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At least 343 records · Page 19

Machine learning approaches for integrating multi-omics data to expand microbiome annotation (Final Technical Report)

We fulfilled all original three aims of the proposal. Following the earlier release (during the first phase of the project at Montana) of software that identifies and fills gaps in the annotation of metabolic proteins within bacterial genomes, we have nearly completed a second gap-filling tool that improves accuracy and explainability. We completed software for alignment-based annotation of protein coding DNA, allowing for coding frameshifts caused by sequencing error. Finally, we completed a neural embedding model for identifying similarities between protein sequences based on amino-wise latent vectors.

59 BASIC BIOLOGICAL SCIENCES↗

Report for the DOE Office of Science Workshop on Envisioning Frontiers in AI and Computing for Biological Research

Artificial intelligence (AI), machine learning (ML), and high-performance computing (HPC) are poised to transform biological research, spurring innovation in biotechnology and biosystems design. "is transformation will bring an explosion of new capabilities to control the expression of genomic information in living organisms and harness that information to invent new biobased technologies (Jinek et al. 2012; NASEM 2025).

59 BASIC BIOLOGICAL SCIENCES↗

Partial Support of the Fast-Track Consensus Study on Foundational Research Gaps and Future Directions for Digital Twins (Final Report)

This study from the National Academies of Sciences, Engineering, and Medicine was launched to explore the foundational research gaps and opportunities for digital twins. As part of the information gathering process, the committee organized three targeted workshops—in engineering, climate sciences, and biomedical sciences—to better understand domain-specific nuances and barriers to developing digital twins. These sessions enabled cross-sector experts to surface field-specific needs, challenges, and open questions related to digital twins. Thousands of participants across multiple domains engaged in the discussions, which workshops were summarized in three separate Proceedings-in-Brief.

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Comparative Analysis of DNA LLM Classification Techniques Using Intra-Layer Feature Extraction with Autoencoder Stacks [Poster]

This project conducts a comparative analysis of DNA LLM classification techniques using Evo2, Grover, and UTRML, focusing on intra-layer feature extraction in Evo2. By extracting features from multiple layers of Evo2 and integrating them into an autoencoder stack with a binary classification head, we evaluate its effectiveness in classifying genomic sequences compared to smaller DNA language models. My findings demonstrate that Evo2 outperforms Grover and UTRML in classification accuracy on a dataset provided by department 08625, CAO2021, while UTRML offers competitive performance with lower computational costs. This study highlights the potential of advanced embedding techniques in enhancing genomic data analysis and informs future research in bioinformatics.

59 BASIC BIOLOGICAL SCIENCES↗

Characterizing Integrase-Attachment Site Pairs: A Machine Learning Approach

Genomic islands (GIs) are mobile genetic elements that integrate into host genomes via self-encoded integrases at specific DNA sequences known as attachment (att) sites. The ability to predict the target att site from an integrase's protein sequence is a central challenge in genomics due to the sequence diversity of integrases and the subtlety of their DNA recognition motifs.

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A spatially regularized detector for emergent/re-emergent disease outbreaks

Early detection of outbreaks caused by emergent pathogens, using epidemiological surveillance data i.e., daily case counts, is difficult. This is because the data tend to be noisy during the early epoch of the outbreak. In contrast, the spread-rate of the disease tends to be well-behaved, as it depends only on the mixing patterns of the population and the characteristics of the pathogen, neither of which behave erratically in space-time. In this report, we explore whether the spread-rate can be used for epidemiological surveillance, conditional on case count data. Estimating the spread-rate from case count data allows us to exploit exogenous information, e.g., incubation period distributions etc., which can considerably smooth out any erratic temporal behavior. Further, epidemiological dynamics are spatially correlated, and if case counts are available for multiple areal units e.g., counties, these correlations could potentially be used to suppress noise in the early epoch data. These exogenous information and structure are not exploited by conventional syndromic surveillance detectors to extract a well-behaved latent variable for monitoring purposes. The technical challenge lies in the estimation of the spread-rate field jointly over a collection of areal units; further, the spread-rate varies over time. We develop a method based on mean-field variational inference to approximately estimate the spread-rate field, using a Gaussian Random Field Model for spatial regularization. The method is tested on the estimation of spread-rate in the thirty-three counties of New Mexico and detect the arrival of the Fall 2020 COVID-19 wave in September 2020. We find that the method is scalable, but underestimates the uncertainty in the estimated spread-rate field. We detect the arrival of the Fall 2020 wave a week ahead of conventional syndromic surveillance algorithms, but our simplistic detection algorithm, based on simple anomaly detection, suffers from a high false positive rate, similar to conventional detectors.

59 BASIC BIOLOGICAL SCIENCES↗

Modular Autonomous Experimentation for Biological Applications

The Modular Autonomous Research System (MARS) was created to address a key challenge in scientific discovery: experiments are often slow, require significant manual labor, and generate data that is not easily integrated across different tools. This limits how quickly scientists can explore new materials, processes, and chemical reactions. Our motivation was to design a system that makes research faster, more reliable, and adaptable by combining automation with artificial intelligence. By doing so, we aimed to reduce human error, accelerate discovery, and allow researchers to quickly test many possibilities that would otherwise take months or years. Our approach was to build a flexible platform that connects laboratory robots, measurement instruments, and a central data system, all guided by artificial intelligence. MARS integrates liquid handling robots, robotic arms, and plate readers with an intelligent decision-making system that chooses the most informative experiments to run next. This creates a closed loop where experiments are performed automatically, the data is analyzed in real time, and new conditions are immediately tested. Through this work, we demonstrated that MARS can carry out multiple experiments with little or no human intervention, adapt to different scientific problems, and handle uncertain or noisy measurements in a robust way. The results show that modular and intelligent automation can significantly accelerate the pace of discovery, providing a model for future self-driving laboratories. This approach addresses the growing scientific need for adaptable, data-driven research platforms that can keep up with the complexity and scale of modern science.

59 BASIC BIOLOGICAL SCIENCES↗

Modular Autonomous Experimentation for Biological Applications (Full Report)

The Modular Autonomous Research System (MARS) was developed to address the pressing need for faster, more reliable, and more adaptable scientific discovery. Traditional experimentation is limited by manual labor, long cycle times, and fragmented data streams, which constrain the ability to explore complex chemical and materials design spaces. To overcome these limitations, we created an integrated, modular platform that combines laboratory robotics, diverse measurement instruments, and a central data infrastructure with artificial intelligence–driven decision-making. The system links liquid handling robots, robotic arms, and optical plate readers into a closed loop where experiments are executed automatically, data is analyzed in real time, and subsequent experimental conditions are adaptively chosen to maximize information gain. Over the course of the project, MARS was validated on two primary test cases—spectroscopic metal–ligand binding assays and peptide-directed mineralization—which highlighted the system’s ability to handle uncertainty and variability in experimental measurements. To further demonstrate modularity and extensibility, we also established additional testbeds in electrochemistry for catalyst discovery and electrolyte formulation for advanced batteries. The results show that MARS can reliably conduct autonomous campaigns with minimal human intervention, adapt to distinct scientific domains, and provide a scalable model for future self-driving laboratories. This work establishes new capabilities for modular, uncertainty-aware automation and directly supports the need for advanced, data-driven research platforms capable of accelerating discovery across a wide range of scientific and national security missions.

59 BASIC BIOLOGICAL SCIENCES↗

HBET V3.0 Installation Manual

The Hydropower Biological Evaluation Toolset (HBET) V3.0 now requires Python v3.11.0 to be installed, following the addition of the absolute fish injury rate prediction feature. This version introduces two new strike metrics—based on velocity and pressure—to provide a more precise understanding of the biological effects of fish collisions with rigid structures within the fish passage system. Additionally, SQL Server 2019 is the supported database for this release. This installation guide will walk users through the process of installing HBET V3.0 along with all necessary dependencies.

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Hydropower Biological Evaluation Toolset (HBET) Version 3.0: User Guide

The Hydropower Biological Evaluation Tools (HBET) software package, developed by Pacific Northwest National Laboratory (PNNL), is designed to assemble, organize, and process data collected by Sensor Fish and live fish. HBET enable users to characterize the hydraulic conditions of hydropower structures and estimate fish injury and mortality rates from various stressors. Future updates of the software may support other technologies, such as bead tracking in physical models and computational fluid dynamics. The HBET program can be customized to analyze different hydraulic applications, including turbines, spillways, weirs, pumped storage, and other user-defined functions, and therefore, help researchers, turbine designers, hydropower operators, and regulators better evaluate hydropower structures regarding their environmental sustainability and cost-effectiveness. Added content to the user guide about the new feature for predicting absolute injury rates.

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Modeling COVID-19 Impacts on Prison Population

The goal of this project was to develop a unique, high-level, concept model that will (1) help examine the consequences COVID-19 has had on prison population and flow dynamics in Illinois and (2) explore (to the extent possible) how that will unfold in the short- and mid-term future. Argonne has unique expertise in dynamic systems modeling and highly specialized simulation capabilities, which will be helpful in developing such a model. The ultimate objective of this CRADA is to develop with the Illinois Public Sentencing Policy Advisory Council (SPAC) the capability to identify and understand factors and interactions associated with prison population and flow dynamics in Illinois. This understanding will then potentially lead to improvements in the allocation of various resources and services. This approach would also be useful to other states.

59 BASIC BIOLOGICAL SCIENCES↗

CRCNS22 Learning Rules in the Hippocampus and their Mapping to Neuromorphic Systems (Final Technical Report)

Large scale biologically-realistic computational models are key to investigating the interplay between structure and function in nervous systems, thus paving the way to new clinical methods and neuro-inspired computing solutions. This project focuses on the hippocampus, in particular the CA3-CA1 regions, due to their role in associative learning and memory, pattern separation and completion, and spatial navigation. Investigations into the neuronal organization and learning rule(s) of this circuit can shed light into how declarative memories are formed, stored, recalled and forgotten and inform computational, experimental and clinical neuroscience work. Our project aims at developing a novel data-driven methodology supported by a broad heterogeneous base of neuroscience experimental knowledge and inspired from advances in computer science and engineering. Specifically, this work will benchmark existing and new learning rules within a full-scale spiking neural network simulation of the CA3-CA1 region. The model will be based on an open-source repository, called the Hippocampome, which contains neuronal morphologies, firing patterns, synapse probabilities, and most other required parameters for all known neuron types in the rodent hippocampal formation. The model will be first trained in a supervised fashion for associative memory tasks using backpropagation through time traditionally used in computer science, enhanced with a new technique called the surrogate gradient method. This optimization method will be used to obtain a global loss minimization, but it is not biologically inspired as it assumes the use of data not locally available to the synapses. However, we propose its use as a benchmarking tool, to compare the training performance of local biologically plausible and hardware-mappable learning rules at scale. New rules or combinations will be proposed and tested as needed, based on the obtained results. Progress in this area will also drive the development of novel hardware-mappable algorithms for continual lifelong learning and categorization of new events from few presented examples. This project goes beyond the existing state-of-the-art by looking at large scale realistic neuronal circuits as networks trainable via global optimization methods such as surrogate gradient descent. The objective function of the brain that supports learning is largely unknown, but it is likely that it operates through local learning rules. Studying network trajectories around local minima as proposed in this work represents a useful strategy for understanding whether a network is training by using a specific (set of) learning rule(s). Starting from a completely untrained network is a challenging test since it is difficult to determine how the learning rule affects the trajectory of the network. This interdisciplinary project will help understand what rule governs learning in these regions or if multiple learning rules are involved. The work will develop a robust methodology to measure if the network is converging to the target solution, oscillating around it, or diverging away.

59 BASIC BIOLOGICAL SCIENCES↗

Finding the missing pieces: filling gaps that impede the translation of omics data into models

High-throughput omics technologies such as DNA sequencing have made the sequencing and computational assembly of microbial genomes recovered from the environment relatively routine. Computational inference of the protein products encoded by these genomes, and the associated biochemical functions, should enable the accurate prediction and modeling of microbial metabolism, organismal interactions, and ecosystem processes. However, a lack of scalable, probabilistic protein annotation tools limits the full potential of modeling for understanding the metabolism and biogeochemical cycles of microbial communities. Our approach to improve inference of protein annotations and metabolic models relied on learning from and emulating expert manual curation, leveraging software engineering and data science best practices to scale up the throughput and accuracy of annotations and metabolic model construction, building software to objectively evaluate different annotation strategies, and more closely linking the protein annotation and metabolic model inference process. Outcomes of this research include several improved or new computational tools, including DRAM (Distilled and Refined Annotation of Metabolism) for annotating microbial genomes with protein function and metabolic traits, CAMPER (Curated Annotations for Microbial Polyphenol Enzymes and Reactions) for annotating key polyphenol metabolisms, EC-Bench for comprehensive and unbiased benchmarking of annotation tools, and several apps available via the DOE Systems Biology Knowledgebase (KBase) for building genome-scale metabolic models. We demonstrate that these tools allow us to scalably annotate and understand thousands of genomes for microbial communities from a variety of systems and test cases, including rivers, thawing permafrost, and gut microbiomes. All of these computational tools are available as open-source software, with most broadly and easily accessible to the scientific community via KBase apps.

59 BASIC BIOLOGICAL SCIENCES↗

CRCNS21 Computational Models of Multisensory Integration by Upper Limb in Humanoids and Amputees

This international collaborative research project between Johns Hopkins University (JHU) and the Technical University of Munich (TUM) investigated how the human brain processes and integrates multiple types of sensory information, such as touch and force, with the goal of improving prosthetic limbs for amputees and advancing sensory capabilities in humanoid robots. The research advanced our understanding of how the brain responds to sensory feedback in upper-limb amputees. Through experiments in which amputees received electrical stimulation while performing phantom hand movements, we demonstrated that sensory feedback activates the cortical sensorimotor and multisensory regions, and that these regions communicate dynamically during stimulation. Experiments with intact-limb participants explored the integration of visual, haptic, and force feedback, as well as in virtual reality motor training, further showing how the brain processes multimodal sensory information. In addition, this research inspired work on examining the reliability of where amputees perceive sensations over time, which contributed to a successful doctoral fellowship for continued investigation. Our collaborators at TUM improved multimodal sensor technology combining tactile and thermal feedback for humanoid robots, demonstrating the feasibility of integrating multiple sensor types into a unified system for detecting and responding to environmental stimuli. The experimental methods and analysis techniques developed across both teams, including functional network analysis and multimodal sensor integration, provide a foundation for future research in prosthetics and robotics. This research benefits the public by generating knowledge about how amputees process restored sensory information. Advances in humanoid sensing contribute to safer human-robot interaction. The project also fostered international collaboration and cross-disciplinary training: one TUM doctoral student spent a summer at JHU working on multimodal sensor integration, while two JHU students traveled to TUM to host workshops on neuromorphic sensory encoding and sensory integration.

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Multimodal Approaches for Leveraging Domain Knowledge with State-of-the-Art Machine Learning to Engineer Biocatalysts

This grant aimed to accelerate the development of specialized enzymes—biological catalysts essential for sustainable manufacturing and medicine—by integrating traditional laboratory evolution with cutting-edge artificial intelligence. To achieve this, we developed a suite of high-throughput sequencing tools and a centralized database to bridge the gap between a protein’s genetic "code" and its physical function. By training machine learning models on large datasets, we also demonstrated the ability to move beyond slow, trial-and-error testing to a "generative" approach, where AI can independently design new, versatile enzymes like tryptophan synthases. Ultimately, these findings demonstrate that combining laboratory data with computer-guided design enables the engineering of highly efficient biological tools with unprecedented speed and precision.

59 BASIC BIOLOGICAL SCIENCES↗

A Computational Workflow of Elucidating Viral Impact on Mediating Microbial Response to In-situ Experimental Warming: Bridging microbial modeling to carbon and mineral modeling

Viruses are abundant in soils and shape microbial communities in ways that can potentially influence ecosystem processes, yet their contributions to carbon cycling and mineral transformations remain poorly understood. Here we present a multi-phase framework that links virus-host interactions to soil biogeochemistry by combining ecological simulations, genome- and community-scale metabolic modeling, and statistical and machine-learning analyses. We first calibrated microbial abundance profiles under explicit infection scenarios to capture how viral pressure alters community structure, then explored alternative interaction strategies, including kill-the-winner, piggyback-the-winner, and mixed lytic-lysogenic modes, through forward simulations. These ecological shifts were translated into metabolic consequences using exchange fluxes summarized into biologically meaningful categories, while integrated statistical and machine-learning screens elevated subtle but consistent signals. Application of this framework revealed that viral infections shift the balance between organic and inorganic fluxes, redirecting metabolism from diffuse organic transformations toward inorganic pools such as protons and CO 2 , directly linking viral regulation to respiration and soil carbon balance. The roll-up analysis also isolated perturbations in critical mineral ions, including magnesium, manganese, zinc, and copper, which serve as essential enzymatic cofactors. In piggyback-the-winner scenarios, uptake of these ions was strongly suppressed. Contrasting viral strategies produced distinct community structures and metabolic outcomes, from broad suppression under kill-the-winner dynamics to dramatic redistributions under high-lytic and high-gain lysogenic regimes that collapsed vulnerable microbial populations while promoting opportunists. Together, these results provide a tractable path to trace viral perturbations from host abundance shifts to metabolic flux adjustments and ecosystem-scale processes, offering a practical way to include viruses in earth system models.

54 ENVIRONMENTAL SCIENCES↗

Predicting Intensive Care Unit Length of Stay and Mortality Using Patient Vital Signs: Machine Learning Model Development and Validation

Background: Patient monitoring is vital in all stages of care. In particular, intensive care unit (ICU) patient monitoring has the potential to reduce complications and morbidity, and to increase the quality of care by enabling hospitals to deliver higher-quality, cost-effective patient care, and improve the quality of medical services in the ICU. Objective: We here report the development and validation of ICU length of stay and mortality prediction models. The models will be used in an intelligent ICU patient monitoring module of an Intelligent Remote Patient Monitoring (IRPM) framework that monitors the health status of patients, and generates timely alerts, maneuver guidance, or reports when adverse medical conditions are predicted. Methods: We utilized the publicly available Medical Information Mart for Intensive Care (MIMIC) database to extract ICU stay data for adult patients to build two prediction models: one for mortality prediction and another for ICU length of stay. For the mortality model, we applied six commonly used machine learning (ML) binary classification algorithms for predicting the discharge status (survived or not). For the length of stay model, we applied the same six ML algorithms for binary classification using the median patient population ICU stay of 2.64 days. For the regression-based classification, we used two ML algorithms for predicting the number of days. We built two variations of each prediction model: one using 12 baseline demographic and vital sign features, and the other based on our proposed quantiles approach, in which we use 21 extra features engineered from the baseline vital sign features, including their modified means, standard deviations, and quantile percentages. Results: We could perform predictive modeling with minimal features while maintaining reasonable performance using the quantiles approach. The best accuracy achieved in the mortality model was approximately 89% using the random forest algorithm. The highest accuracy achieved in the length of stay model, based on the population median ICU stay (2.64 days), was approximately 65% using the random forest algorithm. Conclusions: The novelty in our approach is that we built models to predict ICU length of stay and mortality with reasonable accuracy based on a combination of ML and the quantiles approach that utilizes only vital signs available from the patient’s profile without the need to use any external features. This approach is based on feature engineering of the vital signs by including their modified means, standard deviations, and quantile percentages of the original features, which provided a richer dataset to achieve better predictive power in our models.

59 BASIC BIOLOGICAL SCIENCES↗

Multi-Species Complex and Standard Metabolomic Samples with Verified Truth Annotations Dataset

This dataset contains 4523251 (~6.35 GB) metabolite-spectra matches following identification with CoreMS. Data were manually curated as true positives, true negatives, or unknowns. Calculations for spectral similarity scores were carried out with two methods for a total of ~12.7 GB (6.35 * 2) of data. They are all .tsv files, though can easily be changed to .txt. The file types are: * human cerebrospinal fluid (CSF), human blood plasma human urine: already published here https://www.nature.com/articles/s41597-021-00894-y, • purchased FAMES standards • fungi species (A. niger, A. nidulans, T. reesei) • soil crust

59 BASIC BIOLOGICAL SCIENCES↗