An Introduction to Programming for Bioscientists: A Python-based Primer

Computing has revolutionized the biological sciences over the past several decades, such that virtually all contemporary research in the biosciences utilizes computer programs. The computational advances have come on many fronts, spurred by fundamental developments in hardware, software, and algorithms. These advances have influenced, and even engendered, a phenomenal array of bioscience fields, including molecular evolution and bioinformatics; genome-, proteome-, transcriptome- and metabolome-wide experimental studies; structural genomics; and atomistic simulations of cellular-scale molecular assemblies as large as ribosomes and intact viruses. In short, much of post-genomic biology is increasingly becoming a form of computational biology. The ability to design and write computer programs is among the most indispensable skills that a modern researcher can cultivate. Python has become a popular programming language in the biosciences, largely because (i) its straightforward semantics and clean syntax make it a readily accessible first language; (ii) it is expressive and well-suited to object-oriented programming, as well as other modern paradigms; and (iii) the many available libraries and third-party toolkits extend the functionality of the core language into virtually every biological domain (sequence and structure analyses, phylogenomics, workflow management systems, etc.). This primer offers a basic introduction to coding, via Python, and it includes concrete examples and exercises to illustrate the language's usage and capabilities; the main text culminates with a final project in structural bioinformatics. A suite of Supplemental Chapters is also provided. Starting with basic concepts, such as that of a 'variable', the Chapters methodically advance the reader to the point of writing a graphical user interface to compute the Hamming distance between two DNA sequences.Comment: 65 pages total, including 45 pages text, 3 figures, 4 tables, numerous exercises, and 19 pages of Supporting Information; currently in press at PLOS Computational Biolog

Type-2 fuzzy logic system applications for power systems

PhD ThesisIn the move towards ubiquitous information & communications technology, an opportunity for further optimisation of the power system as a whole has arisen. Nonetheless, the fast growth of intermittent generation concurrently with markets deregulation is driving a need for timely algorithms that can derive value from these new data sources. Type-2 fuzzy logic systems can offer approximate solutions to these computationally hard tasks by expressing non-linear relationships in a more flexible fashion. This thesis explores how type-2 fuzzy logic systems can provide solutions to two of these challenging power system problems; short-term load forecasting and voltage control in distribution networks. On one hand, time-series forecasting is a key input for economic secure power systems as there are many tasks that require a precise determination of the future short-term load (e.g. unit commitment or security assessment among others), but also when dealing with electricity as commodity. As a consequence, short-term load forecasting becomes essential for energy stakeholders and any inaccuracy can be directly translated into their financial performance. All these is reflected in current power systems literature trends where a significant number of papers cover the subject. Extending the existing literature, this work focuses in how these should be implemented from beginning to end to bring to light their predictive performance. Following this research direction, this thesis introduces a novel framework to automatically design type-2 fuzzy logic systems. On the other hand, the low-carbon economy is pushing the grid status even closer to its operational limits. Distribution networks are becoming active systems with power flows and voltages defined not only by load, but also by generation. As consequence, even if it is not yet absolutely clear how power systems will evolve in the long-term, all plausible future scenarios claim for real-time algorithms that can provide near optimal solutions to this challenging mixed-integer non-linear problem. Aligned with research and industry efforts, this thesis introduces a scalable implementation to tackle this task in divide-and-conquer fashio

Deep R Programming

Deep R Programming is a comprehensive course on one of the most popular languages in data science (statistical computing, graphics, machine learning, data wrangling and analytics). It introduces the base language in-depth and is aimed at ambitious students, practitioners, and researchers who would like to become independent users of this powerful environment. This textbook is a non-profit project. Its online and PDF versions are freely available at . This early draft is distributed in the hope that it will be useful.Comment: Draft: v0.2.1 (2023-04-27

Automated Testing and Debugging for Big Data Analytics

The prevalence of big data analytics in almost every large-scale software system has generated a substantial push to build data-intensive scalable computing (DISC) frameworks such as Google MapReduce and Apache Spark that can fully harness the power of existing data centers. However, frameworks once used by domain experts are now being leveraged by data scientists, business analysts, and researchers. This shift in user demographics calls for immediate advancements in the development, debugging, and testing practices of big data applications, which are falling behind compared to the DISC framework design and implementation. In practice, big data applications often fail as users are unable to test all behaviors emerging from interleaving dataflow operators, user-defined functions, and framework's code. "Testing based on a random sample" rarely guarantees the reliability and "trial and error" and "print" debugging methods are expensive and time-consuming. Thus, the current practice of developing a big data application must be improved and the tools built to enhance the developer's productivity must adapt to the distinct characteristics of data-intensive scalable computing. By synthesizing ideas from software engineering and database systems, our hypothesis is that we can design effective and scalable testing and debugging algorithms for big data analytics without compromising the performance and efficiency of the underlying DISC framework. To design such techniques, we investigate how we can build interactive and responsive debugging primitives that significantly reduce the debugging time, yet do not pose much performance overhead on big data applications. Furthermore, we investigate how we can leverage data provenance techniques from databases and fault-isolation algorithms from software engineering to pinpoint the minimal subset of failure-inducing inputs efficiently. To improve the reliability of big data analytics, we investigate how we can abstract the semantics of dataflow operators and use them in tandem with the semantics of user-defined functions to generate a minimum set of synthetic test inputs capable of revealing more defects than the entire input dataset.To examine the first hypothesis, we introduce interactive, real-time debugging primitives for big data analytics through innovative and scalable debugging features such as simulated breakpoint, dynamic watchpoint, and crash culprit identification. Second, we design a new automated fault localization approach that combines insights from both the software engineering and database literature to bring delta debugging closer to a reality in the big data applications by leveraging data provenance and by constructing systems optimizations for debugging provenance queries. Lastly, we devise a new symbolic-execution based white-box testing algorithm for big data applications that abstracts the implementation of dataflow operators using logical specifications instead of modeling their implementations and combines them with the semantics of any arbitrary user-defined function. We instantiate the idea of an interactive debugging algorithm as BigDebug, the idea of an automated debugging algorithm as BigSift, and the idea of symbolic execution-based testing as BigTest. Our investigation shows that the interactive debugging primitives can scale to terabytes---our record-level tracing incurs less than 25% overhead on average and provides up to 100% time saving compared to the baseline replay debugger. Second, we observe that by combining data provenance with delta debugging, we can identify the minimum faulty input in just under 30% of the original job execution time. Lastly, we verify that by abstracting dataflow operators using logical specifications, we can efficiently generate the most concise test data suitable for local testing while revealing twice as many faults as prior approaches. Our investigations collectively demonstrate that developer productivity can be significantly improved through effective and scalable testing and debugging techniques for big data analytics, without impacting the DISC framework's performance. This dissertation affirms the feasibility of automated debugging and testing techniques for big data analytics---techniques that were previously considered infeasible for large-scale data processing

Computer Aided Verification

This open access two-volume set LNCS 11561 and 11562 constitutes the refereed proceedings of the 31st International Conference on Computer Aided Verification, CAV 2019, held in New York City, USA, in July 2019. The 52 full papers presented together with 13 tool papers and 2 case studies, were carefully reviewed and selected from 258 submissions. The papers were organized in the following topical sections: Part I: automata and timed systems; security and hyperproperties; synthesis; model checking; cyber-physical systems and machine learning; probabilistic systems, runtime techniques; dynamical, hybrid, and reactive systems; Part II: logics, decision procedures; and solvers; numerical programs; verification; distributed systems and networks; verification and invariants; and concurrency

Fine-Grained Provenance And Applications To Data Analytics Computation

Data provenance tools seek to facilitate reproducible data science and auditable data analyses by capturing the analytics steps used in generating data analysis results. However, analysts must choose among workflow provenance systems, which allow arbitrary code but only track provenance at the granularity of files; prove-nance APIs, which provide tuple-level provenance, but incur overhead in all computations; and database provenance tools, which track tuple-level provenance through relational operators and support optimization, but support a limited subset of data science tasks. None of these solutions are well suited for tracing errors introduced during common ETL, record alignment, and matching tasks – for data types such as strings, images, etc.Additionally, we need a provenance archival layer to store and manage the tracked fine-grained prove-nance that enables future sophisticated reasoning about why individual output results appear or fail to appear. For reproducibility and auditing, the provenance archival system should be tamper-resistant. On the other hand, the provenance collecting over time or within the same query computation tends to be repeated partially (i.e., the same operation with the same input records in the middle computation step). Hence, we desire efficient provenance storage (i.e., it compresses repeated results). We address these challenges with novel formalisms and algorithms, implemented in the PROVision system, for reconstructing fine-grained provenance for a broad class of ETL-style workflows. We extend database-style provenance techniques to capture equivalences, support optimizations, and enable lazy evaluations. We develop solutions for storing fine-grained provenance in relational storage systems while both compressing and protecting it via cryptographic hashes. We experimentally validate our proposed solutions using both scientific and OLAP workloads