Time-Varying Optimization of Networked Systems With Human Preferences
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Automation & Control Systems↗
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Practical and Optimal Sequential Bayesian Experimental Design for Complex Systems Incorporating Human Experimenter Preferences (Final Scientific/Technical Report)
Experiments are indispensable for developing models of complex systems. Carefully designed experiments can provide substantial savings for these expensive data-acquisition opportunities. However, designs based on heuristics are often suboptimal for systems with multiphysics, nonlinear dynamics, and uncertain and noisy environments. Optimal experimental design, while leveraging predictive models, seeks to systematically quantify and maximize the value of experiments. In this project, we focused on the design of multiple experiments, where current approaches are largely suboptimal: batch-design does not adapt to new data acquired during the experiment campaign (no feedback), and greedy/myopic design ignores future dynamics and consequences (no lookahead). We developed the mathematical framework and computational methods for sequential optimal experimental design (sOED) for complex systems. We enabled tractable model-based sOED in a rigorous manner through novel algorithms based on reinforcement learning, and investigated the effects of human experimenters on the design process. Our methods are fully Bayesian, able to quantify and update uncertainty in a principled manner. The traits aimed by our approach—mathematical rigor and optimality, human effects and uncertainty quantification, computational practicality—are crucial for elevating the standards of artificial intelligence (AI) to support decision-making in scientific domains, and contribute toward trust and realistic adoption of AI in experimental design practice.
97 MATHEMATICS AND COMPUTING↗
A Preferences Corpus and Annotation Scheme for Human-Guided Alignment of Time-Series GPTs
The process of time-series forecasting such as predicting trajectories of silicon content in blast furnaces is a difficult task. Most time-series approaches today focus on scalar-type MSE loss optimization. This optimization approach, while widely common, could benefit from the use of human expert or process-level preferences. In this paper, we introduce a novel alignment and fine-tuning approach that involves learning from a corpus of preferred and dis-preferred time-series prediction trajectories. Our contributions include (1) a preference annotation pipeline for time-series forecasts, (2) the application of Score-based Preference Optimization (SPO) to train decoder-only transformers from preferences, and (3) results showing improvements in forecast quality. The approach is validated on both proprietary blast furnace data and the UCI Appliances Energy dataset. The proposed preference corpus and training strategy offer a new option for fine-tuning sequence models in industrial settings.
DPO↗
Large Game Distribution Camera Study at Los Alamos National Laboratory [Poster]
The unique habitats at the Laboratory support a diverse community of wildlife. The habitat types that include Pinon Juniper, Ponderosa Pine, and Mixed-conifer forests each provide different resources important for a variety of species. Wildlife monitoring for large game animals can be challenging because they avoid interactions with humans, and prefer undeveloped areas. This study was conducted to analyze the distribution of predators and other game animals seasonally across the Laboratory. The data gathered will be used to make recommendations regarding wildlife management for conservation and protection. Utilizing game cameras to remotely monitor wildlife was determined to be the most effective, noninvasive method to gather the necessary data. As camera technology has advanced, game cameras have become adequate for documenting individuals, and are commonly used in wildlife studies on predation, abundance, occupancy, diversity, and endangered species detection. Twenty cameras were placed across the LANL landscape using a modified systematic sampling design. They were deployed in February 2018 and retrieved in January 2019, thus each camera sampled for one full year. All images were reviewed and the species, number, age, and sex of all animals in the photo were recorded. Here we present data for the most abundant species encountered: deer, elk, coyote, bear, bobcat, mountain lion, and fox respectively. The data were summarized by species and season. Future work will include occupancy modelling for each species. This will allow the development of heat maps showing species distributions across the Laboratory.
54 ENVIRONMENTAL SCIENCES↗
Large Game Distribution Camera Study at Los Alamos National Laboratory
The unique habitats at the Laboratory support a diverse community of wildlife. The habitat types that include Pinon Juniper, Ponderosa Pine, and Mixed-conifer forests each provide different resources important for a variety of species. Wildlife monitoring for large game animals can be challenging because they avoid interactions with humans, and prefer undeveloped areas. This study was conducted to analyze the distribution of predators and other game animals seasonally across the Laboratory. This research informs decisions regarding wildlife management recommendations for conservation and protection. This study utilized game cameras to remotely monitor wildlife. As camera technology has advanced, game cameras have become adequate for documenting individuals, and are commonly used in wildlife studies on predation, abundance, occupancy, diversity, and endangered species detection. Twenty cameras were placed across the LANL landscape using a modified systematic sampling design. They were deployed in February 2018 and retrieved in January 2019, thus each camera sampled for one full year. All images were reviewed and the species, number, age, and sex of all animals in the photo were recorded. Here we present data for the most abundant species encountered: deer, elk, coyote, bear, bobcat, mountain lion, and fox respectively. The data were summarized by species and season. Future work will include occupancy modelling for each species. This will allow the development of heat maps showing species distributions across the Laboratory.
59 BASIC BIOLOGICAL SCIENCES↗
Origins of glycan selectivity in streptococcal Siglec-like adhesins suggest mechanisms of receptor adaptation
Bacterial binding to host receptors underlies both commensalism and pathogenesis. Many streptococci adhere to protein-attached carbohydrates expressed on cell surfaces using Siglec-like binding regions (SLBRs). The precise glycan repertoire recognized may dictate whether the organism is a strict commensal versus a pathogen. However, it is currently not clear what drives receptor selectivity. Here, we use five representative SLBRs and identify regions of the receptor binding site that are hypervariable in sequence and structure. We show that these regions control the identity of the preferred carbohydrate ligand using chimeragenesis and single amino acid substitutions. We further evaluate how the identity of the preferred ligand affects the interaction with glycoprotein receptors in human saliva and plasma samples. As point mutations can change the preferred human receptor, these studies suggest how streptococci may adapt to changes in the environmental glycan repertoire.
59 BASIC BIOLOGICAL SCIENCES↗
Do Programmers Prefer Predictable Expressions in Code?
Source code is a form of human communication, albeit one where the information shared between the programmers reading and writing the code is constrained by the requirement that the code executes correctly. Programming languages are more syntactically constrained than natural languages, but they are also very expressive, allowing a great many different ways to express even very simple computations. Still, code written by developers is highly predictable, and many programming tools have taken advantage of this phenomenon, relying on language model surprisal as a guiding mechanism. Additionally, while surprisal has been validated as a measure of cognitive load in natural language, its relation to human cognitive processes in code is still poorly understood. In this paper, we explore the relationship between surprisal and programmer preference at a small granularity—do programmers prefer more predictable expressions in code? Using meaning-preserving transformations, we produce equivalent alternatives to developer-written code expressions and run a corpus study on Java and Python projects. In general, language models rate the code expressions developers choose to write as more predictable than these transformed alternatives. Then, we perform two human subject studies asking participants to choose between two equivalent snippets of Java code with different surprisal scores (one original and transformed). We find that programmers do prefer more predictable variants, and that stronger language models like the transformer align more often and more consistently with these preferences.
97 MATHEMATICS AND COMPUTING↗
Interactive Mesh Generation and Comparison Tools for Nuclear Energy Advanced Modeling & Simulation Phase I. Final Report
The promise of computer simulations for nuclear reactor designs is the opportunity to speed up the design process while also improving safety, providing more detail and higher fidelity, reducing cost, minimizing schedule risk, and avoiding many other potential problems; because simulations have the potential to be much less expensive and time-consuming than traditional development – where scale models and physical tests require construction and long lead times – it is possible to consider more alternatives and complete more comprehensive assessments before the design is finalized and constructed. As more design scenarios are studied by simulation, the speed that simulations promise is only available as long as bottlenecks are addressed for these scenarios. A frequent bottleneck is the amount of human labor required to describe the shape of the objects being designed and decompose the shape into simple elements, such as hexahedra, that are small enough to capture the physical phenomena of interest without being so small that even fast computers cannot perform the simulation in a reasonable amount of time. Recently, techniques for creating all-hexahedral decompositions have been developed, but they require some human input. Many simulation codes prefer all-hexahedral decompositions, so we proposed to evaluate the feasibility of these techniques on nuclear reactor geometries to see whether they required too much human input to be commercially viable. Our study concluded that they can be made viable with some additional software tools to reduce the amount of user input required.
22 GENERAL STUDIES OF NUCLEAR REACTORS↗
Visual Style Elements in Human–System Interface Design for Nuclear Power Operations: Does Style Affect Performance and Preference?
As the world increasingly adopts renewable and sustainable energy systems, transitionary solutions include nuclear power, which currently provides 20% of the United States’ electricity and is the largest single source of carbon-free electricity generation. Advanced reactors are a critical component of a carbon-free mixed energy portfolio that require careful design of first-of-a-kind control rooms. The application of Human Factors Engineering (HFE) is essential for scientific and iterative testing of novel human–system interface (HSI) concepts to ensure effective, efficient, and safe plant operations. Microworlds are simulators that use simplified physics models and control systems to distill nuclear power operations into essential functions. HFE scientists used the Rancor Microworld Simulator to obtain preference and performance metrics for novel and traditional static HSI design styles. Participants comprised advanced reactor company employees and nuclear industry consultants. A mixture of quantitative and qualitative data was captured. There was a preference for the basic graphical style that included high contrast and traditional color scheme elements. No single HSI design outperformed the others, and the participants did not perform better using their preferred HSI style. We report this experiment is the first in a series of HFE testing for HSIs in advanced reactor control room development. Clear user preferences emerged for elements within static displays. The cutting-edge neumorphic style was the least preferred. Future directions include tests of dynamic displays. HFE is used in evaluating and designing HSI devices that will improve the efficiency and safety of advanced nuclear power operations.
99 GENERAL AND MISCELLANEOUS↗
Learning from Crowds by Modeling Common Confusions
Crowdsourcing provides a practical way to obtain large amounts of labeled data at a low cost. However, the annotation quality of annotators varies considerably, which imposes new challenges in learning a high-quality model from the crowdsourced annotations. In this work, we provide a new perspective to decompose annotation noise into common noise and individual noise and differentiate the source of confusion based on instance difficulty and annotator expertise on a per-instance-annotator basis. We realize this new crowdsourcing model by an end-to-end learning solution with two types of noise adaptation layers: one is shared across annotators to capture their commonly shared confusions, and the other one is pertaining to each annotator to realize individual confusion. To recognize the source of noise in each annotation, we use an auxiliary network to choose from the two noise adaptation layers with respect to both instances and annotators. Extensive experiments on both synthesized and real-world benchmarks demonstrate the effectiveness of our proposed common noise adaptation solution.
96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
Caught in motion: human NTHL1 undergoes interdomain rearrangement necessary for catalysis
Abstract Base excision repair (BER) is the main pathway protecting cells from the continuous damage to DNA inflicted by reactive oxygen species. BER is initiated by DNA glycosylases, each of which repairs a particular class of base damage. NTHL1, a bifunctional DNA glycosylase, possesses both glycolytic and β-lytic activities with a preference for oxidized pyrimidine substrates. Defects in human NTHL1 drive a class of polyposis colorectal cancer. We report the first X-ray crystal structure of hNTHL1, revealing an open conformation not previously observed in the bacterial orthologs. In this conformation, the six-helical barrel domain comprising the helix-hairpin-helix (HhH) DNA binding motif is tipped away from the iron sulphur cluster-containing domain, requiring a conformational change to assemble a catalytic site upon DNA binding. We found that the flexibility of hNTHL1 and its ability to adopt an open configuration can be attributed to an interdomain linker. Swapping the human linker sequence for that of Escherichia coli yielded a protein chimera that crystallized in a closed conformation and had a reduced activity on lesion-containing DNA. This large scale interdomain rearrangement during catalysis is unprecedented for a HhH superfamily DNA glycosylase and provides important insight into the molecular mechanism of hNTHL1.
59 BASIC BIOLOGICAL SCIENCES↗
The Development of the Pooled Rideshare Acceptance Model (PRAM)
Due to the advancements in real-time information communication technologies and sharing economies, rideshare services have gained significant momentum by offering dynamic and/or on-demand services. Rideshare service companies evolved from personal rideshare, where riders traveled solo or with known individuals, into pooled rideshare (PR), where riders can travel with one to multiple unknown riders. Similar to other shared economy services, pooled rideshare is beneficial as it efficiently utilizes resources, resulting in reduced energy usage, as well as reduced costs for the riders. However, previous research has demonstrated that riders have concerns about using pooled rideshare, especially regarding personal safety. A U.S. national survey with 5385 participants was used to understand human factor-related barriers and user preferences to develop a novel Pooled Rideshare Acceptance Model (PRAM). This model used a covariance-based structural equation model (CB-SEM) to identify the relationships between willingness to consider PR factors (time/cost, privacy, safety, service experience, and traffic/environment) and optimizing one’s experience of PR factors (vehicle technology/accessibility, convenience, comfort/ease of use, and passenger safety), resulting in the higher-order factor trust service. We examined the factors’ relative contribution to one’s willingness/attitude towards PR and user acceptance of PR. Privacy, safety, trust service, and convenience were statistically significant factors in the model, as were the comfort/ease of use factor and the service experience, traffic/environment, and passenger safety factors. The only two non-significant factors in the model were time/cost and vehicle technology/accessibility; it is only when a rider feels safe that individuals then consider the additional non-significant variables of time, cost, technology, and accessibility. Privacy, safety, and service experience were factors that discouraged the use of PR, whereas the convenience factor greatly encouraged the acceptance of PR. Despite the time/cost factor’s lack of significance, individual items related to time and cost were crucial when viewed within the context of convenience. This highlights that while user perceptions of privacy and safety are paramount to their attitude towards PR, once safety concerns are addressed, and services are deemed convenient, time and cost elements significantly enhance their trust in pooled rideshare services. This study provides a comprehensive understanding of user acceptance of PR services and offers actionable insights for policymakers and rideshare companies to improve their services and increase user adoption.
dynamic rideshare system↗
Cryo-EM structure of the human Sirtuin 6–nucleosome complex
Sirtuin 6 (SIRT6) is a multifaceted protein deacetylase/deacylase and a major target for small-molecule modulators of longevity and cancer. In the context of chromatin, SIRT6 removes acetyl groups from histone H3 in nucleosomes, but the molecular basis for its nucleosomal substrate preference is unknown. Our cryo–electron microscopy structure of human SIRT6 in complex with the nucleosome shows that the catalytic domain of SIRT6 pries DNA from the nucleosomal entry-exit site and exposes the histone H3 N-terminal helix, while the SIRT6 zinc-binding domain binds to the histone acidic patch using an arginine anchor. In addition, SIRT6 forms an inhibitory interaction with the C-terminal tail of histone H2A. The structure provides insights into how SIRT6 can deacetylate both H3 K9 and H3 K56.
59 BASIC BIOLOGICAL SCIENCES↗
A treatment-effect model to quantify human dimensions of disaster impacts: the case of Hurricane Maria in Puerto Rico
Here, we propose a supervised learning approach using publicly available panel data to statistically quantify the specific manifestations of human impacts of an extreme event, such as changes number of suicides, substance abuse, excess mortality, and unemployment. This allows us to conceptually focus our framework on human impacts and how by attributing them to disaster events along widely accepted psychological, economic, and social dimensions. Our modified treatment-effect model allows counterfactual baseline conditions to be posited for each manifestation from which an aggregated quantitative multi-faceted measure of human impacts can be determined. The developed statistical methodology could be beneficial to policymakers who must allocate scarce resources to those communities in greater need. We illustrate the applicability of our approach using annual and monthly panel data from 2012 to 2018 encompassing the 2017 Hurricane Maria event across various municipalities in Puerto Rico. Our statistical modeling methodology stands apart since (i) it explicitly and more realistically captures the effect of different human-oriented manifestations of an actual event and (ii) it is flexible enough to accommodate individual preferences of various stakeholders in how they assign importance to multiple manifestations of human impacts.
54 ENVIRONMENTAL SCIENCES↗
Three-dimensional spheroid culture induces apical-basal polarity and the original characteristics of immortalized human renal proximal tubule epithelial cells
Highlights: • Immortalized proximal tubule cells (HK-2 cells) formed a tubule-like structure. • The 3D spheroid culture enhanced apical-basal polarity of HK-2 cells. • The 3D spheroid culture induced Na transport function of HK-2 cells. • The 3D spheroid culture promoted up-regulation of kidney development-related genes. The proximal tubules, which are part of the kidney, maintain blood homeostasis by absorbing amino acids, glucose, water, and ions such as sodium (Na), potassium, and bicarbonate. Proximal tubule dysfunction is associated with the pathogenesis of many kidney diseases. Renal proximal tubular epithelial cells (RPTECs) are responsible for the main functions of the proximal tubules. Therefore, in vitro experiments using RPTECs would greatly enhance our understanding of nephron physiology and pathobiology. It is preferable to use immortalized cell lines, such as human kidney-2 (HK-2) cells, because they are derived from humans and maintain growth indefinitely. However, tissue-specific RPTEC phenotypes, including apical-basal polarization, are frequently lost in conventional two-dimensional culture methods in part due to microenvironmental deficiencies. To overcome this limitation, we developed a three-dimensional (3D) spheroid culture method for HK-2 cells using an extracellular matrix. HK-2 spheroids in 3D culture formed a tubule-like architecture with cellular polarity and showed markedly restored Na transport function. 3D culture of HK-2 cells also increased expression of kidney development–related genes, including WNT9B. Models of human renal tubules using HK-2 spheroids will greatly improve our understanding of the physiology and pathobiology of the kidney.
60 APPLIED LIFE SCIENCES↗
Cytogenetic follow-up studies on humans with internal and external exposure to ionizing radiation
Cells exposed to ionizing radiation have a wide spectrum of DNA lesions that include DNA single-strand breaks, DNA double-strand breaks (DSBs), oxidative base damage and DNA-protein crosslinks. Among them, DSB is the most critical lesion, which when mis-repaired leads to unstable and stable chromosome aberrations. Currently, chromosome aberration analysis is the preferred method for biological monitoring of radiation-exposed humans. Here, stable chromosome aberrations, such as inversions and balanced translocations, persist in the peripheral blood lymphocytes of radiation-exposed humans for several years and, therefore, are potentially useful tools to prognosticate the health risks of radiation exposure, particularly in the hematopoietic system. In this review, we summarize the cytogenetic follow-up studies performed by REAC/TS (Radiation Emergency Assistance Center/Training site, Oak Ridge, USA) on humans exposed to internal and external radiation. In the light of our observations as well as the data existing in the literature, this review attempts to highlight the importance of follow-up studies for predicting the extent of genomic instability and its impact on delayed health risks in radiation-exposed victims.
61 RADIATION PROTECTION AND DOSIMETRY↗
Evolution of Thyroglobulin Loop Kinetics in EpCAM
Epithelial cell-activating molecule (EpCAM) is an important cancer biomarker and therapeutic target given its elevated expression in epithelial cancers. EpCAM is a type I transmembrane protein that forms cis-dimers along the thyroglobulin type-1A-like domain (TYD) in the extracellular region. The thyroglobulin loop (TY loop) within the TYD is structurally dynamic in the monomer state of human EpCAM, binding reversibly to a TYD site. However, it is not known if this flexibility is prevalent across different species. Here, we conduct over 17 μs of all-atom molecular dynamics simulations to study EpCAM TY loop kinetics of five different species, including human, mouse, chicken, frog, and fish. We find that the TY loop remains dynamic across evolution. In addition to the TYD binding site, we discover a second binding site for the TY loop in the C-terminal domain (CTD). Calculations of the dissociation rate constants from the simulation trajectories suggest a differential binding pattern of fish EpCAM and other organisms. Whereas fish TY loop has comparable binding for both TYD and CTD sites, the TY loops of other species preferably bind the TYD site. A hybrid construct of fish EpCAM with human TY loop restores the TYD binding preference, suggesting robust effects of the TY loop sequence on its dynamic behavior. Our findings provide insights into the structural dynamics of EpCAM and its implication in physiological functions.
59 BASIC BIOLOGICAL SCIENCES↗
Microbiome Comparison and Pathogen Identification for Three Migrating Passerines Captured During Spring Season in Jordan Using 16S rRNA Sequencing
Jordan is located on an important spot along the Mediterranean and Black Sea Flyway. Hundreds of migratory bird species have been identified stopping over in Jordan during spring and autumn migratory seasons. Compared to mammals and economically important birds, the microbiomes of wild bird species are severely understudied. Gut microbial composition is a valuable source of information that reflects food preferences, foraging behavior, and the risk of pathogen transmission to humans and other animals. In this study, we assessed the microbiome composition of three species of migrating passerines (willow warblers, lesser whitethroats, and common reed warblers) captured during the spring migration stopover in Jordan in 2023. A total of 59 fecal samples were selected evenly from the three species and subjected to 16S sequencing and microbiome analysis. Our objectives were to determine the diversity of bacteria in these three species, assess the amount of intra- and inter-specific variation, and detect pathogenic genera and species that could pose health risks to humans, domestic animals, and wildlife. Bacteria mainly belonged to the phyla Proteobacteria (62%), Actinobacteriota (18%), Firmicutes (13%), Cyanobacteria (5%), and Bacteroidota (1%). The results reveal that lesser whitethroats had the greatest variation in bacterial genus richness, Shannon diversity, and microbial composition compared to willow warblers and common reed warblers. The three bird species harbored several pathogenic genera and species, including Campylobacter, Enterococcus, Escherichia-Shigella, Mycoplasma, Rickettsia, Clostridium perfringens, and Vibrio cholerae. We suggest further investigation to understand the relationship between migratory behavior and their gut microbiome. We advocate for the use of advanced molecular techniques to characterize the pathogens found in migratory birds that might have public and environmental health impacts in addition to economic loss.
59 BASIC BIOLOGICAL SCIENCES↗