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41	A Machine Learning Model of Perturb-Seq Data for use in Space Flight Gene Expression Profile Analysis Liam Fitzpatric Johnson (18437556) 27 April 2024 (has links) <p dir="ltr">The genetic perturbations caused by spaceflight on biological systems tend to have a system-wide effect which is often difficult to deconvolute into individual signals with specific points of origin. Single cell multi-omic data can provide a profile of the perturbational effects but does not necessarily indicate the initial point of interference within a network. The objective of this project is to take advantage of large scale and genome-wide perturbational or Perturb-Seq datasets by using them to pre-train a generalist machine learning model that is capable of predicting the effects of unseen perturbations in new data. Perturb-Seq datasets are large libraries of single cell RNA sequencing data collected from CRISPR knock out screens in cell culture. The advent of generative machine learning algorithms, particularly transformers, make it an ideal time to re-assess large scale data libraries in order to grasp cell and even organism-wide genomic expression motifs. By tailoring an algorithm to learn the downstream effects of the genetic perturbations, we present a pre-trained generalist model capable of predicting the effects of multiple perturbations in combination, locating points of origin for perturbation in new datasets, predicting the effects of known perturbations in new datasets, and annotation of large-scale network motifs. We demonstrate the utility of this model by identifying key perturbational signatures in RNA sequencing data from spaceflown biological samples from the NASA Open Science Data Repository.</p> Bioinformatic methods development Genomics and transcriptomics Modelling and simulation Neural networks Perturb-Seq Machine Learning scRNA-seq GSEA RNA-seq Multi-Layer Perceptron Convolutional Neural Network Random Forest multi-class classification multi-label multi-class classification UMAP Leiden clustering K562 cell line RPE1 cell line spaceflight space environment effects differentially expressed gene (DGE) machine learning prediction models gene expression transcriptomics
42	Characterization of Quasi-Periodic Orbits for Applications in the Sun-Earth and Earth-Moon Systems Brian P. McCarthy (5930747) 17 January 2019 (has links) <div>As destinations of missions in both human and robotic spaceﬂight become more exotic, a foundational understanding the dynamical structures in the gravitational environments enable more informed mission trajectory designs. One particular type of structure, quasi-periodic orbits, are examined in this investigation. Speciﬁcally, eﬃcient computation of quasi-periodic orbits and leveraging quasi-periodic orbits as trajectory design alternatives in the Earth-Moon and Sun-Earth systems. First, periodic orbits and their associated center manifold are discussed to provide the background for the existence of quasi-periodic motion on n-dimensional invariant tori, where n corresponds to the number of fundamental frequencies that deﬁne the motion. Single and multiple shooting diﬀerential corrections strategies are summarized to compute families 2-dimensional tori in the Circular Restricted Three-Body Problem (CR3BP) using a stroboscopic mapping technique, originally developed by Howell and Olikara. Three types of quasi-periodic orbit families are presented: constant energy, constant frequency ratio, and constant mapping time families. Stability of quasi-periodic orbits is summarized and characterized with a single stability index quantity. For unstable quasi-periodic orbits, hyperbolic manifolds are computed from the diﬀerential of a discretized invariant curve. The use of quasi-periodic orbits is also demonstrated for destination orbits and transfer trajectories. Quasi-DROs are examined in the CR3BP and the Sun-Earth-Moon ephemeris model to achieve constant line of sight with Earth and avoid lunar eclipsing by exploiting orbital resonance. Arcs from quasi-periodic orbits are leveraged to provide an initial guess for transfer trajectory design between a planar Lyapunov orbit and an unstable halo orbit in the Earth-Moon system. Additionally, quasi-periodic trajectory arcs are exploited for transfer trajectory initial guesses between nearly stable periodic orbits in the Earth-Moon system. Lastly, stable hyperbolic manifolds from a Sun-Earth L<sub>1</sub> quasi-vertical orbit are employed to design maneuver-free transfer from the LEO vicinity to a quasi-vertical orbit.</div> Aerospace Engineering aerospace engineering trajectory trajectory design astrodynamics three body three body mechanics circular restricted three body problem CR3BP quasi-periodic orbits periodic orbits orbit mechanics celestial mechanics dynamical systems dynamical systems theory dynamics applications orbits astronautics differential corrections invariance invariant circle invariant torus torus invariant tori stroboscopic mapping manifolds Sun-Earth system Earth-Moon system stability multiple shooting stroboscopic map eclipse avoidance vertical orbit halo orbit distant retrograde orbit quasi-halo quasi-vertical lissajous quasi-DRO DRO NRHO quasi-NRHO synodic resonance trajectory arcs mission design astromechanics spaceflight mechanics dynamical structures

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A Machine Learning Model of Perturb-Seq Data for use in Space Flight Gene Expression Profile Analysis

Characterization of Quasi-Periodic Orbits for Applications in the Sun-Earth and Earth-Moon Systems