Related papers: BioStatFlow -Statistical Analysis Workflow for "Om…
The utilization of online stochastic algorithms is popular in large-scale learning settings due to their ability to compute updates on the fly, without the need to store and process data in large batches. When a constant step-size is used,…
Motivation: Omics data, such as transcriptomics or phosphoproteomics, are broadly used to get a snap-shot of the molecular status of cells. In particular, changes in omics can be used to estimate the activity of pathways, transcription…
The notion of complex systems is common to many domains, from Biology to Economy, Computer Science, Physics, etc. Often, these systems are made of sets of entities moving in an evolving environment. One of their major characteristics is the…
Statistical mechanics is one of the most powerful and elegant tools in the quantitative sciences. One key virtue of statistical mechanics is that it is designed to examine large systems with many interacting degrees of freedom, providing a…
We propose an online debiased lasso (ODL) method for statistical inference in high-dimensional linear models with streaming data. The proposed ODL consists of an efficient computational algorithm for streaming data and approximately normal…
Simulations play important and diverse roles in statistical workflows, for example, in model specification, checking, validation, and even directly in model inference. Over the past decades, the application areas and overall potential of…
Similar to managing software packages, managing the ontology life cycle involves multiple complex workflows such as preparing releases, continuous quality control checking, and dependency management. To manage these processes, a diverse set…
Up-to-date meta-databases are vital for the analysis of biological data. However,the current exponential increase in biological data leads to exponentially increasing meta-database sizes. Large-scale meta-database management is therefore an…
Background and objective: Cell migration is essential for many biological phenomena with direct impact on human health and disease. One conventional approach to study cell migration involves the quantitative analysis of individual cell…
Datalog has become a popular language for writing static analyses. Because Datalog is very limited, some implementations of Datalog for static analysis have extended it with new language features. However, even with these features it is…
With the proliferation of data across various domains, there is a critical demand for tools that enable non-experts to derive meaningful insights without deep data analysis skills. To address this need, existing automatic fact sheet…
BioSimplify is an open source tool written in Java that introduces and facilitates the use of a novel model for sentence simplification tuned for automatic discourse analysis and information extraction (as opposed to sentence simplification…
In the AI-for-science era, scientific computing scenarios such as concurrent learning and high-throughput computing demand a new generation of infrastructure that supports scalable computing resources and automated workflow management on…
RooFit and RooStats, the toolkits for statistical modelling in ROOT, are used in most searches and measurements at the Large Hadron Collider as well as at $B$ factories. Larger datasets to be collected at e.g. the High-Luminosity LHC will…
We introduce linear-state dataflows, a canonical model for a large set of visualization algorithms that we call data-linear visualizations. Our model defines a fixed dataflow architecture: partitioning and subpartitioning of input data,…
The proliferation of physiological sensors opens new opportunities to explore interactions, conduct experiments and evaluate the user experience with continuous monitoring of bodily functions. Commercial devices, however, can be costly or…
An approach for simulating bionanosystems, such as viruses and ribosomes, is presented. This calibration-free approach is based on an all-atom description for bionanosystems, a universal interatomic force field, and a multiscale…
Static analysis approximates the results of a program by examining only its syntax. For example, control-flow analysis (CFA) determines which syntactic lambdas (for functional languages) or (for object-oriented) methods may be invoked at…
Data-flow analysis is a critical component of security research. Theoretically, accurate data-flow analysis in binary executables is an undecidable problem, due to complexities of binary code. Practically, many binary analysis engines offer…
Building multiscale biological models requires integrating independently developed submodels, which involves sharing variables and coordinating execution. Most existing tools focus on isolated mechanisms and numerical methods, but rarely…