Engineering topics
Krishnakumar, Raga
Publications and source records attributed to Krishnakumar, Raga.
MAPLE v.1.0
SAND2025-00659O MAPLE is a software tool that uses epigenomic data to predict gene expression. MAPLE uses a set of epigenomic modifications to determine the effect on gene expression in a specific subset of species. The algorithm can be trained on additional species and epigenomic modifications, enhancing its predictive capabilities. EAGLE employs a hybrid neural network architecture, featuring a convolutional front-end and a multi-head attention layer, to process pre-processed signal data as input. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-NA0003525.
Poplar
SAND2025-00683O Poplar is a software tool that generates a phylogenetic tree from input gene and genome sequences. It integrates established tools to identify genes within genomes, group sequences, construct gene trees, and infer a species tree. Poplar processes nucleotide sequences, identifies similar sequences using Nucleotide BLAST, groups them with DBSCAN, aligns sequences with MAFFT, constructs gene trees with RAxML-NG, and infers a species tree using ASTRAL-Pro3. This pipeline provides a structured approach to phylogenetic analysis, facilitating the study of evolutionary relationships among species. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.
A Framework for Evaluating the Maturity Level of Machine Learning Explanations
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Applied machine learning for elucidating complex relationships between epigenomic regulatory design rules and gene expression between fungal species across phylogenetic distances
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Applied machine learning for elucidating complex relationships between epigenomic regulatory design rules and gene expression between fungal species across phylogenetic distances
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From the bench to mass production: multi-omic analyses to reveal a roadmap for optimal prediction tools of algal culture scale-up
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Membrane-localized neoantigens predict the efficacy of cancer immunotherapy
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MalGen: Malware Generation with Specific Behaviors to Improve Machine Learning-based Detectors
In recent years, infections and damage caused by malware have increased at exponential rates. At the same time, machine learning (ML) techniques have shown tremendous promise in many domains, often out performing human efforts by learning from large amounts of data. Results in the open literature suggest that ML is able to provide similar results for malware detection, achieving greater than 99% classifcation accuracy [49]. However, the same detection rates when applied in deployed settings have not been achieved. Malware is distinct from many other domains in which ML has shown success in that (1) it purposefully tries to hide, leading to noisy labels and (2) often its behavior is similar to benign software only differing in intent, among other complicating factors. This report details the reasons for the diffcultly of detecting novel malware by ML methods and offers solutions to improve the detection of novel malware.
Electrochemically Tunable Mixed Valence Conduction in Ruthenium Hexacyanoruthenate.
Abstract not provided.
All Models are Wrong, but Some(times) are Useful: Evaluating when Machine Learning Models are Useful for Detecting Novel Malware in the Wild.
Abstract not provided.
Combined Imaging and RNA-Seq on a Microfluidic Platform for Viral Infection Studies
The goal of this work was to pioneer a novel, low-overhead protocol for simultaneously assaying cell-surface markers and intracellular gene expression in a single mammalian cell. The purpose of developing such a method is to be able to understand the mechanisms by which pathogens engage with individual mammalian cells, depending on their cell surface proteins, and how both host and pathogen gene expression changes are reflective of these mechanisms. The knowledge gained from such analyses of single cells will ultimately lead to more robust pathogen detection and countermeasures. Our method was aimed at streamlining both the upstream cell sample preparation using microfluidic methods, as well as the actual library making protocol. Specifically, we wanted to implement a random hexamer-based reverse transcription of all RNA within a single cell (as opposed to oligo dT-based which would only capture polyadenylated transcripts), and then use a CRISPR-based method called scDash to deplete ribosomal DNAs (since ribosomal RNAs make up the majority of the RNA in a mammalian cell). After significant troubleshooting, we demonstrate that we are able to prepare cDNA from RNA using the random hexamer primer, and perform the rDNA depletion. We also show that we can visualize individually stained cells, setting up the pipeline for connecting surface markers to RNA-sequencing profiles. Finally, we test a number of devices for various parts of the pipeline, including bead generation, optical barcoding and cell dispensing, and demonstrate that while some of these have potential, more work is needed to optimize this part of the pipeline.
Proton Tunable Analog Transistor for Low Power Computing
This project was broadly motivated by the need for new hardware that can process information such as images and sounds right at the point of where the information is sensed (e.g. edge computing). The project was further motivated by recent discoveries by group demonstrating that while certain organic polymer blends can be used to fabricate elements of such hardware, the need to mix ionic and electronic conducting phases imposed limits on performance, dimensional scalability and the degree of fundamental understanding of how such devices operated. As an alternative to blended polymers containing distinct ionic and electronic conducting phases, in this LDRD project we have discovered that a family of mixed valence coordination compounds called Prussian blue analogue (PBAs), with an open framework structure and ability to conduct both ionic and electronic charge, can be used for inkjet-printed flexible artificial synapses that reversibly switch conductance by more than four orders of magnitude based on electrochemically tunable oxidation state. Retention of programmed states is improved by nearly two orders of magnitude compared to the extensively studied organic polymers, thus enabling in-memory compute and avoiding energy costly off-chip access during training. We demonstrate dopamine detection using PBA synapses and biocompatibility with living neurons, evoking prospective application for brain - computer interfacing. By application of electron transfer theory to in-situ spectroscopic probing of intervalence charge transfer, we elucidate a switching mechanism whereby the degree of mixed valency between N-coordinated Ru sites controls the carrier concentration and mobility, as supported by density functional theory (DFT) .
Data Science and Machine Learning for Genome Security
This report describes research conducted to use data science and machine learning methods to distinguish targeted genome editing versus natural mutation and sequencer machine noise. Genome editing capabilities have been around for more than 20 years, and the efficiencies of these techniques has improved dramatically in the last 5+ years, notably with the rise of CRISPR-Cas technology. Whether or not a specific genome has been the target of an edit is concern for U.S. national security. The research detailed in this report provides first steps to address this concern. A large amount of data is necessary in our research, thus we invested considerable time collecting and processing it. We use an ensemble of decision tree and deep neural network machine learning methods as well as anomaly detection to detect genome edits given either whole exome or genome DNA reads. The edit detection results we obtained with our algorithms tested against samples held out during training of our methods are significantly better than random guessing, achieving high F1 and recall scores as well as with precision overall.
Malware Generation with Specific Behaviors to Improve Machine Learning-based Detectors.
Abstract not provided.
Malware Generation with Specific Behaviors to Improve Machine Learning-based Detectors.
Abstract not provided.
CERES: CRISPR Engineering for the Rapid Enhancement of Strains
Previous strain development efforts for cyanobacteria have failed to achieve the necessary productivities needed to support economic biofuel production. We proposed to develop CRISPR Engineering for Rapid Enhancement of Strains (CERES). We developed genetic and computational tools to enable future high-throughput screening of CRISPR interference (CRISPRi) libraries in the cyanobacterium Synechococcus sp. PCC 7002, including: (1) Operon- SEQer: an ensemble of algorithms for predicting operon pairs using RNA-seq data, (2) experimental characterization and machine learning prediction of gRNA design rules for CRISPRi, and (3) a shuttle vector for gene expression. These tools lay the foundation for CRISPR library screening to develop cyanobacterial strains that are optimized for growth or metabolite production under a wide range of environmental conditions. The optimization of cyanobacterial strains will directly advance U.S. energy and climate security by enabling domestic biofuel production while simultaneously mitigating atmospheric greenhouse gases through photoautotrophic fixation of carbon dioxide.
Therapeutic phages and methods thereof
The present invention relates, in part, to engineered viruses (e.g., engineered phages), phage cocktails, and methods of producing and/or identifying viruses for targeting pathogenic bacteria.