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All sources NASA NTRS DOE OSTI

DOE OSTI2025

Conflict Detection in Open RAN with Recurrent Neural Networks Using Geometric Manifolds

Allowing third-party applications on Radio Access Network (RAN) Intelligent Controllers (RICs) within the OpenRAN (O-RAN) framework introduces conflicting interactions that are often difficult to detect in advance. These conflicts, occurring between third-party applications in the Near RealTime RIC (Near-RT RIC), known as xApps, can lead to performance degradation and instability in O-RAN if not identified early. Existing conflict detection and mitigation solutions in the literature assume that the conflicts are known beforehand, which is not always accurate due to the complex and often hidden relationships between control parameters and Key Performance Indicators (KPIs). In this paper, we propose a novel Recurrent Neural Network (RNN) to detect both known and unknown conflicts in O-RAN xApps as specified in the O-RAN standards. We model the xApps, control parameters, and KPIs with nodes and edges to create graph structures and use the hidden nonEuclidean geometric properties of the Riemannian manifold to train the RNN model. The performance of this proposed model is validated using evaluation metrics and compared with benchmarks. Results demonstrate that the proposed RNN model, leveraging Riemannian geometric properties, can achieve 100% of the F1-score provided by an optimal solution in just 20 iterations.

5G↗

DOE OSTI2025

Conflict Detection in Open RAN with Recurrent Neural Networks Using Geometric Manifolds

5G↗

DOE OSTI2025

Multimodal super-resolution: discovering hidden physics and its application to fusion plasmas

Understanding complex physical systems often requires integrating data from multiple diagnostics, each with limited resolution or coverage. We present a machine learning framework that reconstructs synthetic high-temporal-resolution data for a target diagnostic using information from other diagnostics, without direct target measurements during the inference. This multimodal super-resolution technique improves diagnostic robustness and enables monitoring even in case of measurement failures or degradation. Applied to fusion plasmas, our method targets edge-localized modes (ELMs), which can damage plasma-facing materials. By reconstructing super-resolution Thomson Scattering data from complementary diagnostics, we uncover fine-scale plasma dynamics and validate the role of resonant magnetic perturbations (RMPs) in ELM suppression through magnetic island formation. The approach provides new observation supporting the plasma profile flattening due to these islands. Our results demonstrate the framework’s ability to generate high-fidelity synthetic diagnostics, offering a powerful tool for ELM control development in future reactors like ITER. The approach is broadly transferable to other domains facing sparse, incomplete, or degraded diagnostic data, opening new avenues for discovery.

Jalalvand, Azarakhsh [Princeton Univ., NJ (United ↗

DOE OSTI2021

Risk Assessment and Management Workflow—An Example of the Southwest Regional Partnership

This paper summarizes the risk assessment and management workflow developed and applied to the Southwest Regional Partnership on Carbon Sequestration (SWP) Phase III Demonstration Project. The risk assessment and management workflow consists of six primary tasks, including management planning, identification, qualitative analysis, quantitative analysis, response planning, and monitoring. Within the workflow, the SWP assembled and iteratively updated a risk registry that identifies risks for all major activities of the project. Risk elements were ranked with respect to the potential impact to the project and the likelihood of occurrence. Both qualitative and quantitative risk analyses were performed. To graphically depict the interactions among risk elements and help building risk scenarios, process influence diagrams were used to represent the interactions. The SWP employed quantitative methods of risk analysis including Response Surface Method (RSM), Polynomial Chaos Expansion (PCE), and the National Risk Assessment Partnership (NRAP) toolset. The SWP also developed risk response planning and performed risk control and monitoring to prevent the risks from affecting the project and ensure the effectiveness of risk management. As part of risk control and monitoring, existing and new risks have been tracked and the response plan was subsequently evaluated. Findings and lessons learned from the SWP’s risk assessment and management efforts will provide valuable information for other commercial geological CO2 storage projects.

Lee, Si-Yong↗

NASA NTRS2005

Distributed Adaptive Control: Beyond Single-Instant, Discrete Variables

In extensive form noncooperative game theory, at each instant t, each agent i sets its state x, independently of the other agents, by sampling an associated distribution, q(sub i)(x(sub i)). The coupling between the agents arises in the joint evolution of those distributions. Distributed control problems can be cast the same way. In those problems the system designer sets aspects of the joint evolution of the distributions to try to optimize the goal for the overall system. Now information theory tells us what the separate q(sub i) of the agents are most likely to be if the system were to have a particular expected value of the objective function G(x(sub 1),x(sub 2), ...). So one can view the job of the system designer as speeding an iterative process. Each step of that process starts with a specified value of E(G), and the convergence of the q(sub i) to the most likely set of distributions consistent with that value. After this the target value for E(sub q)(G) is lowered, and then the process repeats. Previous work has elaborated many schemes for implementing this process when the underlying variables x(sub i) all have a finite number of possible values and G does not extend to multiple instants in time. That work also is based on a fixed mapping from agents to control devices, so that the the statistical independence of the agents' moves means independence of the device states. This paper also extends that work to relax all of these restrictions. This extends the applicability of that work to include continuous spaces and Reinforcement Learning. This paper also elaborates how some of that earlier work can be viewed as a first-principles justification of evolution-based search algorithms.

Wolpert, David H.↗

DOE OSTI2020

Advancing Fusion with Machine Learning Research Needs Workshop Report

Abstract Machine learning and artificial intelligence (ML/AI) methods have been used successfully in recent years to solve problems in many areas, including image recognition, unsupervised and supervised classification, game-playing, system identification and prediction, and autonomous vehicle control. Data-driven machine learning methods have also been applied to fusion energy research for over 2 decades, including significant advances in the areas of disruption prediction, surrogate model generation, and experimental planning. The advent of powerful and dedicated computers specialized for large-scale parallel computation, as well as advances in statistical inference algorithms, have greatly enhanced the capabilities of these computational approaches to extract scientific knowledge and bridge gaps between theoretical models and practical implementations. Large-scale commercial success of various ML/AI applications in recent years, including robotics, industrial processes, online image recognition, financial system prediction, and autonomous vehicles, have further demonstrated the potential for data-driven methods to produce dramatic transformations in many fields. These advances, along with the urgency of need to bridge key gaps in knowledge for design and operation of reactors such as ITER, have driven planned expansion of efforts in ML/AI within the US government and around the world. The Department of Energy (DOE) Office of Science programs in Fusion Energy Sciences (FES) and Advanced Scientific Computing Research (ASCR) have organized several activities to identify best strategies and approaches for applying ML/AI methods to fusion energy research. This paper describes the results of a joint FES/ASCR DOE-sponsored Research Needs Workshop on Advancing Fusion with Machine Learning, held April 30–May 2, 2019, in Gaithersburg, MD (full report available at https://science.osti.gov/-/media/fes/pdf/workshop-reports/FES_ASCR_Machine_Learning_Report.pdf ). The workshop drew on broad representation from both FES and ASCR scientific communities, and identified seven Priority Research Opportunities (PRO’s) with high potential for advancing fusion energy. In addition to the PRO topics themselves, the workshop identified research guidelines to maximize the effectiveness of ML/AI methods in fusion energy science, which include focusing on uncertainty quantification, methods for quantifying regions of validity of models and algorithms, and applying highly integrated teams of ML/AI mathematicians, computer scientists, and fusion energy scientists with domain expertise in the relevant areas.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2025

Combining Deep Learning and scatterControl for High-Throughput X-ray CT Based Non-Destructive Characterization of Large-Scale Casted Metallic Components

X-ray computed tomography (XCT) is essential for nondestructive evaluation and quality control of large-scale metal components. XCT imaging, however, faces significant challenges from metal artifacts, particularly those caused by Compton scattering, which degrade image quality and obscure critical details. Hardware-based solutions (e.g. scatterControl) offer advancements by intercepting scattered photons and reducing artifacts, but they can be time-consuming and require additional processing. Here, we propose modifying and leveraging a novel deep learning (DL) framework, Simurgh, to enhance and accelerate scatter correction in XCT. By combining scatterControl with DL-based artifact removal, we demonstrate significant reduction in scan time while producing high-quality reconstructions. Through extensive evaluation on industrial XCT data, we show that our methods reduce scan time by up to more than 10 x while preserving flaw detectability. Quantitative analysis across multiple segmentation techniques confirms that Simurgh-based reconstructions consistently outperform traditional Feldkamp-Davis-Kress, model-based iterative reconstruction, and commercial DL models in both pixel-level and task-specific evaluations, enabling scalable, high-throughput XCT workflows for characterization of large scale components in applications such as casting and metal additive manufacturing.

Complex metal parts↗

DOE OSTI2023

Deployment of Dynamic Neural Network Optimization to Minimize Heat Rate During Ramping for Coal Power Plants (Final Technical Report)

Much success was achieved throughout the course of this project. A successful implementation of Dynamic Neural Network Optimization (D-NNO) was coupled with Adaptive Predictive Controls (APC) and a novel hardware installation comprised of an advanced sensor network (ASN) measuring mass-weighted averages of flue gas constituents above the horizontal superheater of a coal-fired utility boiler. From 2019 through 2023 (including an extension due to COVID delays), the team was able to prototype, evaluate, deploy, iterate, and ultimately finalize an advanced closed-loop control D-NNO system which demonstrated the ability to: •improve unit efficiency ~2.0% relative to unoptimized operation (represented as total fuel fired per MWh generated) •improve unit NOx emission rates 10%+ beyond static optimization baselines •improve unit temperature stability as much as 58% and on average 12% •improve operating load stability as much as 35% The culmination of this project has generated an advanced methodology of deploying specially designed recurrent neural networks (long short-term memory, gated recurrent unit, encoder-decoder networks, transformers, etc.), customized trajectory planning and closed-loop optimization modules capable of adapting to live electric grid responses and demands, self-tuning and adaptive expert controls constantly adjusting prediction parameters to real-time unit behavior, and a hardware/software package able to reliably calculate net unit heat rate (NUHR) in real-time using flue gas constituents, machine learning, and known combustion relationships. Through this real-time NUHR value, immediate feedback on system adjustments relative to operating efficiency was available, allowing for rapid improvements to system performance. In addition to development and deployment of the advanced D-NNO system, the approach methodology has been readily commercialized through the project platform Griffin Open Systems, LLC, the D-NNO software platform host. Similar methodologies to those developed by this project have already been deployed at 5 other units across the United States, with another 6 implementations scheduled, and more expected. Over the course of the project, multiple academic papers were submitted and accepted for publication within esteemed academic journals, and PhD students were trained and graduated, as well as undergraduate students becoming involved and participating to project objectives.

01 COAL, LIGNITE, AND PEAT↗

DOE OSTI2025

Graph-based Reversible Evaluation and Tangents Library

GRETL is a C++ library for evaluation, re-evaluation and algorithmic differentiation of functional operations on an arbitrary computational graph with limited memory usage. Similar to popular machine learning frameworks in Python, like PyTorch and JAX, it tracks and stores both operations and output data as functions are evaluated. Once this composition of functions is built up, the entire chain of operations can be back propagated to compute sensitivities of the final result with respect to any number of inputs. In contrast to most machine learning applications, memory usage becomes the bottleneck for back propagation in many physics applications, especially for time-dependent PDEs. Dynamic check pointing becomes essential. An important distinguishing feature of GRETL is its ability to limit the maximum memory usage by automatically dynamic checkpointing the data output for each graph operation (see Wang, Moin, Iaccarino, 2009). During backpropagation, parts of the graph that are no longer in memory are automatically re-evaluated from upstream checkpointed states as needed for derivative sensitivity calculations (or more precisely, for vector-Jacobian products). GRETL is particularly beneficial for applications, such as coupled multi-physics, where deriving adjoint-based sensitivities and managing checkpoint memory across modules becomes onerous. Cases which can be readily handled by the GRETL library include: different time-integration algorithms per physics (e.g., coupled predictor-corrector algorithms, IMEX, etc.), sub-cycling, asynchronous integrators, state dependent timestep sizes, iterative solvers and coupling algorithms, controller algorithms, and more.

Tupek, MichaelR [Lawrence Livermore National Labor↗

NASA NTRSDate not supplied

Having a Come-Apart: Lessons Learned from Additively Manufactured Hardware Failures

NASA has been engaged with additively manufactured (AM) process and component development since the 2000’s. AM offers various technical advantages, such as enhanced hardware design complexity, part consolidation, and processing of novel alloys in addition to programmatic advantages for reduction in processing time and cost. The focus of much of the AM development at NASA has been to mature the various processes, characterize material properties, develop standards, produce demonstrator parts, and integrate AM hardware in liquid rocket engines. These aspects have been demonstrated through process and design iterations using a methodical characterization, test-fail-fix cycles, as well as application and dissemination of lessons learned. In addition to these fundamental demonstrations of the AM process and hardware development, alloys that provide performance advantages in the high temperature and high-pressure environments have been matured for use in rocket engines. These environments are challenging for any alloy and any design, and the AM process is required to fully meet the intended design requirements. The importance of proper AM process was made evident in the failure of a Laser Powder Bed Fusion (L-PBF) copper-alloy combustion chamber during a hot-fire test due to a degraded material quality resulted from an AM process issue. The hot-fire test aimed to demonstrate high duty cycle under a risk-tolerant development project, where consequences of component failure would be minimal. However, the unintentional component failure emphasized the necessity of robust material characterization and rigorous process control procedures for the safe use of AM components in critical applications. In part, such concerns motivate the AM certification approach that NASA has recently adopted in NASA-STD-6030 “Additive Manufacturing Requirements for Spaceflight Systems”. This presentation provides an overview of the previously mentioned failure, a discussion on the evaluation of the failed chamber and supplemental chambers produced at the same time, a representative material samples that included intentional build witness lines, and a summary of the key results and recommendations from the evaluations. NASA continues to approach AM processes and designs with a level of risk and acceptance of failures that is appropriate for the project objectives, with the overall goal of safe implementation of AM technology and transferring AM technology into commercial space applications. The objective of this presentation is to provide awareness to the community working critical and non-critical AM components and the lessons learned on proper implementation of AM.

Additive Manufacturing↗

DOE OSTI2025

Optimizing Management of Persistent Data Structures in High-Performance Analytics

Large-scale data analytics workflows ingest massive input data into various data structures, including graphs and key-value datastores. These data structures undergo multiple transformations and computations and are typically reused in incremental and iterative analytics workflows. Persisting in-memory views of these data structures enables reusing them beyond the scope of a single program run while avoiding repetitive raw data ingestion overheads. Memory-mapped I/O enables persisting in-memory data structures without data serialization and deserialization overheads. However, memory-mapped I/O lacks the key feature of persisting consistent snapshots of these data structures for incremental ingestion and processing. The obstacles to efficient virtual memory snapshots using memory-mapped I/O include background writebacks outside the application’s control, and the significantly high storage footprint of such snapshots. To address these limitations, we present Privateer, a memory and storage management tool that enables storage-efficient virtual memory snapshotting while also optimizing snapshot I/O performance. Here, we integrated Privateer into Metall, a state-of-the-art persistent memory allocator for C++, and the Lightning Memory-Mapped Database (LMDB), a widely-used key-value datastore in data analytics and machine learning. Privateer optimized application performance by 1.22× when storing data structure snapshots to node-local storage, and up to 16.7× when storing snapshots to a parallel file system. Privateer also optimizes storage efficiency of incremental data structure snapshots by up to 11× using data deduplication and compression.

Computer science↗

DOE OSTI2025

Tensorized Interior Radiative Heat Transfer for a Scalable and Calibrated Building Energy Simulator

Building energy simulation is a critical tool for developing and testing advanced control strategies, such as Reinforcement Learning (RL), to provide demand flexibility and affordable energy costs. The recently introduced Smart Buildings Control Suite (sbsim) provides a lightweight, scalable, and data-calibrated simulation environment based on a 2D finite-difference model. However, the initial model primarily focused on conductive and convective heat transfer, neglecting the significant impact of long-wave radiative heat exchange between interior surfaces. This paper presents a significant extension to the sbsim framework by incorporating a physically-grounded model for interior radiative heat transfer. Our primary contribution is the development and integration of a fully tensorized radiative heat transfer module, which preserves the computational efficiency and scalability of the original simulator. This was achieved by developing a pipeline for view factor calculation, including an algorithm to identify directly seeing surfaces within complex floor plans, and formulating the net radiation equations for efficient execution on modern hardware accelerators. We validate the numerical accuracy of our tensorized implementation by comparing its results against a traditional iterative approach, demonstrating identical outcomes. This enhancement increases the physical fidelity of sbsim, enabling more accurate training of RL agents for building energy optimization.

Ham, Sang woo↗

DOE OSTI2025

Machine Learning for Real-time Fusion Plasma Behavior Prediction and Manipulation (Final Report)

The goal of this project is to implement real-time analysis of 2D Beam Emission Spectroscopy (BES) data to predict and control transient and high-bandwidth events at DIII-D. In essence, we wish to bring high-bandwidth fluctuation diagnostics into the realm of real-time measurements and control. The BES ML models will necessarily be deep neural networks (DNN) with a “data flow” architecture for compatibility with high-throughput, low-latency evaluation on a field-programmable gate array (FPGA) or other emerging processor technologies. The real-time output will be fed to the plasma control system (PCS) for real-time control tasks, specifically for ELM control and avoidance and for QH-mode access and sustainment. We anticipate that the real-time analysis of fluctuation diagnostics will create new enabling technologies to predict and control transient events such as confinement mode transitions, edge-localized modes, Alfven eigenmode events, and disruptions. The proposed research is aligned with ITER research needs and DIII-D programmatic goals. For instance, the prediction and avoidance of ELM events is critical for ITER machine safety. Also, H-mode access with RMP ELM suppression in ITER is an active research area due to high separatrix density, narrow SOL width, and elevated LH transition power threshold.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

NASA NTRS2006

Leadership Challenges in ISS Operations: Lessons Learned from Junior and Senior Mission Control Personnel

The International Space Station (ISS) is operated by a multi-national, multi-organizational team that is dispersed across multiple locations, time zones, and work schedules. At NASA, both junior and senior mission control personnel have had to find ways to address the leadership challenges inherent in such work, but neither have had systematic training in how to do so. The goals of this study were to examine the major leadership challenges faced by ISS mission control personnel and to highlight the approaches that they have found most effective to surmount them. We pay particular attention to the approaches successfully employed by the senior personnel and to the training needs identified by the junior personnel. We also evaluate the extent to which responses are consistent across the junior and senior samples. Further, we compare the issues identified by our interview survey to those identified by a standardized questionnaire survey of mission control personnel and a contrasting group of space station crewmembers. We studied a sample of 14 senior ISS flight controllers and a contrasting sample of 12 more junior ISS controllers. Data were collected using a semi-structured qualitative interview and content analyzed using an iterative process with multiple coders and consensus meetings to resolve discrepancies. To further explore the meaning of the interview findings, we also conducted new analyses of data from a previous questionnaire study of 13 American astronauts, 17 Russian cosmonauts, and 150 U.S. and 36 Russian mission control personnel supporting the ISS or Mir space stations. The interview data showed that the survey respondents had substantial consensus on several leadership challenges and on key strategies for dealing with them, and they offered a wide range of specific tactics for implementing these strategies. Interview data from the junior respondents will be presented for the first time at the meeting. The questionnaire data showed that the US mission control sample reported a level of support from their management that compared favorably to national norms. American mission control personnel and Russian crewmembers reported higher supervisor support than American crewmembers and Russian mission control personnel. We will present the specific issues underlying these findings and compare and contrast the results from the two datasets. Although specific to space station personnel, our results are consistent with recent management, cultural, and aerospace research. We aim to use our results to improve training for current and future mission control personnel.

Clement, James L.↗

NASA NTRS1994

SCOS 2: An object oriented software development approach

The Spacecraft Control and Operations System 2 (SCOS 2), is intended to provide the generic mission control system infrastructure for future ESA missions. It represents a bold step forward in order to take advantage of state-of-the-art technology and current practices in the area of software engineering. Key features include: (1) use of object oriented analysis and design techniques; (2) use of UNIX, C++ and a distributed architecture as the enabling implementation technology; (3) goal of re-use for development, maintenance and mission specific software implementation; and (4) introduction of the concept of a spacecraft control model. This paper touches upon some of the traditional beliefs surrounding Object Oriented development and describes their relevance to SCOS 2. It gives rationale for why particular approaches were adopted and others not, and describes the impact of these decisions. The development approach followed is discussed, highlighting the evolutionary nature of the overall process and the iterative nature of the various tasks carried out. The emphasis of this paper is on the process of the development with the following being covered: (1) the three phases of the SCOS 2 project - prototyping & analysis, design & implementation and configuration / delivery of mission specific systems; (2) the close cooperation and continual interaction with the users during the development; (3) the management approach - the split between client staff, industry and some of the required project management activities; (4) the lifecycle adopted being an enhancement of the ESA PSS-05 standard with SCOS 2 specific activities and approaches defined; and (5) an examination of some of the difficulties encountered and the solutions adopted. Finally, the lessons learned from the SCOS 2 experience are highlighted, identifying those issues to be used as feedback into future developments of this nature. This paper does not intend to describe the finished product and its operation, but focusing on the journey to arrive there, concentrating therefore on the process and not the products of the SCOS 2 software development.

Symonds, Martin↗

NASA NTRS2014

Anomalous Thrust Production from an RF Test Device Measured on a Low-Thrust Torsion Pendulum

This paper describes the eight-day August 2013 test campaign designed to investigate and demonstrate viability of using classical magnetoplasmadynamics to obtain a propulsive momentum transfer via the quantum vacuum virtual plasma. This paper will not address the physics of the quantum vacuum plasma thruster, but instead will describe the test integration, test operations, and the results obtained from the test campaign. Approximately 30-50 micro-Newtons of thrust were recorded from an electric propulsion test article consisting primarily of a radio frequency (RF) resonant cavity excited at approximately 935 megahertz. Testing was performed on a low-thrust torsion pendulum that is capable of detecting force at a single-digit micronewton level, within a stainless steel vacuum chamber with the door closed but at ambient atmospheric pressure. Several different test configurations were used, including two different test articles as well as a reversal of the test article orientation. In addition, the test article was replaced by an RF load to verify that the force was not being generated by effects not associated with the test article. The two test articles were designed by Cannae LLC of Doylestown, Pennsylvania. The torsion pendulum was designed, built, and operated by Eagleworks Laboratories at the NASA Johnson Space Center of Houston, Texas. Approximately six days of test integration were required, followed by two days of test operations, during which, technical issues were discovered and resolved. Integration of the two test articles and their supporting equipment was performed in an iterative fashion between the test bench and the vacuum chamber. In other words, the test article was tested on the bench, then moved to the chamber, then moved back as needed to resolve issues. Manual frequency control was required throughout the test. Thrust was observed on both test articles, even though one of the test articles was designed with the expectation that it would not produce thrust. Specifically, one test article contained internal physical modifications that were designed to produce thrust, while the other did not (with the latter being referred to as the "null" test article). Test data gathered includes torsion pendulum displacement measurements which are used to calculate generated force, still imagery in the visible spectrum to document the physical configuration, still imagery in the infrared spectrum to characterize the thermal environment, and video imagery. Post-test data includes static and animated graphics produced during RF resonant cavity characterization using the COMSOL Multiphysics® software application. Excerpts from all of the above are included and discussed in this paper. Lessons learned from test integration and operations include identification of the need to replace manual control of the resonant cavity target frequency with an automated frequency control capability. Future test plans include the development of an automatic frequency control circuit. Test results indicate that the RF resonant cavity thruster design, which is unique as an electric propulsion device, is producing a force that is not attributable to any classical electromagnetic phenomenon and therefore is potentially demonstrating an interaction with the quantum vacuum virtual plasma. Future test plans include independent verification and validation at other test facilities.

Brady, David↗

DOE OSTI2026

Lyapunov-Based Iterative Learning of the Region of Attraction for Autonomous Systems

This presentation introduces a novel algorithm for estimating the region of attraction of equilibrium points for nonlinear discrete-time autonomous systems. The method iteratively expands an initial estimate of the region of attraction by constructing unions of sublevel sets of learned functions parametrized as neural networks. Unlike conventional techniques that rely on a single global Lyapunov function, the proposed approach provides a collection of local Lyapunov-like functions, enabling richer representations and potentially larger region of attraction estimates. These functions are trained using sampled state-space data, and their Lipschitz continuity ensures that desirable properties extend beyond the training samples. The devised strategy is tested via numerical simulations, demonstrating the effectiveness of the proposed approach.

97 MATHEMATICS AND COMPUTING↗

NASA NTRS2020

Amino Acid Encoding for Deep Learning Applications

Background: The number of applications of deep learning algorithms in bioinformatics is increasing as they usually achieve superior performance over classical approaches, especially, when bigger training datasets are available. In deep learning applications, discrete data, e.g. words or n-grams in language, or amino acids or nucleotides in bioinformatics, are generally represented as a continuous vector through an embedding matrix. Recently, learning this embedding matrix directly from the data as part of the continuous iteration of the model to optimize the target prediction – a process called ‘end-to-end learning’ – has led to state-ofthe-art results in many fields. Although usage of embeddings is well described in the bioinformatics literature, the potential of end-to-end learning for single amino acids, as compared to more classical manually-curated encoding strategies, has not been systematically addressed. To this end, we compared classical encoding matrices, namely one-hot, VHSE8 and BLOSUM62, to end-to-end learning of amino acid embeddings for two different prediction tasks using three widely used architectures, namely recurrent neural networks (RNN), convolutional neural networks (CNN), and the hybrid CNN-RNN. Results: By using different deep learning architectures, we show that end-to-end learning is on par with classical encodings for embeddings of the same dimension even when limited training data is available, and might allow for a reduction in the embedding dimension without performance loss, which is critical when deploying the models to devices with limited computational capacities. We found that the embedding dimension is a major factor in controlling the model performance. Surprisingly, we observed that deep learning models are capable of learning from random vectors of appropriate dimension. Conclusion: Our study shows that end-to-end learning is a flexible and powerful method for amino acid encoding. Further, due to the flexibility of deep learning systems, amino acid encoding schemes should be benchmarked against random vectors of the same dimension to disentangle the information content provided by the encoding scheme from the distinguishability effect provided by the scheme.

Hesham ElAbd↗