Assessing Comment Quality in Object-Oriented Languages

Previous studies have shown that high-quality code comments support developers in software maintenance and program comprehension tasks. However, the semi-structured nature of comments, several conventions to write comments, and the lack of quality assessment tools for all aspects of comments make comment evaluation and maintenance a non-trivial problem. To understand the specification of high-quality comments to build effective assessment tools, our thesis emphasizes acquiring a multi-perspective view of the comments, which can be approached by analyzing (1) the academic support for comment quality assessment, (2) developer commenting practices across languages, and (3) developer concerns about comments. Our findings regarding the academic support for assessing comment quality showed that researchers primarily focus on Java in the last decade even though the trend of using polyglot environments in software projects is increasing. Similarly, the trend of analyzing specific types of code comments (method comments, or inline comments) is increasing, but the studies rarely analyze class comments. We found 21 quality attributes that researchers consider to assess comment quality, and manual assessment is still the most commonly used technique to assess various quality attributes. Our analysis of developer commenting practices showed that developers embed a mixed level of details in class comments, ranging from high-level class overviews to low-level implementation details across programming languages. They follow style guidelines regarding what information to write in class comments but violate the structure and syntax guidelines. They primarily face problems locating relevant guidelines to write consistent and informative comments, verifying the adherence of their comments to the guidelines, and evaluating the overall state of comment quality. To help researchers and developers in building comment quality assessment tools, we contribute: (i) a systematic literature review (SLR) of ten years (2010–2020) of research on assessing comment quality, (ii) a taxonomy of quality attributes used to assess comment quality, (iii) an empirically validated taxonomy of class comment information types from three programming languages, (iv) a multi-programming-language approach to automatically identify the comment information types, (v) an empirically validated taxonomy of comment convention-related questions and recommendation from various Q&A forums, and (vi) a tool to gather discussions from multiple developer sources, such as Stack Overflow, and mailing lists. Our contributions provide various kinds of empirical evidence of the developer’s interest in reducing efforts in the software documentation process, of the limited support developers get in automatically assessing comment quality, and of the challenges they face in writing high-quality comments. This work lays the foundation for future effective comment quality assessment tools and techniques

Assessing Comment Quality in Object-Oriented Languages

Previous studies have shown that high-quality code comments support developers in software maintenance and program comprehension tasks. However, the semi-structured nature of comments, several conventions to write comments, and the lack of quality assessment tools for all aspects of comments make comment evaluation and maintenance a non-trivial problem. To understand the specification of high-quality comments to build effective assessment tools, our thesis emphasizes acquiring a multi-perspective view of the comments, which can be approached by analyzing (1) the academic support for comment quality assessment, (2) developer commenting practices across languages, and (3) developer concerns about comments. Our findings regarding the academic support for assessing comment quality showed that researchers primarily focus on Java in the last decade even though the trend of using polyglot environments in software projects is increasing. Similarly, the trend of analyzing specific types of code comments (method comments, or inline comments) is increasing, but the studies rarely analyze class comments. We found 21 quality attributes that researchers consider to assess comment quality, and manual assessment is still the most commonly used technique to assess various quality attributes. Our analysis of developer commenting practices showed that developers embed a mixed level of details in class comments, ranging from high-level class overviews to low-level implementation details across programming languages. They follow style guidelines regarding what information to write in class comments but violate the structure and syntax guidelines. They primarily face problems locating relevant guidelines to write consistent and informative comments, verifying the adherence of their comments to the guidelines, and evaluating the overall state of comment quality. To help researchers and developers in building comment quality assessment tools, we contribute: (i) a systematic literature review (SLR) of ten years (2010–2020) of research on assessing comment quality, (ii) a taxonomy of quality attributes used to assess comment quality, (iii) an empirically validated taxonomy of class comment information types from three programming languages, (iv) a multi-programming-language approach to automatically identify the comment information types, (v) an empirically validated taxonomy of comment convention-related questions and recommendation from various Q&A forums, and (vi) a tool to gather discussions from multiple developer sources, such as Stack Overflow, and mailing lists. Our contributions provide various kinds of empirical evidence of the developer’s interest in reducing efforts in the software documentation process, of the limited support developers get in automatically assessing comment quality, and of the challenges they face in writing high-quality comments. This work lays the foundation for future effective comment quality assessment tools and techniques

On the challenges and rewards of analyzing molecular dynamics at the terabyte and millisecond scale

Molecular Dynamics (MD) and Markov state models (MSMs) are powerful tools for estimating and concisely representing the conformational ensemble accessible to biological macromolecules, particularly proteins. Conformational ensembles are of special importance biological function, both in health and disease, because biology derives from molecules’ entire conformational distribution rather than any single structure. Consequently, MD is poised to become a powerful tool for personalized medicine and for the study of molecular sequence-function relationships generally. However, because of their hyperdimensionality and size, just generating MD datasets and Markov state models (MSMs) that represent biologically relevant molecules is a substantive technical challenge. Then, even once these models are generated, it is not immediately obvious how the conformational ensemble represented by an MSM encodes function. In this thesis, I first present enspara, a python library that makes it possible to build and analyze MSMs at an unprecedented scale. Then, I present “exposons,” an unsupervised machine learning method for discovering substructure these colossal datasets by searching for cooperative changes in a protein’s surface. This method is applied to several small systems of biological interest. Finally, I demonstrate the power these technologies to analyze the kinetic diversity of motor protein myosin, the longest-studied protein in all biochemistry, and in so doing address a longstanding mystery in the field of myosin biochemistry. The applicability of these technologies is almost certainly not limited to the handful of systems I study here. Therefore, this work likely has broad implications for the future of biochemistry, personalized medicine, and the study of biology

FAST-Forward Protein Folding and Design: Development, Analysis, and Applications of the FAST Sampling Algorithm

Molecular dynamics simulations are a powerful tool to explore conformational landscapes, though limitations in computational hardware commonly thwart observation of biologically relevant events. Since highly specialized or massively parallelized distributed supercomputers are not available to most scientists, there is a strong need for methods that can access long timescale phenomena using commodity hardware. In this thesis, I present the goal-oriented sampling method, Fluctuation Amplification of Specific Traits (FAST), that takes advantage of Markov state models (MSMs) to adaptively explore conformational space using equilibrium-based simulations. This method follows gradients in conformational space to quickly explore relevant conformational transitions with orders of magnitude less aggregate simulation time than traditional simulations. Since each of the individual simulations are at equilibrium, all of the thermodynamics and kinetics in the final MSM are preserved. Here, I first describe the FAST method then demonstrate that it can be used for a variety of tasks, from folding proteins to finding cryptic pockets. Next, I validate that FAST discovers appropriate transition pathways between states. Lastly, I apply FAST in detailing the mechanism of stabilization for a clinically relevant mutation in TEM-1 β-lactamase. This mechanistic understanding is then used to design other stabilizing mutations, which are all supported experimentally

Q(sqrt(-3))-Integral Points on a Mordell Curve

We use an extension of quadratic Chabauty to number fields,recently developed by the author with Balakrishnan, Besser and M ̈uller,combined with a sieving technique, to determine the integral points overQ(√−3) on the Mordell curve y2 = x3 − 4

New resources and ideas for semantic parser induction

In this thesis, we investigate the general topic of computational natural language understanding (NLU), which has as its goal the development of algorithms and other computational methods that support reasoning about natural language by the computer. Under the classical approach, NLU models work similar to computer compilers (Aho et al., 1986), and include as a central component a semantic parser that translates natural language input (i.e., the compiler’s high-level language) to lower-level formal languages that facilitate program execution and exact reasoning. Given the difficulty of building natural language compilers by hand, recent work has centered around semantic parser induction, or on using machine learning to learn semantic parsers and semantic representations from parallel data consisting of example text-meaning pairs (Mooney, 2007a). One inherent difficulty in this data-driven approach is finding the parallel data needed to train the target semantic parsing models, given that such data does not occur naturally “in the wild” (Halevy et al., 2009). Even when data is available, the amount of domain- and language-specific data and the nature of the available annotations might be insufficient for robust machine learning and capturing the full range of NLU phenomena. Given these underlying resource issues, the semantic parsing field is in constant need of new resources and datasets, as well as novel learning techniques and task evaluations that make models more robust and adaptable to the many applications that require reliable semantic parsing. To address the main resource problem involving finding parallel data, we investigate the idea of using source code libraries, or collections of code and text documentation, as a parallel corpus for semantic parser development and introduce 45 new datasets in this domain and a new and challenging text-to-code translation task. As a way of addressing the lack of domain- and language-specific parallel data, we then use these and other benchmark datasets to investigate training se- mantic parsers on multiple datasets, which helps semantic parsers to generalize across different domains and languages and solve new tasks such as polyglot decoding and zero-shot translation (i.e., translating over and between multiple natural and formal languages and unobserved language pairs). Finally, to address the issue of insufficient annotations, we introduce a new learning framework called learning from entailment that uses entailment information (i.e., high-level inferences about whether the meaning of one sentence follows from another) as a weak learning signal to train semantic parsers to reason about the holes in their analysis and learn improved semantic representations. Taken together, this thesis contributes a wide range of new techniques and technical solutions to help build semantic parsing models with minimal amounts of training supervision and manual engineering effort, hence avoiding the resource issues described at the onset. We also introduce a diverse set of new NLU tasks for evaluating semantic parsing models, which we believe help to extend the scope and real world applicability of semantic parsing and computational NLU