Related papers: PEtab -- interoperable specification of parameter …
The dynamics of systems biological processes are usually modeled by a system of ordinary differential equations (ODEs) with many unknown parameters that need to be inferred from noisy and sparse measurements. Here, we introduce…
Peptide therapeutics are widely regarded as the "third generation" of drugs, yet progress in peptide Machine Learning (ML) are hindered by the absence of standardized benchmarks. Here we present PepBenchmark, which unifies datasets,…
Scientific software is often driven by multiple parameters that affect both accuracy and performance. Since finding the optimal configuration of these parameters is a highly complex task, it extremely common that the software is used…
Pathway Tools is a bioinformatics software environment with a broad set of capabilities. The software provides genome-informatics tools such as a genome browser, sequence alignments, a genome-variant analyzer, and comparative-genomics…
The rise of Artificial Intelligence (AI)-and particularly Large Language Models (LLMs) for code-has reshaped Software Engineering (SE) by enabling the automation of tasks such as code generation, bug detection, and repair. However, these…
In the SysLab project we develop a software engineering method based on a mathematical foundation. The SysLab system model serves as an abstract mathematical model for information systems and their components. It is used to formalize the…
While scientists increasingly recognize the importance of metadata in describing their data, spreadsheets remain the preferred tool for supplying this information despite their limitations in ensuring compliance and quality. Various tools…
Context: Over the last decade, software researchers and engineers have developed a vast body of methodologies and technologies in requirements engineering for self-adaptive systems. Although existing studies have explored various aspects of…
While a large number of adaptive Differential Evolution (DE) algorithms have been proposed, their Parameter Adaptation Methods (PAMs) are not well understood. We propose a Target function-based PAM simulation (TPAM) framework for evaluating…
Predictions for physical systems often rely upon knowledge acquired from ensembles of entities, e.g., ensembles of cells in biological sciences. For qualitative and quantitative analysis, these ensembles are simulated with parametric…
Background: The study of genome-scale metabolic models and their underlying networks is one of the most important fields in systems biology. The complexity of these models and their description makes the use of computational tools an…
Dynamic modelling is one of the cornerstones of systems biology. Many research efforts are currently being invested in the development and exploitation of large-scale kinetic models. The associated problems of parameter estimation (model…
Both experimental and computational biology is becoming increasingly automated. Laboratory experiments are now performed automatically on high-throughput machinery, while computational models are synthesized or inferred automatically from…
The rapid expansion of large foundation models within the pre-training and fine-tuning framework has underscored that larger models often yield better results. However, the scaling up of large foundation models has led to soaring costs in…
Due to the large number of submissions that more and more conferences experience, finding an automatized way to well distribute the submitted papers among reviewers has become necessary. We model the peer-reviewing matching problem as a…
Models of biological systems often have many unknown parameters that must be determined in order for model behavior to match experimental observations. Commonly-used methods for parameter estimation that return point estimates of the…
Parameter-efficient fine-tuning (PEFT) is an effective methodology to unleash the potential of large foundation models in novel scenarios with limited training data. In the computer vision community, PEFT has shown effectiveness in image…
Structural biology has made significant progress in determining membrane proteins, leading to a remarkable increase in the number of available structures in dedicated databases. The inherent complexity of membrane protein structures,…
MATLAB has emerged as one of the languages most commonly used by scientists and engineers for technical computing, with ~1,000,000 users worldwide. The compute intensive nature of technical computing means that many MATLAB users have codes…
Computational experiments have become essential for scientific discovery, allowing researchers to test hypotheses, analyze complex datasets, and validate findings. However, as computational experiments grow in scale and complexity, ensuring…