Physical Sciences and Mathematics Commons^™

Using Ensemble Learning Techniques To Solve The Blind Drift Calibration Problem, Devin Scott Drake

Computer Science Theses & Dissertations

Large sets of sensors deployed in nearly every practical environment are prone to drifting out of calibration. This drift can be sensor-based, with one or several sensors falling out of calibration, or system-wide, with changes to the physical system causing sensor-reading issues. Recalibrating sensors in either case can be both time and cost prohibitive. Ideally, some technique could be employed between the sensors and the final reading that recovers the drift-free sensor readings. This paper covers the employment of two ensemble learning techniques — stacking and bootstrap aggregation (or bagging) — to recover drift-free sensor readings from a suite of …

Transparscit: A Transformer-Based Citation Parser Trained On Large-Scale Synthesized Data, Md Sami Uddin

Computer Science Theses & Dissertations

Accurately parsing citation strings is key to automatically building large-scale citation graphs, so a robust citation parser is an essential module in academic search engines. One limitation of the state-of-the-art models (such as ParsCit and Neural-ParsCit) is the lack of a large-scale training corpus. Manually annotating hundreds of thousands of citation strings is laborious and time-consuming. This thesis presents a novel transformer-based citation parser by leveraging the GIANT dataset, consisting of 1 billion synthesized citation strings covering over 1500 citation styles. As opposed to handcrafted features, our model benefits from word embeddings and character-based embeddings by combining the bidirectional long …

Highly Accurate Fragment Library For Protein Fold Recognition, Wessam Elhefnawy

Computer Science Theses & Dissertations

Proteins play a crucial role in living organisms as they perform many vital tasks in every living cell. Knowledge of protein folding has a deep impact on understanding the heterogeneity and molecular functions of proteins. Such information leads to crucial advances in drug design and disease understanding. Fold recognition is a key step in the protein structure discovery process, especially when traditional computational methods fail to yield convincing structural homologies. In this work, we present a new protein fold recognition approach using machine learning and data mining methodologies.

First, we identify a protein structural fragment library (Frag-K) composed of a …

Deep Learning For Segmentation Of 3d Cryo-Em Images, Devin Reid Haslam

Computer Science Theses & Dissertations

Cryo-electron microscopy (cryo-EM) is an emerging biophysical technique for structural determination of protein complexes. However, accurate detection of secondary structures is still challenging when cryo-EM density maps are at medium resolutions (5-10 Å). Most existing methods are image processing methods that do not fully utilize available images in the cryo-EM database. In this paper, we present a deep learning approach to segment secondary structure elements as helices and β-sheets from medium- resolution density maps. The proposed 3D convolutional neural network is shown to detect secondary structure locations with an F1 score between 0.79 and 0.88 for six simulated test cases. …

Machine Learning Methods For Medical And Biological Image Computing, Rongjian Li

Computer Science Theses & Dissertations

Medical and biological imaging technologies provide valuable visualization information of structure and function for an organ from the level of individual molecules to the whole object. Brain is the most complex organ in body, and it increasingly attracts intense research attentions with the rapid development of medical and bio-logical imaging technologies. A massive amount of high-dimensional brain imaging data being generated makes the design of computational methods for efficient analysis on those images highly demanded. The current study of computational methods using hand-crafted features does not scale with the increasing number of brain images, hindering the pace of scientific discoveries …

A Computational Framework For Learning From Complex Data: Formulations, Algorithms, And Applications, Wenlu Zhang

Computer Science Theses & Dissertations

Many real-world processes are dynamically changing over time. As a consequence, the observed complex data generated by these processes also evolve smoothly. For example, in computational biology, the expression data matrices are evolving, since gene expression controls are deployed sequentially during development in many biological processes. Investigations into the spatial and temporal gene expression dynamics are essential for understanding the regulatory biology governing development. In this dissertation, I mainly focus on two types of complex data: genome-wide spatial gene expression patterns in the model organism fruit fly and Allen Brain Atlas mouse brain data. I provide a framework to explore …

Machine Learning Methods For Brain Image Analysis, Ahmed Fakhry

Computer Science Theses & Dissertations

Understanding how the brain functions and quantifying compound interactions between complex synaptic networks inside the brain remain some of the most challenging problems in neuroscience. Lack or abundance of data, shortage of manpower along with heterogeneity of data following from various species all served as an added complexity to the already perplexing problem. The ability to process vast amount of brain data need to be performed automatically, yet with an accuracy close to manual human-level performance. These automated methods essentially need to generalize well to be able to accommodate data from different species. Also, novel approaches and techniques are becoming …