Search NASA⌕ Search

SEARCH · Search NASA

Results for “Biological neural networks”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 271 records · Page 15
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Leveraging Prior Concept Learning Improves Generalization From Few Examples in Computational Models of Human Object Recognition

Humans quickly and accurately learn new visual concepts from sparse data, sometimes just a single example. The impressive performance of artificial neural networks which hierarchically pool afferents across scales and positions suggests that the hierarchical organization of the human visual system is critical to its accuracy. These approaches, however, require magnitudes of order more examples than human learners. We used a benchmark deep learning model to show that the hierarchy can also be leveraged to vastly improve the speed of learning. We specifically show how previously learned but broadly tuned conceptual representations can be used to learn visual concepts from as few as two positive examples; reusing visual representations from earlier in the visual hierarchy, as in prior approaches, requires significantly more examples to perform comparably. These results suggest techniques for learning even more efficiently and provide a biologically plausible way to learn new visual concepts from few examples.

Rule, Joshua S.↗
DOE OSTI2023

A Hardware and Software Co-design Framework for Energy Efficient Neuromorphic Systems

Neuromorphic systems can be realized by a variety of algorithms and architectures. A common understanding is that spiking neuromorphic designs, which encode information into spatio-temporal spiking events, are both a biologically-accurate and efficient way of processing information. However, representing the information through timing relationships induces sophisticated circuit designs in traditional CMOS-based implementations. In recent years, high-capacity resistive memory (RRAM, aka, memristor) has demonstrated great potential in mimicking synaptic behaviors. Several RRAM-based spiking neuromorphic designs exist, most of which focus on rate coding schemes. These designs simplify circuit implementations of neuron models and explore challenges such as unsatisfactory speed, resolution, and performance. As an alternative, we will explore temporal coding spiking neuromorphic systems that encode information as the relative timing of neuron activations (spikes), which have been proven to be more adaptive and energy-efficient. Developing a neuromorphic system for spiking neural network (SNN) inference and online training, however, faces some major technical challenges: (1) It lacks circuit implementation support for temporal-coding SNN to achieve satisfying power efficiency and accuracy; (2) Although existing research works have investigated memristive synapse and neuron designs for spike-timing-dependent plasticity, the non-ideal conditions in implementation, such as device variations and signal degradation, degrade online learning accuracy of large scale systems; and (3) Non-optimized, inter-layer data traffic in SNNs, leads to unnecessary data communication costs. In this project, we plan to address these challenges by a hardware and software co-design framework that incorporates solutions at the circuit, architecture, and algorithm levels. At the circuit-level, we will elaborate on the in-situ SNN processing element designs for supporting both inference and online training modes. Variation-aware schemes will be studied to improve reliability. At the architecture level, we propose a pipelined, asynchronous architecture to retain the timing resolution of spikes. At the algorithm level, we will investigate an innovative SNN training algorithm for enabling activation sparsification and reducing unnecessary data communication costs. This neuromorphic system will provide an effective solution to real-life energy-constrained applications and significantly contribute to the exploration of next-generation high-performance computing systems under the DOE context.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Predictive Skill of Deep Learning Models Trained on Limited Sequence Data

In this report we investigate the utility of one-dimensional convolutional neural network (CNN) models in epidemiological forecasting. Deep learning models, especially variants of recurrent neural networks (RNNs) have been studied for influenza forecasting, and have achieved higher forecasting skill compared to conventional models such as ARIMA models. In this study, we adapt two neural networks that employ one-dimensional temporal convolutional layers as a primary building block temporal convolutional networks and simple neural attentive meta-learner for epidemiological forecasting and test them with influenza data from the US collected over 2010-2019. We find that epidemiological forecasting with CNNs is feasible, and their forecasting skill is comparable to, and at times, superior to, RNNs. Thus CNNs and RNNs bring the power of nonlinear transformations to purely data-driven epidemiological models, a capability that heretofore has been limited to more elaborate mechanistic/compartmental disease models.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗
DOE OSTI2021

Accurate prediction of protein structures and interactions using a three-track neural network

DeepMind presented notably accurate predictions at the recent 14th Critical Assessment of Structure Prediction (CASP14) conference. We explored network architectures that incorporate related ideas and obtained the best performance with a three-track network in which information at the one-dimensional (1D) sequence level, the 2D distance map level, and the 3D coordinate level is successively transformed and integrated. The three-track network produces structure predictions with accuracies approaching those of DeepMind in CASP14, enables the rapid solution of challenging x-ray crystallography and cryo–electron microscopy structure modeling problems, and provides insights into the functions of proteins of currently unknown structure. The network also enables rapid generation of accurate protein-protein complex models from sequence information alone, short-circuiting traditional approaches that require modeling of individual subunits followed by docking. Here, we make the method available to the scientific community to speed biological research.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Building molecular model series from heterogeneous CryoEM structures using Gaussian mixture models and deep neural networks

Cryogenic electron microscopy (CryoEM) produces structures of macromolecules at near-atomic resolution. However, building molecular models with good stereochemical geometry from those structures can be challenging and time-consuming, especially when many structures are obtained from datasets with conformational heterogeneity. Here we present a model refinement protocol that automatically generates series of molecular models from CryoEM datasets, which describe the dynamics of the macromolecular system and have near-perfect geometry scores. This method makes it easier to interpret the movement of the protein complex from heterogeneity analysis and to compare the structural dynamics observed from CryoEM data with results from other experimental and simulation techniques.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

PersGNN: Applying Topological Data Analysis and Geometric Deep Learning to Structure-Based Protein Function Prediction

Understanding protein structure-function relationships is a key challenge in computational biology, with applications across the biotechnology and pharmaceutical industries. While it is known that protein structure directly impacts protein function, many functional prediction tasks use only protein sequence. In this work, we isolate protein structure to make functional annotations for proteins in the Protein Data Bank in order to study the expressiveness of different structure-based prediction schemes. We present PersGNN - an end-to-end trainable deep learning model that combines graph representation learning with topological data analysis to capture a complex set of both local and global structural features. While variations of these techniques have been successfully applied to proteins before, we demonstrate that our hybridized approach, PersGNN, outperforms either method on its own as well as a baseline neural network that learns from the same information. PersGNN achieves a 9.3% boost in area under the precision recall curve (AUPR) compared to the best individual model, as well as high F1 scores across different gene ontology categories, indicating the transferability of this approach.

Swenson, Nicolas↗
DOE OSTI2023

Digital holography for real-time non-invasive monitoring of larval fish at power plant intakes

Effective evaluation of technological and operational approaches to reduce entrainment of marine organisms at cooling water intake structures (CWIS) requires accurate organism-sensing systems. Current detection methods lead to large temporal data gaps, require tedious manual analysis, and are fatal to organisms. In this report we describe integrating deep learning with a non-lethal, non-intrusive imaging method—digital holography—to rapidly detect fish larvae. Laboratory experiments demonstrated that the instrument could successfully image fish larvae at flow rates exceeding ranges seen in CWIS. Holograms of two fish larvae species, in the presence of bubbles and detritus, were collected to build a large database for training a lightweight convolutional neural network. The model achieves 97% extraction accuracy in quantifying larvae, and distinguishing them from other particles, including detritus and bubbles, when applied to a dataset of manually classified images, exceeding previous metrics for non-lethal, accurate, and real-time detection. These results demonstrate the potential of in situ holographic imaging for monitoring endangered larval fish species at power plant intake structures, and for high-fidelity, real-time applications in monitoring aquatic ichthyoplankton.

endangered species↗
DOE OSTI2022

Path sampling of recurrent neural networks by incorporating known physics

Recurrent neural networks have seen widespread use in modeling dynamical systems in varied domains such as weather prediction, text prediction and several others. Often one wishes to supplement the experimentally observed dynamics with prior knowledge or intuition about the system. While the recurrent nature of these networks allows them to model arbitrarily long memories in the time series used in training, it makes it harder to impose prior knowledge or intuition through generic constraints. In this work, we present a path sampling approach based on principle of Maximum Caliber that allows us to include generic thermodynamic or kinetic constraints into recurrent neural networks. We show the method here for a widely used type of recurrent neural network known as long short-term memory network in the context of supplementing time series collected from different application domains. These include classical Molecular Dynamics of a protein and Monte Carlo simulations of an open quantum system continuously losing photons to the environment and displaying Rabi oscillations. Our method can be easily generalized to other generative artificial intelligence models and to generic time series in different areas of physical and social sciences, where one wishes to supplement limited data with intuition or theory based corrections.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

CrossMP: Enabling Cross-Modality Translation between Single-Cell RNA-Seq and Single-Cell ATAC-Seq through Web-Based Portal

In recent years, there has been a growing interest in profiling multiomic modalities within individual cells simultaneously. One such example is integrating combined single-cell RNA sequencing (scRNA-seq) data and single-cell transposase-accessible chromatin sequencing (scATAC-seq) data. Integrated analysis of diverse modalities has helped researchers make more accurate predictions and gain a more comprehensive understanding than with single-modality analysis. However, generating such multimodal data is technically challenging and expensive, leading to limited availability of single-cell co-assay data. Here, we propose a model for cross-modal prediction between the transcriptome and chromatin profiles in single cells. Our model is based on a deep neural network architecture that learns the latent representations from the source modality and then predicts the target modality. It demonstrates reliable performance in accurately translating between these modalities across multiple paired human scATAC-seq and scRNA-seq datasets. Additionally, we developed CrossMP, a web-based portal allowing researchers to upload their single-cell modality data through an interactive web interface and predict the other type of modality data, using high-performance computing resources plugged at the backend.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Deep Learning Approaches to Surrogates for Solving the Diffusion Equation for Mechanistic Real-World Simulations

In many mechanistic medical, biological, physical, and engineered spatiotemporal dynamic models the numerical solution of partial differential equations (PDEs), especially for diffusion, fluid flow and mechanical relaxation, can make simulations impractically slow. Biological models of tissues and organs often require the simultaneous calculation of the spatial variation of concentration of dozens of diffusing chemical species. One clinical example where rapid calculation of a diffusing field is of use is the estimation of oxygen gradients in the retina, based on imaging of the retinal vasculature, to guide surgical interventions in diabetic retinopathy. Furthermore, the ability to predict blood perfusion and oxygenation may one day guide clinical interventions in diverse settings, i.e., from stent placement in treating heart disease to BOLD fMRI interpretation in evaluating cognitive function (Xie et al., 2019; Lee et al., 2020). Since the quasi-steady-state solutions required for fast-diffusing chemical species like oxygen are particularly computationally costly, we consider the use of a neural network to provide an approximate solution to the steady-state diffusion equation. Machine learning surrogates, neural networks trained to provide approximate solutions to such complicated numerical problems, can often provide speed-ups of several orders of magnitude compared to direct calculation. Surrogates of PDEs could enable use of larger and more detailed models than are possible with direct calculation and can make including such simulations in real-time or near-real time workflows practical. Creating a surrogate requires running the direct calculation tens of thousands of times to generate training data and then training the neural network, both of which are computationally expensive. Often the practical applications of such models require thousands to millions of replica simulations, for example for parameter identification and uncertainty quantification, each of which gains speed from surrogate use and rapidly recovers the up-front costs of surrogate generation. We use a Convolutional Neural Network to approximate the stationary solution to the diffusion equation in the case of two equal-diameter, circular, constant-value sources located at random positions in a two-dimensional square domain with absorbing boundary conditions. Such a configuration caricatures the chemical concentration field of a fast-diffusing species like oxygen in a tissue with two parallel blood vessels in a cross section perpendicular to the two blood vessels. To improve convergence during training, we apply a training approach that uses roll-back to reject stochastic changes to the network that increase the loss function. The trained neural network approximation is about 1000 times faster than the direct calculation for individual replicas. Because different applications will have different criteria for acceptable approximation accuracy, we discuss a variety of loss functions and accuracy estimators that can help select the best network for a particular application. We briefly discuss some of the issues we encountered with overfitting, mismapping of the field values and the geometrical conditions that lead to large absolute and relative errors in the approximate solution.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Building an ab initio solvated DNA model using Euclidean neural networks

Accurately modeling large biomolecules such as DNA from first principles is fundamentally challenging due to the steep computational scaling of ab initio quantum chemistry methods. This limitation becomes even more prominent when modeling biomolecules in solution due to the need to include large numbers of solvent molecules. We present a machine-learned electron density model based on a Euclidean neural network framework that includes a built-in understanding of equivariance to model explicitly solvated double-stranded DNA. By training the machine learning model using molecular fragments that sample the key DNA and solvent interactions, we show that the model predicts electron densities of arbitrary systems of solvated DNA accurately, resolves polarization effects that are neglected by classical force fields, and captures the physics of the DNA-solvent interaction at the ab initio level.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

A global lipid map defines a network essential for Zika virus replication

>Zika virus (ZIKV), an arbovirus of global concern, remodels intracellular membranes to form replication sites. How ZIKV dysregulates lipid networks to allow this, and consequences for disease, is poorly understood. Here, we performed comprehensive lipidomics to create a lipid network map during ZIKV infection. We found that ZIKV significantly alters host lipid composition, with the most striking changes seen within subclasses of sphingolipids. Ectopic expression of ZIKV NS4B protein resulted in similar changes, demonstrating a role for NS4B in modulating sphingolipid pathways. Disruption of sphingolipid biosynthesis in various cell types, including human neural progenitor cells, blocked ZIKV infection. Additionally, the sphingolipid ceramide redistributes to ZIKV replication sites and increasing ceramide levels by multiple pathways sensitizes cells to ZIKV infection. Thus, we identify a sphingolipid metabolic network with a critical role in ZIKV replication and show that ceramide flux is a key mediator of ZIKV infection.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Harnessing large language models’ zero-shot and few-shot learning capabilities for regulatory research

Abstract Large language models (LLMs) are sophisticated AI-driven models trained on vast sources of natural language data. They are adept at generating responses that closely mimic human conversational patterns. One of the most notable examples is OpenAI's ChatGPT, which has been extensively used across diverse sectors. Despite their flexibility, a significant challenge arises as most users must transmit their data to the servers of companies operating these models. Utilizing ChatGPT or similar models online may inadvertently expose sensitive information to the risk of data breaches. Therefore, implementing LLMs that are open source and smaller in scale within a secure local network becomes a crucial step for organizations where ensuring data privacy and protection has the highest priority, such as regulatory agencies. As a feasibility evaluation, we implemented a series of open-source LLMs within a regulatory agency’s local network and assessed their performance on specific tasks involving extracting relevant clinical pharmacology information from regulatory drug labels. Our research shows that some models work well in the context of few- or zero-shot learning, achieving performance comparable, or even better than, neural network models that needed thousands of training samples. One of the models was selected to address a real-world issue of finding intrinsic factors that affect drugs' clinical exposure without any training or fine-tuning. In a dataset of over 700 000 sentences, the model showed a 78.5% accuracy rate. Our work pointed to the possibility of implementing open-source LLMs within a secure local network and using these models to perform various natural language processing tasks when large numbers of training examples are unavailable.

Biochemistry & Molecular Biology↗
DOE OSTI2022

Objective Phenotyping of Root System Architecture Using Image Augmentation and Machine Learning in Alfalfa (Medicago sativa L.)

Active breeding programs specifically for root system architecture (RSA) phenotypes remain rare; however, breeding for branch and taproot types in the perennial crop alfalfa is ongoing. Phenotyping in this and other crops for active RSA breeding has mostly used visual scoring of specific traits or subjective classification into different root types. While image-based methods have been developed, translation to applied breeding is limited. This research is aimed at developing and comparing image-based RSA phenotyping methods using machine and deep learning algorithms for objective classification of 617 root images from mature alfalfa plants collected from the field to support the ongoing breeding efforts. Our results show that unsupervised machine learning tends to incorrectly classify roots into a normal distribution with most lines predicted as the intermediate root type. Encouragingly, random forest and TensorFlow-based neural networks can classify the root types into branch-type, taproot-type, and an intermediate taproot-branch type with 86% accuracy. With image augmentation, the prediction accuracy was improved to 97%. Coupling the predicted root type with its prediction probability will give breeders a confidence level for better decisions to advance the best and exclude the worst lines from their breeding program. This machine and deep learning approach enables accurate classification of the RSA phenotypes for genomic breeding of climate-resilient alfalfa.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Growing grasses in unprofitable areas of US Midwest croplands could increase species richness

The US has large potential to grow perennial energy crops, but because these crops are rarely grown in current agricultural landscapes, it is unclear how biodiversity may be affected. Over time, as agriculture has increased, many grassland species have declined. In addition, not all agricultural land is profitable for growing annual crops. Unprofitable areas were responsible for a loss of approximately $110 million USD per year from 2013 to 2016. Based on this, we want to know how converting less-profitable portions of agricultural fields to switchgrass, a native prairie grass, would influence species occurrence. To address this question, we developed an alternative landscape in which clustered corn/soy acres with a low return on investment (ROI) were replaced with grassland. We also developed and validated species distribution models to predict changes in species occurrence for 28 avian species in Iowa in response to landscape management. Furthermore, we compared results for three different models: Random forest (RF), Stochastic gradient boosting (GBM), and Neural network (Nnet) and found that all models performed well and predicted similar species distribution. Predicted species richness increased by 3.66% (RF), 2.79% (GBM), and 7.51% (Nnet) when we simulated a change in management for ~3% of Iowa's low ROI corn/soybean areas to grassland. If harvested, these areas could generate approximately 7.6 million dry tons/year of switchgrass for bioenergy, thereby increasing farmers earnings. Unprofitable areas tended to occur along streams, which suggest that incorporating partially harvested riparian buffers can benefit avian biodiversity, while improving water quality and reducing unnecessary costs for farmers.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Hyperspectral remote sensing-based plant community map for region around NGEE-Arctic intensive research watersheds at Seward Peninsula, Alaska, 2017-2019

Using airborne hyperspectral remote sensing data from NASA Airborne Visible-Infrared Imaging Spectrometer- Next Generation (AVIRIS-NG) platforms in a region near NGEE-Arctic intensive watersheds at Seward peninsula of Alaska, high resolution (5m) maps of plant community distribution were developed and included in this data collected. AVIRIS-NG data collected over 2017-2019 period were used to develop deep neural networks, trained using vegetation plot observations collected at NGEE-Arctic watersheds at Kougarok, Council and Teller. A hierarchical vegetation classification scheme consisting of six classes at Level I, and 16 classes at Level II contained in two .txt files were used to developed the plant community maps for the region. Two geospatial raster data files (.tif) at both thematic levels are shared in this data collection. Data files in this collection use Alaska Albers Equal Area projection. Readme files available in three formats (*.html, *.md, *.pdf) and one *.png visualization map.The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a research effort to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research.The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska.Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

A workflow for segmenting soil and plant X-ray computed tomography images with deep learning in Google’s Colaboratory

X-ray micro-computed tomography (X-ray μCT) has enabled the characterization of the properties and processes that take place in plants and soils at the micron scale. Despite the widespread use of this advanced technique, major limitations in both hardware and software limit the speed and accuracy of image processing and data analysis. Recent advances in machine learning, specifically the application of convolutional neural networks to image analysis, have enabled rapid and accurate segmentation of image data. Yet, challenges remain in applying convolutional neural networks to the analysis of environmentally and agriculturally relevant images. Specifically, there is a disconnect between the computer scientists and engineers, who build these AI/ML tools, and the potential end users in agricultural research, who may be unsure of how to apply these tools in their work. Additionally, the computing resources required for training and applying deep learning models are unique, more common to computer gaming systems or graphics design work, than to traditional computational systems. To navigate these challenges, we developed a modular workflow for applying convolutional neural networks to X-ray μCT images, using low-cost resources in Google’s Colaboratory web application. Here we present the results of the workflow, illustrating how parameters can be optimized to achieve best results using example scans from walnut leaves, almond flower buds, and a soil aggregate. We expect that this framework will accelerate the adoption and use of emerging deep learning techniques within the plant and soil sciences.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Functional and transcriptional characterization of complex neuronal co-cultures

Brain-on-a-chip systems are designed to simulate brain activity using traditional in vitro cell culture on an engineered platform. It is a noninvasive tool to screen new drugs, evaluate toxicants, and elucidate disease mechanisms. However, successful recapitulation of brain function on these systems is dependent on the complexity of the cell culture. In this study, we increased cellular complexity of traditional (simple) neuronal cultures by co-culturing with astrocytes and oligodendrocyte precursor cells (complex culture). We evaluated and compared neuronal activity (e.g., network formation and maturation), cellular composition in long-term culture, and the transcriptome of the two cultures. Compared to simple cultures, neurons from complex co-cultures exhibited earlier synapse and network development and maturation, which was supported by localized synaptophysin expression, up-regulation of genes involved in mature neuronal processes, and synchronized neural network activity. Also, mature oligodendrocytes and reactive astrocytes were only detected in complex cultures upon transcriptomic analysis of age-matched cultures. Functionally, the GABA antagonist bicuculline had a greater influence on bursting activity in complex versus simple cultures. Collectively, the cellular complexity of brain-on-a-chip systems intrinsically develops cell type-specific phenotypes relevant to the brain while accelerating the maturation of neuronal networks, important features underdeveloped in traditional cultures.

59 BASIC BIOLOGICAL SCIENCES↗