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This viewgraph presentation describes Orion mission's automation Guidance, Navigation and Control (GNC) architecture and interfaces. The contents include: 1) Orion Background; 2) Shuttle/Orion Automation Comparison; 3) Orion Mission Sequencing; 4) Orion Mission Sequencing Display Concept; and 5) Status and Forward Plans.
This paper describes the design, development and results from a high fidelity human-in-the-loop simulation of an integrated set of trajectory-based automation tools providing precision scheduling, sequencing and controller merging and spacing functions. These integrated functions are combined into a system called the Terminal Area Precision Scheduling and Spacing (TAPSS) system. It is a strategic and tactical planning tool that provides Traffic Management Coordinators, En Route and Terminal Radar Approach Control air traffic controllers the ability to efficiently optimize the arrival capacity of a demand-impacted airport while simultaneously enabling fuel-efficient descent procedures. The TAPSS system consists of four-dimensional trajectory prediction, arrival runway balancing, aircraft separation constraint-based scheduling, traffic flow visualization and trajectory-based advisories to assist controllers in efficient metering, sequencing and spacing. The TAPSS system was evaluated and compared to today's ATC operation through extensive series of human-in-the-loop simulations for arrival flows into the Los Angeles International Airport. The test conditions included the variation of aircraft demand from a baseline of today's capacity constrained periods through 5%, 10% and 20% increases. Performance data were collected for engineering and human factor analysis and compared with similar operations both with and without the TAPSS system. The engineering data indicate operations with the TAPSS show up to a 10% increase in airport throughput during capacity constrained periods while maintaining fuel-efficient aircraft descent profiles from cruise to landing.
A method for collecting and processing remotely sensed imagery in order to achieve precise spatial co-registration (e.g., matched alignment) between multi-temporal image sets is presented. Such precise alignment or spatial co-registration of imagery can be used for change detection, image fusion, and temporal analysis/modeling. Further, images collected in this manner may be further processed in such a way that image frames or line arrays from corresponding photo stations are matched, co-aligned and if desired merged into a single image and/or subjected to the same processing sequence. A second methodology for automated detection of moving objects within a scene using a time series of remotely sensed imagery is also presented. Specialized image collection and preprocessing procedures are utilized to obtain precise spatial co-registration (image registration) between multitemporal image frame sets. In addition, specialized change detection techniques are employed in order to automate the detection of moving objects.
Most single-stranded RNA (ssRNA) viruses mutate rapidly to generate a large number of strains with highly divergent capsid sequences. Determining the capsid residues or nucleotides that uniquely characterize these strains is critical in understanding the strain diversity of these viruses. RECOVIR (an acronym for "recognize viruses") software predicts the strains of some ssRNA viruses from their limited sequence data. Novel phylogenetic-tree-based databases of protein or nucleic acid residues that uniquely characterize these virus strains are created. Strains of input virus sequences (partial or complete) are predicted through residue-wise comparisons with the databases. RECOVIR uses unique characterizing residues to identify automatically strains of partial or complete capsid sequences of picorna and caliciviruses, two of the most highly diverse ssRNA virus families. Partition-wise comparisons of the database residues with the corresponding residues of more than 300 complete and partial sequences of these viruses resulted in correct strain identification for all of these sequences. This study shows the feasibility of creating databases of hitherto unknown residues uniquely characterizing the capsid sequences of two of the most highly divergent ssRNA virus families. These databases enable automated strain identification from partial or complete capsid sequences of these human and animal pathogens.
Due to the nature of the GRAIL mission, the GRAIL Mission Planning and Sequence Team (MPST) is required to generate ground and uplink products faster than ever done before. The existing correct_transmitter_min_dur tool that provides a similar function to grl_suppdoc lacks the ability to operate accurately or quickly enough to support the rapid turnaround required of the GRAIL MPST. The GRAIL MPST was required to build this new tool to facilitate the ground and uplink generation processes to meet a tight sequence development timeline. The grl_suppdoc tool enables the GRAIL MPST to generate automatically Deep Space Network (DSN) transmitter suppressions based on short uplinks that are found in the ground/modeled Predicted Events File (PEF). The grl_suppdoc script automatically generates applicable DSN uplink suppressions in the form of a Spacecraft Activity Sequence File (SASF) to protect the GRAIL project from short DSN uplink windows, which can be cause for operator error at the DSN antennas. Currently, no software exists that provides this functionality at the efficiency required for GRAIL sequence team operations. Compared to a manual process, this script reduces human error and saves considerable man-hours by automating and streamlining the mission planning and sequencing task for the GRAIL mission.
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Abstract The vast size of chemical space necessitates computational approaches to automate and accelerate the design of molecular sequences to guide experimental efforts for drug discovery. Genetic algorithms provide a useful framework to incrementally generate molecules by applying mutations to known chemical structures. Recently, masked language models have been applied to automate the mutation process by leveraging large compound libraries to learn commonly occurring chemical sequences (i.e., using tokenization) and predict rearrangements (i.e., using mask prediction). Here, we consider how language models can be adapted to improve molecule generation for different optimization tasks. We use two different generation strategies for comparison, fixed and adaptive. The fixed strategy uses a pre-trained model to generate mutations; the adaptive strategy trains the language model on each new generation of molecules selected for target properties during optimization. Our results show that the adaptive strategy allows the language model to more closely fit the distribution of molecules in the population. Therefore, for enhanced fitness optimization, we suggest the use of the fixed strategy during an initial phase followed by the use of the adaptive strategy. We demonstrate the impact of adaptive training by searching for molecules that optimize both heuristic metrics, drug-likeness and synthesizability, as well as predicted protein binding affinity from a surrogate model. Our results show that the adaptive strategy provides a significant improvement in fitness optimization compared to the fixed pre-trained model, empowering the application of language models to molecular design tasks.
When field service engineers go to customer sites to service equipment, they want to diagnose and repair failures quickly and cost effectively. Symptoms exhibited by failed equipment frequently suggest several possible causes which require different approaches to diagnosis. This can lead the engineer to follow several fruitless paths in the diagnostic process before they find the actual failure. To assist in this situation, we have developed the Fault Tree Diagnosis and Optimal Test Sequence (FTDOTS) software system that performs automated diagnosis and ranks diagnostic hypotheses based on failure probability and the time or cost required to isolate and repair each failure. FTDOTS first finds a set of possible failures that explain exhibited symptoms by using a fault tree reliability model as a diagnostic knowledge to rank the hypothesized failures based on how likely they are and how long it would take or how much it would cost to isolate and repair them. This ordering suggests an optimal sequence for the field service engineer to investigate the hypothesized failures in order to minimize the time or cost required to accomplish the repair task. Previously, field service personnel would arrive at the customer site and choose which components to investigate based on past experience and service manuals. Using FTDOTS running on a portable computer, they can now enter a set of symptoms and get a list of possible failures ordered in an optimal test sequence to help them in their decisions. If facilities are available, the field engineer can connect the portable computer to the malfunctioning device for automated data gathering. FTDOTS is currently being applied to field service of medical test equipment. The techniques are flexible enough to use for many different types of devices. If a fault tree model of the equipment and information about component failure probabilities and isolation times or costs are available, a diagnostic knowledge base for that device can be developed easily.
Recently, a knowledge-based approach was used to develop a system called the Command Constraint Checker (CCC) for TRW. CCC was created to automate the process of verifying spacecraft command sequences. To check command files by hand for timing and sequencing errors is a time-consuming and error-prone task. Conventional software solutions were rejected when it was estimated that it would require 36 man-months to build an automated tool to check constraints by conventional methods. Using rule-based representation to model the various timing and sequencing constraints of the spacecraft, CCC was developed and tested in only three months. By applying artificial intelligence techniques, CCC designers were able to demonstrate the viability of AI as a tool to transform difficult problems into easily managed tasks. The design considerations used in developing CCC are discussed and the potential impact of this system on future satellite programs is examined.
Electronic structure calculations in enzymes converge very slowly with respect to the size of the model region that is described using quantum mechanics (QM), requiring hundreds of atoms to obtain converged results and exhibiting substantial sensitivity (at least in smaller models) to which amino acids are included in the QM region. As such, there is considerable interest in developing automated procedures to construct a QM model region based on well-defined criteria. However, testing such procedures is burdensome due to the cost of large-scale electronic structure calculations. Here, we show that semiempirical methods can be used as alternatives to density functional theory (DFT) to assess convergence in sequences of models generated by various automated protocols. The cost of these convergence tests is reduced even further by means of a many-body expansion. We use this approach to examine convergence (with respect to model size) of protein–ligand binding energies. Fragment-based semiempirical calculations afford well-converged interaction energies in a tiny fraction of the cost required for DFT calculations. Two-body interactions between the ligand and single-residue amino acid fragments afford a low-cost way to construct a “QM-informed” enzyme model of reduced size, furnishing an automatable active-site model-building procedure. This provides a streamlined, user-friendly approach for constructing ligand binding-site models that needs neither a priori information nor manual adjustments. Extension to model-building for thermochemical calculations should be straightforward.
This paper describes the Automated Scheduling and Planning Environment (ASPEN). ASPEN encodes complex spacecraft knowledge of operability constraints, flight rules, spacecraft hardware, science experiments and operations procedures to allow for automated generation of low level spacecraft sequences. Using a technique called iterative repair, ASPEN classifies constraint violations (i.e., conflicts) and attempts to repair each by performing a planning or scheduling operation. It must reason about which conflict to resolve first and what repair method to try for the given conflict. ASPEN is currently being utilized in the development of automated planner/scheduler systems for several spacecraft, including the UFO-1 naval communications satellite and the Citizen Explorer (CX1) satellite, as well as for planetary rover operations and antenna ground systems automation. This paper focuses on the algorithm and search strategies employed by ASPEN to resolve spacecraft operations constraints, as well as the data structures for representing these constraints.
High-throughput genetic screening is frequently employed to rapidly associate gene with phenotype and establish sequence-function relationships. With the advent of CRISPR technology, and the ability to functionally interrogate previously genetically recalcitrant organisms, non-model organisms can be investigated using pooled guide RNA (gRNA) libraries and sequencing-based assays to quantitatively assess fitness of every targeted locus in parallel. To aid the construction of pooled gRNA assemblies, we have developed an in silico design workflow for gRNA selection using the gRNA Sequence Region Extraction Tool (gRNA-SeqRET). Built upon the previously developed CCTop, gRNA-SeqRET enables automated, scalable design of gRNA libraries that target user-specified regions or whole genomes of any prokaryote or eukaryote. Additionally, gRNA-SeqRET automates the bulk extraction of any regions of sequence relative to genes or other features, aiding in the design of homology arms for insertion or deletion constructs. We also assess in silico the application of a designed gRNA library to other closely related genomes and demonstrate that for very closely related organisms Average Nucleotide Identity (ANI) > 95% a large fraction of the library may be of relevance. The gRNA-SeqRET web application pipeline can be accessed at https://grna.jgi.doe.gov. The source code is comprised of freely available software tools and customized Python scripts, and is available at https://bitbucket.org/berkeleylab/grnadesigner/src/master/ under a modified BSD open-source license (https://bitbucket.org/berkeleylab/grnadesigner).
Abstract Bacteriophages are viruses that infect bacteria. Many bacteriophages integrate their genomes into the bacterial chromosome and become prophages. Prophages may substantially burden or benefit host bacteria fitness, acting in some cases as parasites and in others as mutualists. Some prophages have been demonstrated to increase host virulence. The increasing ease of bacterial genome sequencing provides an opportunity to deeply explore prophage prevalence and insertion sites. Here we present VIBES (Viral Integrations in Bacterial genomES), a workflow intended to automate prophage annotation in complete bacterial genome sequences. VIBES provides additional context to prophage annotations by annotating bacterial genes and viral proteins in user-provided bacterial and viral genomes. The VIBES pipeline is implemented as a Nextflow-driven workflow, providing a simple, unified interface for execution on local, cluster and cloud computing environments. For each step of the pipeline, a container including all necessary software dependencies is provided. VIBES produces results in simple tab-separated format and generates intuitive and interactive visualizations for data exploration. Despite VIBES’s primary emphasis on prophage annotation, its generic alignment-based design allows it to be deployed as a general-purpose sequence similarity search manager. We demonstrate the utility of the VIBES prophage annotation workflow by searching for 178 Pf phage genomes across 1072 Pseudomonas spp. genomes.
The African swine fever virus (ASFV) is currently causing a world-wide pandemic of a highly lethal disease in domestic swine and wild boar. Currently, recombinant ASF live-attenuated vaccines based on a genotype II virus strain are commercially available in Vietnam. With 25 reported ASFV genotypes in the literature, it is important to understand the molecular basis and usefulness of ASFV genotyping, as well as the true significance of genotypes in the epidemiology, transmission, evolution, control, and prevention of ASFV. Historically, genotyping of ASFV was used for the epidemiological tracking of the disease and was based on the analysis of small fragments that represent less than 1% of the viral genome. The predominant method for genotyping ASFV relies on the sequencing of a fragment within the gene encoding the structural p72 protein. Genotype assignment has been accomplished through automated phylogenetic trees or by comparing the target sequence to the most closely related genotyped p72 gene. To evaluate its appropriateness for the classification of genotypes by p72, we reanalyzed all available genomic data for ASFV. We conclude that the majority of p72-based genotypes, when initially created, were neither identified under any specific methodological criteria nor correctly compared with the already existing ASFV genotypes. Based on our analysis of the p72 protein sequences, we propose that the current twenty-five genotypes, created exclusively based on the p72 sequence, should be reduced to only six genotypes. To help differentiate between the new and old genotype classification systems, we propose that Arabic numerals (1, 2, 8, 9, 15, and 23) be used instead of the previously used Roman numerals. Furthermore, we discuss the usefulness of genotyping ASFV isolates based only on the p72 gene sequence.
Within human factors there is burgeoning interest in the "human-autonomy teaming" (HAT) concept as a way to address the challenges of interacting with complex, increasingly autonomous systems. The HAT concept comes out of an aspiration to interact with increasingly autonomous systems as a team member, rather than simply use automation as a tool. The authors, and others, have proposed core tenets for HAT that include bi-directional communication, automation and system transparency, and advanced coordination between human and automated teammates via predefined, dynamic task sequences known as "plays." It is believed that, with proper implementation, HAT should foster appropriate teamwork, thus increasing trust and reliance on the system, which in turn will reduce workload, increase situation awareness, and improve performance. To this end, HAT has been demonstrated and/or studied in multiple applications including search and rescue operations, healthcare and medicine, autonomous vehicles, photography, and aviation. The current paper presents one such effort to apply HAT. It details the design of a HAT agent, developed by Human Automation Teaming Solutions, Inc., to facilitate teamwork between the automation and the human operator of an advanced ground dispatch station. This dispatch station was developed to support a NASA project investigating a concept called Reduced Crew Operations (RCO); consequently, we have named the agent R-HATS. Part of the RCO concept involves a ground operator providing enhanced support to a large number of aircraft with a single pilot on the flight deck. When assisted by R-HATS, operators can monitor and support or manage a large number of aircraft and use plays to respond in real-time to complicated, workload-intensive events (e.g., an airport closure). A play is a plan that encapsulates goals, tasks, and a task allocation strategy appropriate for a particular situation. In the current implementation, when a play is initiated by a user, R-HATS determines what tasks need to be completed and has the ability to autonomously execute them (e.g., determining diversion options and uplinking new routes to aircraft) when it is safe and appropriate. R-HATS has been designed to both support end users and researchers in RCO and HAT. Additionally, R-HATS and its underlying architecture were developed with generalizability in mind as a modular software applicable outside of RCO/aviation domains. This paper will also discuss future further development and testing of RHATS.
Within human factors there is burgeoning interest in the Human-Autonomy Teaming (HAT) concept as away to address the challenges of interacting with complex, increasingly autonomous systems. The HAT concept comes out of an aspiration to interact with increasingly autonomous automation as a team member, rather than simply use automation as a tool. The authors, and others, have proposed core tenets for HAT that include bi-directional communication, automation and system transparency, and advanced coordination between human and automated teammates via predefined, dynamic task sequences known as plays (Shively et al., 2017). It is believed that, with proper implementation, HAT should foster appropriate teamwork, thus increasing trust and reliance on the system, which in turn will reduce workload, increase situation awareness, and improve performance. To this end, HAT has been demonstrated and/or studied in multiple applications including search and rescue operations (Nourbakhsh et al., 2005), healthcare and medicine (Tsui Yanco, 2007), autonomous vehicles (Parasuraman, Barnes, Cosenzo, Mulgund, 2007), photography (Lachter, Brandt, Sadler, Shively, in press), and aviation (Shively et al., in press). The current paper presents one such effort to apply HAT. It details the design of a R-HAT Agent developed as part of a NASA Research Agreement awarded to Human-Autonomy Teaming Solutions Inc. (HATS Inc), and developed in collaboration with the Human-Autonomy Teaming Laboratory at NASA Ames Research Center. The role of this Agent is to mediate interaction between the automation and the human operator of an advanced ground dispatch station, with this mediation based upon previously mentioned core tenets for HAT and the many lessons learned from the HAT research literature. This dispatch station was developed to support a NASA project investigating a concept called Reduced Crew Operations (RCO; Lachter, Brandt, Battiste, Matessa, Johnson, in press). Part of the RCO concept involves a ground operator providing enhanced support to a large number of aircraft with a single pilot on the flight deck. When assisted by the Agent, operators can monitor and support or manage a large number of aircraft and use plays to respond in real-time to complicated, workload-intensive events (e.g., an airport closure). A play is a plan that encapsulates goals, tasks, and a task allocation strategy appropriate for a particular situation. In the current implementation, when a play is initiated by a user, the Agent determines what tasks need to be done and has the ability to autonomously execute them (e.g., determining diversion options and uplinking new routes to aircraft) when it is safe and appropriate. The R-HAT Agent has been designed to both support end users and research in RCO and HAT. Additionally, the Agent and its underlying architecture were developed with generalizability in mind as a modular piece of software applicable outside of RCO aviation in domains such as those mentioned above. This paper will also discuss future further development and testing of the R-HAT Agent.
Proteins are the molecular machines of life with numerous applications in energy, health, and sustainability. However, engineering proteins with desired functions for practical applications remains slow, expensive, and specialist-dependent. Here we report a generally applicable platform for autonomous enzyme engineering that integrates machine learning and large language models with biofoundry automation to eliminate the need for human intervention, judgement, and domain expertise. Requiring only an input protein sequence and a quantifiable way to measure fitness, this automated platform can be applied to engineer a wide array of proteins. As a proof of concept, we engineer Arabidopsis thaliana halide methyltransferase (AtHMT) for a 90-fold improvement in substrate preference and 16-fold improvement in ethyltransferase activity, along with developing a Yersinia mollaretii phytase (YmPhytase) variant with 26-fold improvement in activity at neutral pH. This is accomplished in four rounds over 4 weeks, while requiring construction and characterization of fewer than 500 variants for each enzyme. This platform for autonomous experimentation paves the way for rapid advancements across diverse industries, from medicine and biotechnology to renewable energy and sustainable chemistry.
Proteins are the molecular machines of life with numerous applications in energy, health, and sustainability. However, engineering proteins with desired functions for practical applications remains slow, expensive, and specialist-dependent. Here we report a generally applicable platform for autonomous enzyme engineering that integrates machine learning and large language models with biofoundry automation to eliminate the need for human intervention, judgement, and domain expertise. Requiring only an input protein sequence and a quantifiable way to measure fitness, this automated platform can be applied to engineer a wide array of proteins. As a proof of concept, we engineer Arabidopsis thaliana halide methyltransferase (AtHMT) for a 90-foldimprovement in substrate preference and 16-fold improvement in ethyl-transferase activity, along with developing a Yersinia mollaretii phytase (YmPhytase) variant with 26-fold improvement in activity at neutral pH. This is accomplished in four rounds over 4 weeks, while requiring construction and characterization of fewer than 500 variants for each enzyme. This platform for autonomous experimentation paves the way for rapid advancements across diverse industries, from medicine and biotechnology to renewable energy and sustainable chemistry.