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In recent years, the research community, but also the general public, has raised serious questions about the reproducibility and replicability of scientific work. Since many studies include some kind of computational work, these issues are…
The advent of modern data processing has led to an increasing tendency towards interdisciplinarity, which frequently involves the importation of different technical approaches. Consequently, there is an urgent need for a unified data…
Iterators are a fundamental programming abstraction for traversing and modifying elements in containers in mainstream imperative languages such as C++. Iterators provide a uniform access mechanism that hides low-level implementation details…
The ubiquity of computation in modern scientific research inflicts new challenges for reproducibility. While most journals now require code and data be made available, the standards for organization, annotation, and validation remain lax,…
Within an increasing number of domains an important emerging need is the ability for technically naive users to compose computational elements into novel configurations. Examples include astronomers who create new analysis pipelines to…
With a view to provide a user-friendly interface for designing, training and developing deep learning frameworks, we have developed Expresso, a GUI tool written in Python. Expresso is built atop Caffe, the open-source, prize-winning…
The work presented in this thesis seeks to improve programmer productivity in the following ways: - by reducing the amount of code that has to be written to construct an application; - by increasing the reliability of the code written; and…
The reproduction and replication of novel results has become a major issue for a number of scientific disciplines. In computer science and related computational disciplines such as systems biology, the issues closely revolve around the…
In many science and engineering settings, system dynamics are characterized by governing PDEs, and a major challenge is to solve inverse problems (IPs) where unknown PDE parameters are inferred based on observational data gathered under…
Using computational notebooks (e.g., Jupyter Notebook), data scientists rationalize their exploratory data analysis (EDA) based on their prior experience and external knowledge such as online examples. For novices or data scientists who…
Designing scientific instrumentation often requires exploring large, highly constrained design spaces using computationally expensive physics simulations. These simulators pose substantial challenges for integrating evolutionary computation…
The fixed parameter tractable (FPT) approach is a powerful tool in tackling computationally hard problems. In this paper, we link FPT results to classic artificial intelligence (AI) techniques to show how they complement each other.…
The Libopt environment is both a methodology and a set of tools that can be used for testing, comparing, and profiling solvers on problems belonging to various collections. These collections can be heterogeneous in the sense that their…
Artificial intelligence (AI) techniques are widely applied in the life sciences. However, applying innovative AI techniques to understand and deconvolute biological complexity is hindered by the learning curve for life science scientists to…
Recently proposed modifications of the standard particle-in-cell (PIC) method resolve long-standing limitations such as exact preservation of physically conserved quantities and unbiased ensemble down-sampling. Such advances pave the way…
Distributed, large-scale quantum computing will need architectures that combine matter-based qubits with photonic links, but today's software stacks target either gate-based chips or linear-optical devices in isolation. We introduce Optyx,…
Motivation: Parameter estimation is a cornerstone of data-driven modeling in systems biology. Yet, constructing such problems in a reproducible and accessible manner remains challenging. The PEtab format has established itself as a powerful…
Online user studies of visualizations, visual encodings, and interaction techniques are ubiquitous in visualization research. Yet, designing, conducting, and analyzing studies effectively is still a major burden. Although various packages…
Interface icons are prevalent in various digital applications. Due to limited time and budgets, many designers rely on informal evaluation, which often results in poor usability icons. In this paper, we propose a unique human-in-the-loop…
The enabling of scientific experiments that are embarrassingly parallel, long running and data-intensive into a cloud-based execution environment is a desirable, though complex undertaking for many researchers. The management of such…