pnnl/gumby-spectral-imaging
Deep Learning models for multi- and hyper-spectral imaging data
Byler, Nell↗
Engineering topics
Central, PNNL Developer
Publications and source records attributed to Central, PNNL Developer.
pnnl/deimos_gui
The DEIMoS Graphical User Interface was created as an interface for DEIMoS: Data Extraction for Integrated Multidimensional Spectrometry. DEIMoS is a Python package to process data from mass spectrometry instrument developed at PNNL.
Oostrom, Marjolein↗
pnnl/parking
Commercial Parking Application is a web-based application that alerts delivery drivers in real time to available parking spaces near their destinations. Parking availability can be viewed on a map in real-time, using sensor data supplied by external services. The app can be viewed with a web browser on a mobile device or PC. Currently the app supports connections to real time sensors from Lacuna, Fybr, Cleverciti, and Automotus
Bleeker, Amelia↗
pnnl/PTMPSI
PTM-Psi is a Python 3 package that combines several capabilities to streamline the workflow to interrogate the impact of PTMs on proteins using well-established software packages. The workflow of the PTM-Psi software package includes input files and launch instances from standard packages such as AlphaFold, NWChem, GROMACS, and the Autodock Suite
Mejia-Rodriguez, Daniel↗
pnnl/frequency_sensitivity
This research code base includes functions to compute statistics of image distributions in (spatial DFT) frequency space, train deep learning image classifiers on these distributions with variable depth and weight decay, and finally measure the sensitivity of the trained models to perturbations along (spatial DFT) frequency components.
Central, PNNL Developer↗
pnnl/PHANTOM
A topology-based anomaly detection tool for temporal varying data. The input is json or CSV formatted data with a timestamp field identified. The algorithm computes vectorizations (using a vectorization config file) of time windows of data and computes a topological measure of anomalousness. The output is a sequence of anomaly scores for each time window
Seppala, Garret↗
pnnl/mlprotein
The molecular graphics program, PyMol, was employed to produce all images in the training/validation/testing datasets. A PyMol script identified the clusters of interest from a list of all proteins containing 1) Fe (III) and Fe (II) ion and 2) FeS, respectively. A PyMol script and a Python webscraper were also used to classify [2Fe-2S] cofactors into three classes: standard, Rieske, and other and to identify iron atoms with four cysteine residues. We also used the pyMol script to rotate amino acids for training
Oostrom, Marjolein↗
pnnl/Pathway_Controlled_Optimization
A method for prediction of cell regulation to maximize cell growth rate while maintaining the solvent capacity of the cell. Prediction is formulated as an optimization problem using a thermodynamic framework that can leverage experimental data. We develop a formulation and variable initialization procedure that allows for computing solutions of the optimization with an interior point method
Central, PNNL Developer↗
pnnl/TransMED
Transfer Learning From Existing Diseases Via Hierarchical Multi-Modal BERT Models
Ham, Colby↗
pnnl/dream_v3
The Designs for Risk Evaluation and Management (DREAM) tool was developed as part of the effort to quantify the risk of geologic storage of carbon dioxide (CO2) under the U.S. Department of Energy’s National Risk Assessment Partnership (NRAP). DREAM is an optimization tool created to identify optimal monitoring schemes that minimize the time to first detection of CO2 leakage from a subsurface storage formation. DREAM acts as a post-processer on user-provided output from subsurface leakage simulations. While DREAM was developed for CO2 leakage scenarios, it is applicable to any subsurface leakage simulation of the same output format
Kupis, Shyla↗
pnnl/memgaze
MemGaze is a memory analysis toolset that combines high-resolution trace analysis and low overhead measurement, both with respect to time and space. It provides high-resolution by collecting world-level memory access traces, where the highest resolution supported is back-to-back sequences. It achieves low-overhead in space and time by leveraging sampling and various methods of hardware support for collecting traces. Its post-mortem trace processing provides multiresolution analysis for locations vs. operations; accesses vs. spatio-temporal reuse, and reuse (distance, rate, volume) vs. access patterns.
Central, PNNL Developer↗
pnnl/portfoliomanager-rb
This invention is a Ruby "gem" (library) that provides clients for ENERGY STAR Portfolio Manager (ESPM) Web Services, Inventive features: 100% coverage of version 18.0 of the ESPM API. Automated mapping between ESPM XML schemas and Ruby objects. Clients for both the "live" and "test" ESPM API environments. Debugging mode with HTTP request/response logging.
Borkum, Mark↗
pnnl/simple-building-calculator
The Simple Building Calculator is a web application that estimates annual energy use using regression models that have been fit to simulation results for the DOE Commercial Prototype Building Models. The tool is a single-page application that will allow a user to rapidly analyze the impact of energy efficiency measures and design options on building performance. As it uses linear regression models rather than more complicated machine learning models or physics based simulation, the tool can deploy easily and run client-side.
Xu, Weili↗
pnnl/eqc
EQC is a software framework for smart distributed quantum computer management and organization for variational quantum algorithms. EQC utilizes smart real time management of multiple independent quantum processors to maximize variational quantum algorithm throughput, for improved converged performance and improved rate of convergance.
Central, PNNL Developer↗
pnnl/COMET
COMET: Domain Specific Compilation in Multi-level IR COMET is a compiler for dense and sparse tensor algebra and a domain-specific-language (DSL) that facilitates development and implementation of high-performance computing, graph analytics, and artificial intelligence (AI) applications.
Kestor, Gokcen↗
pnnl/hydraconda
A framework for developing scientific computing codes for projects was developed that accommodates both explorations as well as, simultaneously, software engineering rigor. This is accomplished by organizing modular yet composable and related computational environments. Also known as Management of Multiple Computational Environments
alDosari, Majid↗
pnnl/Active-Sampling-for-Atomistic-Potentials
This software contains a routine for active sampling of a DFT-generated dataset for training a neural network potential (SchNet). Major updates to the base SchNet code are also included to accommodate large systems (100s of atoms). We also provide code to apply the neural network potential in dynamic shear simulations.
Sprueill, Henry↗