Related papers: RepEx: A Flexible Framework for Scalable Replica E…

Computational models of complex systems are usually elaborate and sensitive to implementation details, characteristics which often affect their verification and validation. Model replication is a possible solution to this issue. It avoids…

Molecular simulations and biophysical experiments can be used to provide independent and complementary insights into the molecular origin of biological processes. A particularly useful strategy is to use molecular simulations as a modelling…

Molecule-text modeling, which aims to facilitate molecule-relevant tasks with a textual interface and textual knowledge, is an emerging research direction. Beyond single molecules, studying reaction-text modeling holds promise for helping…

Reconstructing numerical simulations from control systems research papers is often hindered by underspecified parameters and ambiguous implementation details. We define the task of Paper to Simulation Recoverability, the ability of an…

We developed a replica exchange method that is effectively parallelizable even if the computational cost of the Monte Carlo moves in the parallel replicas are considerably different, for instance, because the replicas run on different type…

Replicability in machine learning (ML) research is increasingly concerning due to the utilization of complex non-deterministic algorithms and the dependence on numerous hyper-parameter choices, such as model architecture and training…

Regular expression (RE) matching is a very common functionality that scans a text to find occurrences of patterns specified by an RE; it includes the simpler function of RE recognition. Here we address RE parsing, which subsumes matching by…

Test-Time Scaling enhances the reasoning capabilities of Large Language Models by allocating additional inference compute to broaden the exploration of the solution space. However, existing search strategies typically treat rollouts as…

Large-scale simulations play a central role in science and the industry. Several challenges occur when building simulation software, because simulations require complex software developed in a dynamic construction process. That is why…

This work presents retQSS, a novel methodology for efficient modeling and simulation of particle systems in reticulated meshed geometries. On the simulation side, retQSS profits from the discrete-event nature of Quantized State System (QSS)…

Inferential methods can be used to integrate experimental informations and molecular simulations. The maximum entropy principle provides a framework for using equilibrium experimental data and it has been shown that replica-averaged…

Deep learning (DL) techniques have gained significant popularity among software engineering (SE) researchers in recent years. This is because they can often solve many SE challenges without enormous manual feature engineering effort and…

Diffusion-based molecular communication (MC) systems experience significant reliability losses. To boost the reliability, an MC scheme where multiple receivers (RXs) work cooperatively to decide the signal of a transmitter (TX) by sending…

Cosimulation methods allow combination of simulation tools of physical systems running in parallel to act as a single simulation environment for a big system. As data is passed across subsystem boundaries instead of solving the system as…

The reproduction and replication of research results has become a major issue for a number of scientific disciplines. In computer science and related computational disciplines such as systems biology, the challenges closely revolve around…

We propose a simple and effective tool for the expression of tasks such as cross-layer optimization strategies or sensors-related applications. The approach is based on what we refer to as "reflective and refractive variables". Both types…

For the study of complex synthetic and biological molecular systems by computer simulations one is still restricted to simple model systems or to by far too small time scales. To overcome this problem multiscale techniques are being…

The computational study of conformational transitions in RNA and proteins with atomistic molecular dynamics often requires suitable enhanced sampling techniques. We here introduce a novel method where concurrent metadynamics are integrated…

Existing Programming-By-Example (PBE) systems often rely on simplified benchmarks that fail to capture the high structural complexity-such as deeper nesting and frequent Unions-of real-world regexes. To overcome the resulting performance…

The formation of biomolecular materials via dynamical interfacial processes such as self-assembly and fusion, for diverse compositions and external conditions, can be efficiently probed using ensemble Molecular Dynamics. However, this…