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Evaluating the Efficacy of Conditional Variational Autoencoders in Generating Synthetic Single Nuclei RNA-Seq Data for Space Biology Research

Astronauts are subject to unique stressors during spaceflight, leading to changes in their cellular function. However, neither astronauts nor model organisms respond the same to spaceflight, and research implicates a contribution of omics components in differential responses. Understanding how gene expression affects astronaut health is critical for the success of long-term space missions, prompting interest in developing personalized predictive models leveraging artificial intelligence (AI) and machine learning (ML) techniques. Developing such models requires extensive data, which is challenging to obtain and share. This study explores the use of conditional variational autoencoders (CVAEs) to synthetically generate single-nuclei RNA-seq (snRNA-seq) data. CVAEs build on standard variational autoencoders (VAEs) by conditioning data generation on covariates like sample identity and mission parameters, enhancing the relevance of generated data for specific contexts. For our work, we built two CVAEs with varying degrees of sparsity to optimize both interpretability and generative power. We train and validate models on existing snRNA-seq data collected from the brain tissue of mice subjected to spaceflight conditions and their ground control counterparts. We evaluate model performance using statistical tests and visualizations to compare synthetic data to real data. We aim to demonstrate that these prototype CVAE architectures could be used in future space biology work and that this is a method worth further exploring.

Sarah Golts

Bayesian Model Selection for Reducing Bloat and Overfitting in Genetic Programming for Symbolic Regression

When performing symbolic regression using genetic programming, overfitting and bloat can negatively impact generalizability and interpretability of the resulting equations as well as increase computation times. A Bayesian fitness metric is introduced and its impact on bloat and overfitting during population evolution is studied and compared to common alternatives in the literature. The proposed approach was found to be more robust to noise and data sparsity in numerical experiments, guiding evolution to a level of complexity appropriate to the dataset. Further evolution of the population resulted not in overfitting or bloat, but rather in slight simplifications in model form. The ability to identify an equation of complexity appropriate to the scale of noise in the training data was also demonstrated. In general, the Bayesian model selection algorithm was shown to be an effective means of regularization which resulted in less bloat and overfitting when any amount of noise was present in the training data.

G F Bomarito

Bayesian Model Selection for Reducing Bloat and Overfitting in Genetic Programming for Symbolic Regression

When performing symbolic regression using genetic programming, overfitting and bloat can negatively impact generalizability and interpretability of the resulting equations as well as increase computation times. A Bayesian fitness metric is introduced and its impact on bloat and overfitting during population evolution is studied and compared to common alternatives in the literature. The proposed approach was found to be more robust to noise and data sparsity in numerical experiments, guiding evolution to a level of complexity appropriate to the dataset. Further evolution of the population resulted not in overfitting or bloat, but rather in slight simplifications in model form. The ability to identify an equation of complexity appropriate to the scale of noise in the training data was also demonstrated. In general, the Bayesian model selection algorithm was shown to be an effective means of regularization which resulted in less bloat and overfitting when any amount of noise was present in the training data.

Uncertainty quantification

Adaptive Pressure Profile Method to Locate the Isolator Shock Train Leading Edge Given Limited Pressure Information

To maximize the performance of high-speed air-breathing engines, such as dual-mode scramjets, the streamwise location of the shock train leading edge (STLE) is ideally placed as far upstream in the isolator as possible while avoiding engine unstart. Thus, it is of interest to quantify and control the STLE location as the vehicle travels along its flight trajectory. The STLE location is typically quantified using wall static pressure measurements but there are often restrictions on the number and placement of transducers, thus reducing the accuracy and overall capability of STLE detection methods. In this work, the Adaptive Pressure Profile (APP) method is introduced to address such sparsity concerns. This method is data driven and does not heavily rely on prior information about the flow regime or engine model. Instead, the \mname method uses real-time pressure measurements from a small number of transducers to adaptively learn the isolator pressure profile. This adaptively-learned profile is fit to the pressure data at each time instance to estimate STLE location. The \mname method produces accurate estimates even when (1) the STLE location is not bounded by two or more transducers or (2) when the STLE location is between two transducers that are situated several duct heights apart. Data from two direct-connect isolator models are used to evaluate the accuracy of the \mname method and demonstrate its robustness for different back-pressure scenarios and transducer configurations.

Robin L Hunt

Adaptive Pressure Profile Method to Locate the Isolator Shock Train Leading Edge Given Limited Pressure Information

To maximize the performance of high-speed air-breathing engines, such as dual-mode scramjets, the streamwise location of the shock train leading edge (STLE) is ideally placed as far upstream in the isolator as possible while avoiding engine unstart. Thus, it is of interest to quantify and control the STLE location as the vehicle travels along its flight trajectory. The STLE location is typically quantified using wall static pressure measurements but there are often restrictions on the number and placement of transducers, thus reducing the accuracy and overall capability of STLE detection methods. In this work, the Adaptive Pressure Profile (APP) method is introduced to address such sparsity concerns. This method is data driven and does not heavily rely on prior information about the flow regime or engine model. Instead, the \mname method uses real-time pressure measurements from a small number of transducers to adaptively learn the isolator pressure profile. This adaptively-learned profile is fit to the pressure data at each time instance to estimate STLE location. The \mname method produces accurate estimates even when (1) the STLE location is not bounded by two or more transducers or (2) when the STLE location is between two transducers that are situated several duct heights apart. Data from two direct-connect isolator models are used to evaluate the accuracy of the \mname method and demonstrate its robustness for different back-pressure scenarios and transducer configurations.

Robin Hunt

Contextualizing Air Traffic Management Conversations using Natural Language Understanding

Efficient management of air traffic and mitigation of delays depend on extracting actionable information from unstructured data, such as dialogues from the Federal Aviation Administration’s (FAA’s) Air Traffic Control System Command Center (ATCSCC) telecons. This study presents a pipeline utilizing Natural Language Processing (NLP) methods for Intent Classification (IC) and Slot Filling (SF) to identify and extract Traffic Management Initiatives (TMIs) from aviation-specific dialogues. We leveraged DeBERTa, a pre-trained transformer model, and fine-tuned it to the nuances of the aviation domain. Despite challenges posed by annotation complexities, the IC model achieved promising results with a weighted average F1-score of 0.81. Our results are close to those of human annotators, which demonstrates the model’s strong alignment with human-level performance. The SF model also showed strong performance, achieving a weighted F1-score of 0.97, which demonstrates its effectiveness in accurately predicting key slots. Our analysis revealed limitations in handling less frequent intents and slot labels due to data sparsity, motivating future efforts to adopt joint IC-SF modeling and data augmentation strategies. This research highlights the potential of domain-specific NLP to streamline decision-making in the aviation industry and improve the management of TMIs.

Air Traffic Control Management

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