Machine learning (ML) and deep learning (DL) models impact our daily lives with applications in natural language modeling, image analysis, healthcare, genomics, and bioinformatics. The exponential growth of biological sequence data necessitates accompanying advances in computational methods. Although deep learning is highly effective for detecting and classifying biological sequences, challenges...
RNA structure prediction is a challenging problem, especially with pseudoknots. Recently, there has been a shift from the classical minimum free energy-based methods (MFE) to partition function-based ones that assemble structures based on base-pairing probabilities. Two typical examples of the latter group are the popular maximum expected accuracy (MEA) method...
Our goal is to build a system to model the RNA sequences that reveals their structural information by using efficient dynamic programming algorithms and deep learning approaches. We aim to 1) achieve linear-time for RNA secondary structure prediction based on existing minimum free energy models; 2) utilize deep neural networks...
Learning Analytics and other branches of Educational Research such as Computing Education Research (CER) implicitly assume that students, especially college students, have no barriers to access learning platforms or software packages. This assumption may be attributed to such pervasive beliefs such as "everyone has a device", or "everyone can access...
Situated cognition theory emphasizes the role that social and material contexts have on learning and knowledge application. Several studies of engineering workplace environments have noted differences between the social and material contexts of the workplace and those of undergraduate engineering education. No existing research has studied the social and material...
Most database users do not know formal query languages, such as SQL, and prefer to express their information needs using usable query languages, such as keyword queries. Keyword queries, however, are inherently ambiguous and challenging for the database systems to understand and answer effectively. We propose a novel approach to...
The advent of deep learning models leads to a substantial improvement in a wide range of NLP tasks, achieving state-of-art performances without any hand-crafted features. However, training deep models requires a massive amount of labeled data. Labeling new data as a new task or domain emerges consumes time and efforts...
Automatic music transcription (AMT) is the task, given an acoustic representation of music, to recover a symbolic notation of the written notes expressed by the sound. Transcribing music with multiple notes sounding simultaneously is difficult for both humans and machines. Much existing work on AMT has focused on suitable acoustic...
Learning novel concepts from relational databases is an important problem with applications in several disciplines, such as data management, natural language processing, and bioinformatics. For a learning algorithm to be effective, the input data should be clean and in some desired representation. However, real-world data is usually heterogeneous – the...
Anomaly detection has been used in variety of applications in practice, including cyber-security, fraud detection and detecting faults in safety critical systems, etc. Anomaly detectors produce a ranked list of statistical anomalies, which are typically examined by human analysts in order to extract the actual anomalies of interest. Unfortunately, most...
A series of laboratory experiments were conducted to study the wave field in the inner lagoon excited by ‘long’ incident waves. Three cases were considered: Cases A, B and C presenting incident waves of wavelength with factors of 1, 2 and 2.5 times the width of the reef respectively. The...
There are growing interests in designing polynomial-time approximation schemes (PTAS) for optimization problems in planar graphs. Many NP-hard problems are shown to admit PTAS in planar graphs in the last decade, including Steiner tree, Steiner forest, two- edge-connected subgraphs and so on. We follow this research line and study several...
Recent advancements in joining operations and additive manufacturing now allow complex metal parts to be built up from raw materials, as opposed to being machined down from solid blocks. This not only opens up the design space, but also allows for much more efficient manufacturing. By decomposing a complex part...
Changes in the global climate and forest management practices have given rise to increasing numbers and severity of wildfires. More than five million acres burned in the United States in 2017, while in Canada 7.4 million acres burned. In particular, an increasing amount of dead woody biomass is a key...
The Rust programming language is a systems programming language with a strong static type system. A central feature of Rust’s type system is its unique concept of “ownership”, which enables Rust to give a user safe, low-level control over resources without the overhead of garbage collection. In Haskell, most data...
Automatic event extraction from natural text is an important and challenging task for natural language understanding. Traditional event detection methods heavily rely on manually engineered rich features. Recent deep learning approaches alleviate this problem by automatic feature engineering. But such efforts, like tradition methods, have so far only focused on...
Although machine learning systems are often effective in real-world applications, there are situations in which they can be even better when provided with some degree of end user feedback. This is especially true when the machine learning system needs to customize itself to the end user's preferences, such as in...
Society faces many complex management problems, particularly in the area of shared public resources such as ecosystems. Existing decision making processes are often guided by personal experience and political ideology rather than state-of-the-art scientific understanding. This dissertation envisions a future in which multiple stakeholders are provided with computational tools for...
There is growing commercial interest in the use of unmanned aerial vehicles (UAVs) in urban environments, specifically for package delivery applications. However, the size, complexity and sheer numbers of expected UAVs makes conventional air traffic management that relies on human air traffic controllers infeasible. To enable UAVs to safely and...
In Intense Pulsed Light (IPL) sintering, pulsed large-area visible light from a xenon lamp is absorbed by nanoparticle films or patterns and converted to heat, resulting in rapid sintering of the nanoparticles. This work experimentally characterizes IPL sintering of silver nanoparticle films. A newly observed turning point in the evolution...