NASA T-2 aircraft, demonstrating that this empirical process allows us to construct cheap and simple models with specific attributes amenable to belief state inference in aerospace applications. While theoretically, we could create a single CVAE with an input space the size of all measurable flight variables and environmental dynamics, it becomes intractable to use such a neural network in an in-situ intelligent multi-agent system. Using the recommendations from our case study, we introduce a technical approach for feasibly describing the belief space by (1) identifying significant statistical relationships among flight variables using rule induction, (2) using a set of rules that cover all features to define the input space of multiple CVAEs, and (3) forming a belief space based on the joint probability density of their collective latent spaces. This results in a series of relatively small matrix multiplications that can be performed in real time, as opposed to large matrix computations in a single CVAE. We demonstrate the application of this approach on the T-2 flight loss-of control experiments, using the architecture and hyperparameter recommendations from the case study. We compare the utilities of an individual CVAE trained on all flight variables and multiple CVAEs defined on subsets of flight variables for detecting qualitative changes in flight. We demonstrate that the use of multiple CVAEs with smaller input spaces permits the CVAE to capture more granular relationships in the latent space, permitting better state space characterization and loss-of-control detection.

Design of experiments↗

Network Analysis of Rodent Transcriptomes in Spaceflight

Network analysis methods leverage prior knowledge of cellular systems and the statistical and conceptual relationships between analyte measurements to determine gene connectivity. Correlation and conditional metrics are used to infer a network topology and provide a systems-level context for cellular responses. Integration across multiple experimental conditions and omics domains can reveal the regulatory mechanisms that underlie gene expression. GeneLab has assembled rich multi-omic (transcriptomics, proteomics, epigenomics, and epitranscriptomics) datasets for multiple murine tissues from the Rodent Research 1 (RR-1) experiment. RR-1 assesses the impact of 37 days of spaceflight on gene expression across a variety of tissue types, such as adrenal glands, quadriceps, gastrocnemius, tibalius anterior, extensor digitorum longus, soleus, eye, and kidney. Network analysis is particularly useful for RR-1 -omics datasets because it reinforces subtle relationships that may be overlooked in isolated analyses and subdues confounding factors. Our objective is to use network analysis to determine potential target nodes for therapeutic intervention and identify similarities with existing disease models. Multiple network algorithms are used for a higher confidence consensus.

genomics↗

Identifying Planetary Transit Candidates in TESS Full-frame Image Light Curves via Convolutional Neural Networks

The Transiting Exoplanet Survey Satellite(TESS)mission measured light from stars in∼75% of the sky throughout its 2 yr primary mission, resulting in millions of TESS 30-minute-cadence light curves to analyze in the search for transiting exoplanets. To search this vast data trove for transit signals, we aim to provide an approach that both is computationally efficient and produces highly performant predictions. This approach minimizes the required human search effort. We present a convolutional neural network, which we train to identify planetary transit signals and dismiss false positives. To make a prediction for a given light curve, our network requires no prior transit parameters identified using other methods. Our network performs inference on a TESS 30-minute-cadence light curve in∼5 ms on a single GPU, enabling large-scale archival searches. We present 181 new planet candidates identified by our network, which pass subsequent human vetting designed to rule out false positives.Our neural network model is additionally provided as open-source code for public use and extension

Gregory Olmschenk↗