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An experimental approach to validating a theory of human error in complex systems

The problem of 'human error' is pervasive in engineering systems in which the human is involved. In contrast to the common engineering approach of dealing with error probabilistically, the present research seeks to alleviate problems associated with error by gaining a greater understanding of causes and contributing factors from a human information processing perspective. The general approach involves identifying conditions which are hypothesized to contribute to errors, and experimentally creating the conditions in order to verify the hypotheses. The conceptual framework which serves as the basis for this research is discussed briefly, followed by a description of upcoming research. Finally, the potential relevance of this research to design, training, and aiding issues is discussed.

Morris, N. M.↗

A Machine Learning Approach to Improve Air Traffic Management Initiatives

Collaborating closely with commercial air carriers and related organizations, the Federal Aviation Administration(FAA) regulates air traffic and ensures the safety and efficiency of air operations. Air traffic controllers make strategic decisions, such as delaying, rerouting, or canceling flights, partly based on guidance provided by the FAA’s Air TrafficControl System Command Center (ATCSCC). The guidance includes, among other things, control measures known asTraffic Management Initiatives (TMIs) designed to enhance safety and improve operational efficiency. TMIs play a crucial role in managing the demand and capacity within the U.S. National Airspace System (NAS). Two major TMIs that are routinely used (primarily to mitigate the adverse effects of bad weather) are Ground Delay Programs (GDPs) andGround Stops (GSs). In a GDP, flights destined for airports facing thunderstorm activity experience delays at their origin airports. This proactive approach minimizes the risk of routing aircraft through hazardous weather conditions and also replaces (fuel burning) airborne delays with ground delays. In a GS, a temporary restriction is imposed on the departure or arrival of aircraft at a specific airport or within a designated airspace. Although other TMIs (e.g., miles-in-trail) are also implemented as part of (air) traffic flow management in the NAS, the focus of this work is on GDPs and GSs. Since TMIs, by design, lead to flight delays or cancellations, it is crucial to put in place the right set of parameters(e.g., scope and duration of the GDP). For example, when the end time of a GDP extends beyond what is necessary, it imposes unnecessary delays on departing flights. This situation could occur as a result of inaccurate prediction of the(required) duration of the GDP based on the weather forecast. On the other hand, if a GDP ends prematurely before the underlying capacity constraints are resolved at the destination airport, it may result in airborne holding. The delicate balance lies in matching the termination of the GDP precisely with the resolution of capacity constraints, avoiding both the imposition of unnecessary ground delays and the need for airborne holding due to premature program termination.Failing to specify the right parameters for TMIs also leads to flight delays, creating a significant obstacle in managing the increasing traffic volumes causing increased work load for the controllers. To address this issue, we propose the integration of Machine Learning (ML) models in the traffic flow management(TFM) pipeline. In current operations, decisions are made by human experts based on extensive training, historical patterns, available traffic and weather data. Since we have an abundance of data from past events that tell us the likely impact of various TMIs, by ingesting historical data, properly trained ML models can offer valuable insights and aid human decision-making. With the FAA increasingly exploring advanced analytics, ML emerges as a focal point for enhancing TFM within the National Airspace System (NAS). As a first step, this study aims to provide traffic controllers with decision-making support for the issuance and adjustment of TMIs. Data analytics and machine learning have been previously employed to address some of the challenges associated with TMIs. Numerous studies have concentrated on various facets of TMI issuance, exploring factors influencing TMI parameters, including arrival rate, airport capacity, and delay prediction. For example, using weather forecasts, several statistical methods were used to produce probabilistic capacity profiles which in conjunction with deterministic models provided insights into the GDP planning process [1–4]. The downside of using deterministic models is that they rely on fixed inputs and predetermined rules, which lack the ability to account for the inherent uncertainty and variability present in real-world scenarios. In a separate series of studies, researchers aimed to predict the occurrences of GDPs and GSs. The majority of these studies utilized various supervised learning methods, including Decision Trees, Naive Bayes, Support VectorMachines, and Random Forests to analyze the influence of weather conditions and arrival demand on TMI incidents[5–8]. However, these studies primarily focused on predicting the incidence of TMIs without explicitly addressing the scope of TMIs, including their duration and their geographical coverage. Furthermore, the emphasis of these studies was largely on GDPs, given their higher frequency and longer duration when compared to GSs. A limited number of studies focused on predicting the parameters of TMIs, specifically addressing their duration and extent. In one such study focusing on optimizing the TMI parameters at San Francisco International Airport (SFO),the authors utilized a probabilistic forecast of fog [9]. They simulated various capacity scenarios based on the (fog)burn-off forecasts, selecting GDP parameters that minimized airborne and overall ground delays. However, this approach exclusively emphasizes stratus (fog) burn-off as the primary determinant of GDP and GS, neglecting other influential factors like severe weather events, runway closures, lower capacity than traffic demand, and other important variables. Given the complexity of predicting the TMI and determining its scope, we seek a more holistic approach. We aim to consider all significant factors that could impact TMIs and their parameters. What sets this research apart is the fusion of all data sources relevant to the issuance and adjustment of TMIs and it represents the first comprehensive attempt to optimize TMIs in this manner. Since this comprehensive solution involves various aspects, we break down the problem into smaller components and input all parameters into a unified model called the “TMI Adjuster”. Figure 1 shows the overall framework and the list of datasets used in each model. The objective of the TMI Adjuster module is to deliver reliable, consistent and expedited recommendations for the progression, adjustment, and termination of TMIs. The ML solution entails developing a pipeline capable of predicting the necessity of a TMI (e.g., GS or GDP) along with its various parameters. For example, in the case of a GS, this includes the scope of the GS either in terms of distance from the destination airport or based on pre-defined airspace sectors. Here, scope refers to those regions and departing airports that are subject to the GS. In this paper, we concentrate on the issuance of GSs in the three major airports in the New York area — LaGuardia(LGA), John F. Kennedy International (JFK), and Newark Liberty International (EWR). We fuse traffic, weather and other relevant aviation data from years 2017 to 2019 to train and validate the ML models. In particular, we use the following datasets: •Terminal Aerodrome Forecast (TAF): meteorological forecasts specific to each airport, issued four times a day, covering predefined time periods. •TMI data: includes all GSs and GDPs along with their respective parameters. •Aviation System Performance Metrics (ASPM): includes traffic related data such as aircraft delays, arrival, and departure rates. •Notices to Airmen (NOTAMs): utilized to extract runway closure data and manage interdependencies between terminals in close proximity. •Flight cancellation data •Airspace Flow Programs (AFP): includes information on flight airborne holdings caused by TMIs. The data preprocessing entails transforming ASPM, TMI, AFP, NOTAMs, and weather data into an hourly format and consolidating all datasets by merging them based on date and time as the primary key. The TMI Adjuster framework comprises two parallel models: one dedicated to GS and a second model focused on GDP. As previously mentioned, our specific focus is on the GS model as a multi-classification problem. In this framework, each data point of the GS model input summarizes ten hours of data. Specifically, the data loader for the GS model generates the input and output of the model as follows: at a given time step, the input includes the actual traffic, weather, and TMI data from the two-hour window before the time step, alongside the weather forecast and scheduled traffic for the next 8 hours starting from the time step. Based on this information, the output of the GS model for each time interval consists of three dimensions. The first dimension represents a binary decision on whether there should be a GS in place for the next hour or not. The second dimension is related to the scope of the GS in the United States, and the third dimension is related to the scope of the GS in Canada (i.e., to determine if the GS impacts airports in Canada).One of the challenges with TMI modeling is the sparsity of TMI events, particularly regarding its scope. To address this challenge in the scope of the GS model output, we implement grouping. The GS scope for the US region is defined based on a list of centers that should be included when the GS is in place. With 20 centers in the US, we utilized historical data to group them into 4 categories. In particular, we summarized our historical data in a graph format where nodes represent centers, and link weights are defined based on the co-occurrence of centers in the scope parameter ofTMIs. By identified strongly connected components in this graph, we were able to partition the centers into four groups. We consider two model structures for the GS Model. Firstly, a hierarchical classification model [10], where the human decision-making for a GS is of hierarchical nature. The decision-maker first decides whether there is a need fora GS, and if the answer is yes, determines the scope. A hierarchical classification model organizes the problem into a class hierarchy, typically a tree or a Directed Acyclic Graph (DAG) structure, and considers the dependency of the decision in the previous step to the next component [10]. Here, we employ the local classifier per level approach, which involves training one multi-class classifier for each level of the class hierarchy. The second structure is the independent structure. In this setting, as the name suggests, we do not consider the dependency of the decisions in the different dimensions of the output of the model. Instead, for each dimension, we train a multi-class classifier independently. Table 1 summarizes GS model statistics for training, validation and testing. The table documents the effect of limiting data to the time steps when there was actually a TMI in place or when a TMI had just terminated. This resulted in a more balanced distribution of the GS class(GS positive class)versus “No GS”(GS negative class), which might help the training process. While JFK and LGA follow very similar distributions, with 40% and 42% GS positive class respectively, EWR has proportionally fewer GS incidents at 28%. Our subsequent phase involves evaluating the performance of both hierarchical structure and independent structure using different state-of-the-art multi-class classifier models such as Random Forest, Decision Trees, K-nearest Neighbors, and Logistic Regression and forecast the duration and scope of the GSs.

Farzan Masrour Shalmani↗

Evaluation of probabilistic photometric redshift estimation approaches for The Rubin Observatory Legacy Survey of Space and Time (LSST)

Many scientific investigations of photometric galaxy surveys require redshift estimates, whose uncertainty properties are best encapsulated by photometric redshift (photo-z) posterior probability density functions (PDFs). A plethora of photo-z PDF estimation methodologies abound, producing discrepant results with no consensus on a preferred approach. We present the results of a comprehensive experiment comparing twelve photo-z algorithms applied to mock data produced forLarge Synoptic Survey Telescope The Rubin Observatory Legacy Survey of Space and Time (lsst) Dark Energy Science Collaboration (desc). By supplying perfect prior information, in the form of the complete template library and a representative training set as inputs to each code, we demonstrate the impact of the assumptions underlying each technique on the output photo-z PDFs. In the absence of a notion of true, unbiased photo-z PDFs, we evaluate and interpret multiple metrics of the ensemble properties of the derived photo-z PDFs as well as traditional reductions to photo-z point estimates. Additionally, we report systematic biases and overall over/under-breadth of the photo-z PDFs of many popular codes, which may indicate avenues for improvement in the algorithms or implementations. Furthermore, we raise attention to the limitations of established metrics for assessing photo-z PDF accuracy; though we identify the conditional density estimate (CDE) loss as a promising metric of photo-z PDF performance in the case where true redshifts are available but true photo-z PDFs are not, we emphasize the need for science-specific performance metrics.

79 ASTRONOMY AND ASTROPHYSICS↗

Evaluate the impact of sensor accuracy on model performance in data-driven building fault detection and diagnostics using Monte Carlo simulation

The performance of data-driven fault detection and diagnostics (FDD) is heavily dependent on sensors. However, sensor inaccuracy and sensor faults are pervasive in building operation: inaccurate and missing sensor readings deteriorate FDD performance; sensor inaccuracy will also affect the selection of sensor for data-driven FDD in the model training process, which is another key factor of data-driven FDD performance. Sensor accuracy and sensor selection individually are well-studied research topics in this field, but the impact of sensor accuracy on sensor selection and its further impact on FDD performance has not been evaluated and quantified. In this paper, we developed a novel analysis methodology that comprehensively evaluates sensor fault on sensor selection and FDD accuracy. Monte Carlo simulation is applied to deal with multiple stochastic sensor inaccuracy and provide probabilistic analysis results of the impact of sensor inaccuracy on sensor selection and FDD accuracy. This methodology focuses on the net impact of fault states across a full sensor set. The developed methodology can be used for the early-stage sensor design and operation-stage sensor maintenance. Furthermore, a case study is conducted to demonstrate the analysis methodology using a commercial building model crated to Flexible Research Platform located at Oak Ridge National Laboratory, USA.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Combining biomarker and virus phylogenetic models improves HIV-1 epidemiological source identification

To identify and stop active HIV transmission chains new epidemiological techniques are needed. Here, we describe the development of a multi-biomarker augmentation to phylogenetic inference of the underlying transmission history in a local population. HIV biomarkers are measurable biological quantities that have some relationship to the amount of time someone has been infected with HIV. To train our model, we used five biomarkers based on real data from serological assays, HIV sequence data, and target cell counts in longitudinally followed, untreated patients with known infection times. The biomarkers were modeled with a mixed effects framework to allow for patient specific variation and general trends, and fit to patient data using Markov Chain Monte Carlo (MCMC) methods. Subsequently, the density of the unobserved infection time conditional on observed biomarkers were obtained by integrating out the random effects from the model fit. This probabilistic information about infection times was incorporated into the likelihood function for the transmission history and phylogenetic tree reconstruction, informed by the HIV sequence data. To critically test our methodology, we developed a coalescent-based simulation framework that generates phylogenies and biomarkers given a specific or general transmission history. Testing on many epidemiological scenarios showed that biomarker augmented phylogenetics can reach 90% accuracy under idealized situations. Under realistic within-host HIV-1 evolution, involving substantial within-host diversification and frequent transmission of multiple lineages, the average accuracy was at about 50% in transmission clusters involving 5–50 hosts. Realistic biomarker data added on average 16 percentage points over using the phylogeny alone. Using more biomarkers improved the performance. Shorter temporal spacing between transmission events and increased transmission heterogeneity reduced reconstruction accuracy, but larger clusters were not harder to get right. More sequence data per infected host also improved accuracy. We show that the method is robust to incomplete sampling and that adding biomarkers improves reconstructions of real HIV-1 transmission histories. The technology presented here could allow for better prevention programs by providing data for locally informed and tailored strategies.

60 APPLIED LIFE SCIENCES↗

Bi-fidelity variational auto-encoder for uncertainty quantification

Quantifying the uncertainty of quantities of interest (QoIs) from physical systems is a primary objective in model validation. However, achieving this goal entails balancing the need for computational efficiency with the requirement for numerical accuracy. To address this trade-off, we propose a novel bi-fidelity formulation of variational auto-encoders (BF-VAE) designed to estimate the uncertainty associated with a QoI from low-fidelity (LF) and high-fidelity (HF) samples of the QoI. Here, this model allows for the approximation of the statistics of the HF QoI by leveraging information derived from its LF counterpart. Specifically, we design a bi-fidelity auto-regressive model in the latent space which is integrated within the VAE’s probabilistic encoder–decoder structure. An effective algorithm is proposed to maximize the variational lower bound of the HF log-likelihood in the presence of limited HF data, resulting in the synthesis of HF realizations with a reduced computational cost. Additionally, we introduce the concept of the bi-fidelity information bottleneck (BF-IB) to provide an information-theoretic interpretation of the proposed BF-VAE model. Our numerical results demonstrate that the BF-VAE leads to considerably improved accuracy, as compared to a VAE trained using only HF data, when limited HF data is available.

42 ENGINEERING↗

A Probabilistic Reasoner Based on Bayes Risk for Damage Detection in Structural Systems

Structural health monitoring (SHM) systems are used to inform operation of structural systems subject to loads and environments that may affect their integrity. SHM systems rely on continuous monitoring of the structure to determine its health state. These systems are often coupled with a model of the deployed structure to determine the consequences of changes in the system by forecasting the response to future states. These models, which may be thought of as digital twins, need to be updated to reflect the latest state of the structural system. This work makes use of an uncertainty-aware machine learning model that enforces distance preservation of the original input space to determine deviations from the training data input space distributions. This workflow enables domain shift detection to determine whether damage is present in the structure. The uncertainty metrics generated by this network are then used in a Bayes risk framework to design an optimal damage detector given cost and risk considerations. The approach is demonstrated on a computational example with simulated damage.

Najera-Flores, David [ATA Engineering, Inc.]↗

IMPACTing Medical System Design with a Risk Analysis Tool [“IMPACT” sur la Conception du Système Médical avec un Outil d'Analyse des Risques]

Background: Following the success of Artemis I, NASA is preparing for human extended duration missions. Ongoing efforts are focused on mitigating mission-related risks, including those affecting crew health and performance. Communication latency, logistics of resupply and time frame of medical evacuation are barriers to provision of healthcare for these missions, especially with respect to constraints in mass, volume, and crew training. An in-depth assessment of medical risks, capabilities and resources for a specific mission design is necessary to determine an optimal balance that maximizes likelihood of mission success. Overview: IMPACT (Informed Mission Planning via Analysis of Complex Tradespaces) is a dynamic tool designed to estimate medical risk and outcomes for a specific mission design. In its current iteration, a list of medical conditions selected based on likelihood of occurrence and/or consequence was linked to a set of clinical capabilities and resources necessary for diagnosis and management. A probabilistic risk analysis tool was then used to identify and estimate the likelihood and consequence of risks through the following outcome metrics: loss of crew life (inflight mortality due to medical conditions), need for medical evacuation (return to definitive care), and crew disability (task time affected based on how medical conditions influence the ability to perform specific exploration mission crew tasks). Finally, the model’s optimization algorithm provides recommendations for medical capabilities that maximize risk mitigation relative to mass and volume constraints. In the Spring of 2023, IMPACT was utilized to estimate outcome metrics for a design reference mission that would be representative of an extended duration Artemis mission. Notional data generated were then used to determine a recommended set of medical capabilities and resources relative to user-defined mass and volume constraints. A multidisciplinary team has also been updating IMPACT to strengthen the model’s fidelity. Figure 1 shows how updates to outcome metric inputs for the conditions resulted in different capability and resource allocation recommendations. Discussion: This presentation will discuss the IMPACT tool and share the latest data generated for a representative extended duration Artemis mission. Efforts to improve the fidelity of data generated by the model’s algorithm will also be discussed.

K A Shair↗

IMPACTing Medical System Design with a Risk Analysis Tool

Background: Following the success of Artemis I, NASA is preparing for human extended duration missions. Ongoing efforts are focused on mitigating mission-related risks, including those affecting crew health and performance. Communication latency, logistics of resupply and time frame of medical evacuation are barriers to provision of healthcare for these missions, especially with respect to constraints in mass, volume, and crew training. An in-depth assessment of medical risks, capabilities and resources for a specific mission design is necessary to determine an optimal balance that maximizes likelihood of mission success. Overview: IMPACT (Informed Mission Planning via Analysis of Complex Tradespaces) is a dynamic tool designed to estimate medical risk and outcomes for a specific mission design. In its current iteration, a list of medical conditions selected based on likelihood of occurrence and/or consequence was linked to a set of clinical capabilities and resources necessary for diagnosis and management. A probabilistic risk analysis tool was then used to identify and estimate the likelihood and consequence of risks through the following outcome metrics: loss of crew life (inflight mortality due to medical conditions), need for medical evacuation (return to definitive care), and crew disability (task time affected based on how medical conditions influence the ability to perform specific exploration mission crew tasks). Finally, the model’s optimization algorithm provides recommendations for medical capabilities that maximize risk mitigation relative to mass and volume constraints. In the Spring of 2023, IMPACT was utilized to estimate outcome metrics for a design reference mission that would be representative of an extended duration Artemis mission. Notional data generated were then used to determine a recommended set of medical capabilities and resources relative to user-defined mass and volume constraints. A multidisciplinary team has also been updating IMPACT to strengthen the model’s fidelity. Figure 1 shows how updates to outcome metric inputs for the conditions resulted in different capability and resource allocation recommendations. Discussion: This presentation will discuss the IMPACT tool and share the latest data generated for a representative extended duration Artemis mission. Efforts to improve the fidelity of data generated by the model’s algorithm will also be discussed.

K A Shair↗

Machine-Learning-Based Adaptive Thinning of CrIS Radiances to Improve Global Tropical Cyclone Analysis and Forecasts

This work is focused on optimizing the assimilation of hyperspectral infrared (IR) radiances from the Cross-track Infrared Sounder (CrIS) with the goal of improving the representation of tropical cyclones (TCs) in global analyses and forecasts. Current operational assimilation systems rely on subsampling IR radiances on a regular thinning grid. A new and improved adaptive methodology based on machine learning (ML) recognizes TCs from geostationary satellite imagery and is implemented in the Goddard Earth Observing System (GEOS) model and data assimilation framework. The ML methodology is extensively trained on existing TC data sets and creates for each TC a dynamic mask, based on the evolving shape and life cycle of that specific event. Once a TC mask is created, a switch is then activated in the data assimilation system to alter the thinning, ingesting more CrIS radiances within the moving mask, thus increasing the TC sampling. After the TC dissipates, the assimilation of CrIS radiances reverts to normal data density. Results of TC segmentation provided by a state-of-the-art generative machine learning model known as the Denoising Diffusion Probabilistic Model (DDPM) are compared to the previously used U-Net model. The new approach surpasses the performance of the previously developed one. The methodology is applied to both clear-sky and cloud-cleared radiances. Benefits from the latter methodology, particularly in improving the structure of TCs and the intensity forecasts, are presented.

Oreste Reale↗

Analysis of human performance differences between students and operators when using the Rancor Microworld simulator

Here, from within the umbrella of the Simplified Human Error Experimental Program (SHEEP) framework, this paper analyzes human performance differences between professional and student operators when using a simplified simulator (i.e., Rancor Microworld). This paper represents a crucial step in understanding the fidelity of the simplified simulators and student operators within the SHEEP study. This paper explores a randomized factorial experimental design that features two independent variables: participant type and event class. Six human performance measurements are considered in the experiment. The experiment is conducted using 20 professional reactor operators employed at actual nuclear power plants (NPPs), along with 20 trained students. The experimental data are analyzed via statistical analysis methods. Finally, this paper examines the differences in human performance between actual operators and students when using Rancor Microworld.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

The Integrated Medical Model: A Risk Assessment and Decision Support Tool for Space Flight Medical Systems

The Integrated Medical Model (IMM) is a decision support tool that is useful to mission planners and medical system designers in assessing risks and designing medical systems for space flight missions. The IMM provides an evidence based approach for optimizing medical resources and minimizing risks within space flight operational constraints. The mathematical relationships among mission and crew profiles, medical condition incidence data, in-flight medical resources, potential crew functional impairments, and clinical end-states are established to determine probable mission outcomes. Stochastic computational methods are used to forecast probability distributions of crew health and medical resource utilization, as well as estimates of medical evacuation and loss of crew life. The IMM has been used in support of the International Space Station (ISS) medical kit redesign, the medical component of the ISS Probabilistic Risk Assessment, and the development of the Constellation Medical Conditions List. The IMM also will be used to refine medical requirements for the Constellation program. The IMM outputs for ISS and Constellation design reference missions will be presented to demonstrate the potential of the IMM in assessing risks, planning missions, and designing medical systems. The implementation of the IMM verification and validation plan will be reviewed. Additional planned capabilities of the IMM, including optimization techniques and the inclusion of a mission timeline, will be discussed. Given the space flight constraints of mass, volume, and crew medical training, the IMM is a valuable risk assessment and decision support tool for medical system design and mission planning.

Kerstman, Eric↗

Probabilistic predictions and uncertainty estimation for radiological and nuclear effects modeling

Better characterization of meteorological uncertainty is needed to predict the effects of radiological and nuclear releases in the atmosphere. Multi-physics ensembles of atmospheric simulations can estimate uncertainty of physical processes, but they are often limited for computational reasons. Because weather uncertainty is important for emergency response applications, but the conventional way of running multi-physics ensembles is infeasible, we have developed new machine learning-based methods that quickly estimate and identify key sources of meteorological uncertainty. Machine learning accelerates the analysis of weather uncertainty by iteratively learning about model physics options that affect plume predictions. We have demonstrated the power of machine learning by creating a large multi-physics weather and dispersion ensemble dataset containing 1,200 simulations for two hypothetical radiological release scenarios. By training on less than 10% of the ensemble, we can quickly and accurately predict different outcomes, including the mass of radiological material deposited and spatial distribution and extent of contaminated areas.

54 ENVIRONMENTAL SCIENCES↗

Scalable statistical inference of photometric redshift via data subsampling

Handling big data has largely been a major bottleneck in traditional statistical models. Consequently, when accurate point prediction is the primary target, machine learning models are often preferred over their statistical counterparts for bigger problems. But full probabilistic statistical models often outperform other models in quantifying uncertainties associated with model predictions. We develop a data-driven statistical modeling framework that combines the uncertainties from an ensemble of statistical models learned on smaller subsets of data carefully chosen to account for imbalances in the input space. We demonstrate this method on a photometric redshift estimation problem in cosmology, which seeks to infer a distribution of the redshift—the stretching effect in observing the light of far-away galaxies—given multivariate color information observed for an object in the sky. Our proposed method performs balanced partitioning, graph-based data subsampling across the partitions, and training of an ensemble of Gaussian process models.

data subsampling↗

NaroNet: Discovery of tumor microenvironment elements from highly multiplexed images

Understanding the spatial interactions between the elements of the tumor microenvironment -i.e. tumor cells. fibroblasts, immune cells- and how these interactions relate to the diagnosis or prognosis of a tumor is one of the goals of computational pathology. We present NaroNet, a deep learning framework that models the multi-scale tumor microenvironment from multiplex-stained cancer tissue images and provides patient-level interpretable predictions using a seamless end-to-end learning pipeline. Trained only with multiplex-stained tissue images and their corresponding patient-level clinical labels, NaroNet unsupervisedly learns which cell phenotypes, cell neighborhoods, and neighborhood interactions have the highest influence to predict the correct label. To this end, NaroNet incorporates several novel and state-of-the-art deep learning techniques, such as patch-level contrastive learning, multi-level graph embeddings, a novel max-sum pooling operation, or a metric that quantifies the relevance that each microenvironment element has in the individual predictions. We validate NaroNet using synthetic data simulating multiplex-immunostained images where a patient label is artificially associated to the -adjustable- probabilistic incidence of different microenvironment elements. We then apply our model to two sets of images of human cancer tissues: 336 seven-color multiplex-immunostained images from 12 high-grade endometrial cancer patients; and 382 35-plex mass cytometry images from 215 breast cancer patients. In both synthetic and real datasets, NaroNet provides outstanding predictions of relevant clinical information while associating those predictions to the presence of specific microenvironment elements.

60 APPLIED LIFE SCIENCES↗

Estimating the Rate of Occurrence of Renal Stones in Astronauts

Changes in urine chemistry, during and post flight, potentially increases the risk of renal stones in astronauts. Although much is known about the effects of space flight on urine chemistry, no inflight incidence of renal stones in US astronauts exists and the question "How much does this risk change with space flight?" remains difficult to accurately quantify. In this discussion, we tackle this question utilizing a combination of deterministic and probabilistic modeling that implements the physics behind free stone growth and agglomeration, speciation of urine chemistry and published observations of population renal stone incidences to estimate changes in the rate of renal stone presentation. The modeling process utilizes a Population Balance Equation based model developed in the companion IWS abstract by Kassemi et al. (2016) to evaluate the maximum growth and agglomeration potential from a specified set of urine chemistry values. Changes in renal stone occurrence rates are obtained from this model in a probabilistic simulation that interrogates the range of possible urine chemistries using Monte Carlo techniques. Subsequently, each randomly sampled urine chemistry undergoes speciation analysis using the well-established Joint Expert Speciation System (JESS) code to calculate critical values, such as ionic strength and relative supersaturation. The Kassemi model utilizes this information to predict the mean and maximum stone size. We close the assessment loop by using a transfer function that estimates the rate of stone formation from combining the relative supersaturation and both the mean and maximum free stone growth sizes. The transfer function is established by a simulation analysis which combines population stone formation rates and Poisson regression. Training this transfer function requires using the output of the aforementioned assessment steps with inputs from known non-stone-former and known stone-former urine chemistries. Established in a Monte Carlo system, the entire renal stone analysis model produces a probability distribution of the stone formation rate and an expected uncertainty in the estimate. The utility of this analysis will be demonstrated by showing the change in renal stone occurrence predicted by this method using urine chemistry distributions published in Whitson et al. 2009. A comparison to the model predictions to previous assessments of renal stone risk will be used to illustrate initial validation of the model.

gravitational physiology↗

A Probabilistic Approach To Selecting Build Configurations in Package Managers

In the past decade software has grown significantly in complexity and scale. Likewise the number of dependencies for most software has increased with typical software packages depending on tens to hundreds of other packages. Such large numbers of dependencies place a significant burden on package managers to correctly maintain dependency lists and constraints between them. Due to this package managers have incorporated sophisticated tooling such as SAT solvers into their dependency management mechanisms. Despite these tools package managers still rely on many human annotated constraints for dependency and version selection. These are error-prone and require a significant amount of labor to constantly update and test. In this paper we propose a methodology to make use of historical build results in selecting the version for package dependencies. Our method utilizes the flexibility of the Spack package manager’s heavily parameterized package configurations to incorporate a machine learning model trained to predict the probability of build outcomes. This work is able to build and install packages with a 13% higher success rate than the default version selection mechanism in Spack.

97 MATHEMATICS AND COMPUTING↗

Probabilistic Inference of Low-Surface-Brightness Galaxy Morphological Parameters Using Simulation-Based Inference

Low-surface-brightness galaxies (LSBGs) are diffuse, often dark-matter-dominated systems whose faintness makes their structural parameters difficult to measure reliably in wide-field imaging surveys. Robust parameter inference, including uncertainty quantification, is important for population studies and for comparisons with models of galaxy formation, as future surveys are expected to produce increasingly large samples of diffuse galaxies. In practice, LSBG profile modeling is sensitive to sky- background errors, masking choices, contaminating background sources, and the computational cost of obtaining posterior-level uncertainties for large samples. Motivated by these questions, we develop a simulation-based inference (SBI) framework for estimating posterior distributions of LSBG morphological parameters from simulated galaxy images. Using PyImfit, we generate DES-like single-Sersic profile LSBG images with known position angle, ellipticity, Sersic index, effective surface brightness, and effective radius. We then train a normalizing-flow-based neural posterior estimator using the sbi package to infer these parameters from the simulated images. For isolated simulated galaxies, the SBI posterior recovers the true input parameters, produces posterior predictive residuals consistent with the assumed noise model, and shows good empirical calibration in a DES-motivated test regime. We also compare SBI with PyImfit-based MCMC inference and find broadly comparable posterior constraints, while SBI enables substantially faster posterior sampling after training. Finally, we test robustness to compact background contaminants. A model trained only on isolated galaxies produces undercovered posteriors on contaminated images, whereas training on simulations with variable contaminant positions and fluxes improves calibration across contaminated test sets. These results demonstrate the promise of SBI for scalable, uncertainty-aware LSBG morphology inference, while emphasizing that posterior reliability strongly depends on whether training simulations include relevant observational complications.

Batbayar, Bilguun [U. Chicago (main)]↗