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Increasing accessibility to deep learning-based analytics for space biology: pretrained models, transfer learning, and analytics platform development

Biological systems react in complex ways to the stressors of spaceflight, and the data capturing these relationships is concomitantly high-dimensional and complex. Deep learning and machine learning approaches are increasingly popular as an analytical approach for space biosciences, due to their ability to model complex relationships in complex data. However, such approaches often require large datasets and extensive computational resources. New approaches that minimize data sizes and computational power needed to leverage machine learning, and resources that make these approaches accessible, are needed to increase accessibility and adoption of machine learning in the space biosciences. Transfer learning, in which a pretrained model of broad utility is trained on a large dataset, and subsequently reused on downstream applications for which data is more limited, is one approach to minimizing data and computational intensity of deep learning applications. This transfer learning approach results in more performant models in high-dimensional, low-sample-size settings such as space biology, as compared to training models on limited data from scratch. This presentation will outline efforts to generate pretrained models for the space biology community, and highlight transfer learning applications modeling microbial antibiotic resistance during spaceflight. Finally, in order to increase accessibility of these models and tools, as well as others, for the broader space biology community, we present a modeling and analysis platform facilitating machine learning applications in space biology. This platform streamlines machine learning training and analysis in a notebook format, facilitates download and use of space biology data from the NASA GeneLab database, and can be utilized on NASA-hosted servers or downloaded and hosted locally. This effort, as part of the AI4LS (Artificial Intelligence for Life in Space) working group, will increase accessibility, feasibility, and performance of machine learning approaches for the space biology community.

Adrienne Hoarfrost

Quantum Hardware-Enabled Molecular Dynamics via Transfer Learning

The ability to perform ab initio molecular dynamics simulations using potential energy surfaces provided by quantum computers would open the door to virtually exact dynamics for a variety of chemical and biochemical systems, with impacts on catalysis and biophysics. Nonetheless, performing molecular dynamics on surfaces produced by quantum hardware has been hampered by the noisy energies typically produced by quantum computers and challenges associated with computing gradients and scaling to large systems interest. A recent set of advances in machine learning, known as transfer learning, provides a new path forward for molecular dynamics simulations on quantum hardware. Transfer learning offers a workaround, where one first trains models on larger, less accurate classical datasets and then refines them on smaller, more accurate quantum datasets. We explore this approach by training machine learning models to predict a molecule's potential energy based on its geometric structure using Behler-Parrinello neural networks. When successfully trained, the model enables energy gradient predictions necessary for dynamic simulations. To reduce the quantum resources needed, the model is initially trained with data derived from classical density functional theory and subsequently refined with a smaller dataset obtained from a variational quantum eigensolver optimization of the unitary coupled cluster ansatz. We show that this approach significantly reduces the size of the needed quantum training dataset while capturing the high accuracies needed within quantum chemistry simulations. The success of this two-step training method opens more opportunities to apply machine learning models on quantum data, a significant stride towards efficient quantum-classical hybrid computational models.

quantum computing

Onboard Hyperspectral Image Classification via Transfer Learning for Communication-Limited Spacecraft

Employing deep-learning and artificial-intelligence (AI) techniques onboard spacecraft can dramatically improve priority data selection to ensure more effective use of the available downlink. However, deployment of effective deep-learning models requires significant training on the ground, which may not be feasible, due to limited data available in an unexplored environment. Therefore, this research explores building robust classification models for onboard data processing where training data is highly limited using transfer-learning techniques. In this paper, we focus on the use case of hyperspectral imaging for remote sensing, a domain where the high dimensionality of the data from the sensor can rapidly saturate the downlink bandwidth. With this bottleneck, there is an impending need to autonomously and robustly classify data onboard to optimize downlink of high-impact measurements, thus maximizing the scientific utility per bit transmitted to the ground. This paper examines the use of deep neural networks onboard for hyperspectral image classification in a communication-limited scenario to analyze how the models perform with limited training data. The use of transfer learning can ameliorate the issue of poor generalization by transferring features learned from training on a large source dataset for one classification task to the target classification task with limited training data. For two deep-learning models from literature, we compare the accuracy of the models trained using transfer learning to models trained from scratch using a random weight initialization with varying amounts of training data. We demonstrate the feasibility and performance of running inference of the deep-learning models on representative flight-like hardware.

Advanced Avionics, Machine Learning, Data Processi

GEONEX: Progressive Conditional Generative Adversarial Training Using Transfer learning

Obtaining accurate segmentation on large scale images is an open problem in deep learning. The main problem is the amount of labeled data that exists for large scale images. Traditionally, the common solution to this problem is to crop the large images into smaller images to increase the amount of available data and train a Conditional Generative Adversarial Network (CGAN). CGANs are currently the state of the art in image to image translation and provide better accuracy than the traditional method of training a encoder based conv-net architecture to minimize the loss at each pixel. This method can produce noisy and discontinuous images with inaccurate results. We seek to solve this problem by utilizing the concepts of transfer learning and progressive training to create a CGAN that can segment large scale images with a limited amount of labeled data. In transfer learning we recognize that many learned features are applicable to many classes from multiple domains. This introduces the concept of feature reusability, which is the basis for finetuning. Progressive training got its start in training models on the same images at different resolutions. In this work we instead train a GAN on increasing image scales by transferring the weights from the smaller scales to the larger scales. The learned features at the smaller scales are continually reused and applied to larger scales to create a CGAN that can perform accurate segmentation on large scale images. We apply this method to detect building footprints on very high-resolution overhead imagery (e.g Digital Globe and high resolution airborne platforms).

GEONEX

Transfer Learning to Generate True Color Images from GOES-16

Along with scientific applications, Geostationary imagery is often used to learn about weather patterns through true color visualizations. NOAA/NASA's GOES-R series of satellites uses the advanced baseline imager with 16-bands which, unlike previous generations, does not include the green wavelength (500-565 nm) and hence cannot directly generate true color images. However, Himawari, Japan's geostationary satellite, uses a similar 16-band advanced Himawari imager that does include a green band (but missing cirrus). In this work, we show how transfer learning with convolutional neural networks can be applied across satellites to generate "virtual sensors". We apply this approach to generate a green band for GOES-16 and present near true color images.

transfer learning

Satellite-Derived Imagery and Transfer Learning: A Novel Technique for Land Cover Classification

Land cover classification is a continuing research topic due to its relevance to land use and land cover changes from impacts such as climate change, agriculture, urbanization, and hazardous weather. Simple access to frequently changing land cover classifications could provide knowledge and decision support to various researchers and agencies across the globe for each of above-mentioned and related influences. This research aims to provide a novel technique for land cover classification of remote sensing imagery; harnessing Artificial Neural Networks and transfer learning (TL). Knowledge sharing techniques within machine learning are typically utilized when training datasets are sparse or transitions between data modalities is required. In this case, two data modalities, multi and hyperspectral data, are considered for knowledge transfer. The large number of continuous spectral bands available from hyperspectral sensors typically provide increased sophisticated land classification capability compared to more traditional multispectral imagery with limited discrete spectral bands. However, large-scale, frequent access to hyperspectral imagery is relatively limited. The proposed classification technique would therefore prove useful in regions in which hyperspectral data are not readily available for classification but multispectral data are. Image segmentation models are trained on each multi and hyperspectral datasets. Knowledge sharing techniques are then applied to each model to understand what knowledge, if any, is gained when moving between the data modalities. The datasets utilized for training and testing a U-Net model include the European Space Agency’s multispectral imager Sentinel-2 and the hyperspectral German Aerospace Center’s Earth Sensing Imaging Spectrometer (DESIS). Initially, only two classes, land and water, are classified for simplicity. However, more complex classes can be added if knowledge sharing is successful. The workflow for image classification through supervised image segmentation with a U-Net model will be discussed along with metrics calculated before and after TL for both Sentinel-2 and DESIS data are applied. Additionally, future steps to advance the sophistication of this technique as well as other applicable methodologies will be explored.

Emily Foshee

Impact Ice Microstructure Segmentation Using Transfer Learned Model

A process of using machine learning to segment impact ice microstructure is presented and analyzed. The segmentation was conducted with the goal of obtaining average grain size estimations. The model was trained on a set of micrographs of impact ice grown at NASA Glenn’s Icing Research Tunnel. The model leveraged a model pre-trained on a large set of micrographs of various materials as a starting point. Post-processing of the segmented images was done to connect broken boundaries. An automatic method of determining grain size following an ASTM standard was implemented. Segmentation results using different training sets as well as different encoder and decoder pairs are presented. Calculated sizes are compared to manual grain size measurement methods. Results show promise in accuracy as well as a possible improvement in repeatability and consistency. Next steps for improving the model are suggested.

Machine learning

Biological Research and Space Health Enabled by Machine Learning to Support Deep Space Missions

A key science goal of the NASA “Moon to Mars” campaign is to understand how biology responds to the Lunar, Martian, and deep space environments in order to advance fundamental knowledge, reduce risk, and support safe, productive human space missions. Through the powerful emerging computer science approaches of artificial intelligence (AI) and machine learning (ML), a paradigm shift has begun in biomedical science and engineered astronaut health systems, to enable Earth-independence and autonomy of mission operations. We present a decadal view of AI/ML architecture to support deep space mission goals, developed in concert with leaders in the field. We describe current AI/ML methods to support 1) fundamental biology, 2) in situ analytics, 3) high performance computing hardware, 4) automated science, 5) self-driving labs, 6) remote data management, 7) integrated real-time mission biomonitoring, and 8) a Precision Space Health system. Cutting-edge AI/ML approaches that can be integrated to support these domains include active learning, explainable AI, adaptive learning, causal inference, knowledge graphs, federated learning, transfer learning, and large language models. Finally, we present results from several current ML projects that are underway in the field to address key challenges of small sample n, high feature count, heterogeneity, and sparse data. These include 1) connecting omics data to phenotypic data using an ensemble model to infer causality of spaceflight rodent liver health disruption, 2) usage of explainable ML to interrogate the muscular underpinnings of spaceflight muscle atrophy, 3) ML models analyzing and determining directed acyclic graphs of human space health risk leveraging rodent bone datasets, 4) usage of large pre-trained models connecting biomedical knowledgebases with small spaceflight datasets to understand gene-to-gene interaction networks, and 5) a suite of benchmarked open science datasets (spaceflight mouse liver; radiation DNA damage) enabling programmers to identify the best ML algorithms to answer space biological science questions.

space biology

Biological Research and Space Health Enabled by Machine Learning to Support Deep Space Missions

A key science goal of the NASA “Moon to Mars” campaign is to understand how biology responds to the Lunar, Martian, and deep space environments in order to advance fundamental knowledge and support human space missions. Through artificial intelligence (AI) and machine learning (ML), a paradigm shift has begun in space biosciences and engineered astronaut health systems, to enable Earth-independence and mission operations autonomy. We describe current AI/ML methods to support 1) fundamental biology, 2) in situ analytics, 3) high performance computing, 4) automated science, 5) self-driving labs, 6) remote data management, 7) integrated mission biomonitoring, and 8) a Precision Space Health system. AI/ML approaches that can be integrated to support these domains include active learning, explainable AI, adaptive learning, causal inference, knowledge graphs, federated learning, transfer learning, and large language models. Finally, we present results from several current ML projects that are underway in the space biology field to address key challenges of small sample n, high feature count, heterogeneity, and sparse data. These include 1) connecting omics to phenotypic data using an ensemble model to infer causality of rodent liver health disruption, 2) usage of explainable ML to interrogate muscular underpinnings of muscle atrophy, 3) ML models analyzing and determining directed acyclic graphs of human health risk leveraging rodent bone datasets, 4) usage of large pre-trained models connecting biomedical knowledgebases with small spaceflight datasets to understand gene-to-gene interactions, and 5) a suite of benchmarked open science datasets enabling programmers to identify best algorithms to answer space biology questions.

space biology

Biological Research and Space Health Enabled by Machine Learning to Support Deep Space Missions

A key science goal of the NASA “Moon to Mars” campaign is to understand how biology responds to the Lunar, Martian, and deep space environments in order to advance fundamental knowledge, reduce risk, and support safe, productive human space missions. Through the powerful emerging computer science approaches of artificial intelligence (AI) and machine learning (ML), a paradigm shift has begun in biomedical science and engineered astronaut health systems, to enable Earth-independence and autonomy of mission operations. We present a decadal view of AI/ML architecture to support deep space mission goals, developed in concert with leaders in the field. We describe current AI/ML methods to support 1) fundamental biology, 2) in situ analytics, 3) high performance computing hardware, 4) automated science, 5) self-driving labs, 6) remote data management, 7) integrated real-time mission biomonitoring, and 8) a Precision Space Health system. Cutting-edge AI/ML approaches that can be integrated to support these domains include active learning, explainable AI, adaptive learning, causal inference, knowledge graphs, federated learning, transfer learning, and large language models. Finally, we present results from several current ML projects that are underway in the field to address key challenges of small sample n, high feature count, heterogeneity, and sparse data. These include 1) connecting omics data to phenotypic data using an ensemble model to infer causality of spaceflight rodent liver health disruption, 2) usage of explainable ML to interrogate the muscular underpinnings of spaceflight muscle atrophy, 3) ML models analyzing and determining directed acyclic graphs of human space health risk leveraging rodent bone datasets, 4) usage of large pre-trained models connecting biomedical knowledgebases with small spaceflight datasets to understand gene-to-gene interaction networks, and 5) a suite of benchmarked open science datasets (spaceflight mouse liver; radiation DNA damage) enabling programmers to identify the best ML algorithms to answer space biological science questions.

space biology

Machine Learning Explainability and Transferability for Path Navigation

Deep neural networks are powerful tools for machine perception. Unfortunately their decisions are difficult to explain due to the complexity and size of the networks. Previously we have alleviated this issue by using the representational portion of a deep neural network and combining it with a k-nearest neighbor (KNN) classifier. Through inspection of the decisions made by the KNN, we can directly see the training data responsible for the decisions, allowing us to determine the quality of the overall decision and the quality of the representational layer of the deep NN. While the technique worked well, it requires tens of thousands of latent vectors to be stored for classification. In addition, it lacks the ability to show how parts of an image influence the classification decision. Here we address these issues by 1) Using a radial basis function network (RBFN) in place of the KNN allowing far fewer images to be used in deployment and 2) Using an auto encoder network for explainability. In addition to these techniques, we examine the effects of transfer learning to determine that results are robust. All results are tested on a domain where an unmanned aerial vehicle (UAV) navigates a forest trail through a single camera.

explainable machine learning

From Simulation to Reality With Random Noise

The challenging environment of autonomous vehicle (AV) navigation necessitates certain functions be performed by deep neural networks. Optimizing these models involves collecting vast quantities of domain-specific training data and ensuring that the dataset is representative of expected conditions. High-fidelity simulation plays a vital role in making this process feasible, allowing a wide range of scenarios to be explored at low cost. However, learning from simulation introduces subtle biases into models, which can degrade real-world performance in unpredictable ways. This effect can be mitigated with learning schemes specialized to bridge distributional shifts (transfer learning). Given the complex nature of these methods, the underlying models, and their environments, meaningfully evaluating performance is notstraight forward. Many unrelated factors can effect an improvement in generalization accuracy, but a full ablation analysis is often difficult. To tease out signal from noise, it is necessary to understand how transfer learning performance is affected by noise itself. The goals of this paper are (i) to establish a domain randomization baseline for a simple classification transfer learning task and (ii) to validate the RRAV testbed as a platform for further research in sim-to-real learning. We generate imagery from a simulation of NASA Ames Research Center and train a small convolutional neural network (ConvNet) to classify position relative to a centerline. Further models are trained with different types of noise progressively added to the data. The models are deployed aboard the on-site test vehicle to test real-world performance. In our experiments, we find that such naive domain randomization raises sim-to-real accuracy from 64% to 79%, while training directly on real data yields an 89% accuracy ceiling. These results suggest that the isolated mechanism of domain randomization can significantly improve generalization.

simulation