Related papers: PEtab -- interoperable specification of parameter …
When employing mechanistic models to study biological phenomena, practical parameter identifiability is important for making accurate predictions across wide range of unseen scenarios, as well as for understanding the underlying mechanisms.…
Table annotation is crucial for making web and enterprise tables usable in downstream NLP applications. Unlike textual data where learning semantically rich token or sentence embeddings often suffice, tables are structured combinations of…
Many optimization algorithm benchmarking platforms allow users to share their experimental data to promote reproducible and reusable research. However, different platforms use different data models and formats, which drastically complicates…
The common utilization-based definition of available bandwidth and many of the existing tools to estimate it suffer from several important weaknesses: i) most tools report a point estimate of average available bandwidth over a measurement…
The increasing availability of high-quality optical and near-infrared spectroscopic data, as well as advances in modelling techniques, have greatly expanded the scientific potential of spectroscopic studies. However, the software tools…
BPMN is a specification language widely used by industry and researchers for business process modeling and execution. It defines clearly how to articulate its concepts, but do not provide mechanism to represent the semantics of the produced…
As the cost of training ever larger language models has grown, so has the interest in reusing previously learnt knowledge. Transfer learning methods have shown how reusing non-task-specific knowledge can help in subsequent task-specific…
Computationally predicting protein-protein interactions (PPIs) is challenging due to the lack of integrated, multimodal protein representations. DPEB is a curated collection of 22,043 human proteins that integrates four embedding types:…
Instruction data is crucial for improving the capability of Large Language Models (LLMs) to align with human-level performance. Recent research LIMA demonstrates that alignment is essentially a process where the model adapts instructions'…
Motivation: The rapid growth of metagenomics sequencing data makes metagenomics increasingly dependent on computational and statistical methods for fast and efficient analysis. Consequently, novel analysis tools for big-data metagenomics…
Accurate protein structural ensembles can be determined with metainference, a Bayesian inference method that integrates experimental information with prior knowledge of the system and deals with all sources of uncertainty and errors as well…
Parameter-Efficient Fine-Tuning (PEFT) methods address the increasing size of Large Language Models (LLMs). Currently, many newly introduced PEFT methods are challenging to replicate, deploy, or compare with one another. To address this, we…
Atomic-level simulations are widely used to study biomolecules and their dynamics. A common goal in such studies is to compare simulations of a molecular system under several conditions -- for example, with various mutations or bound…
Representation learning is a critical ingredient for natural language processing systems. Recent Transformer language models like BERT learn powerful textual representations, but these models are targeted towards token- and sentence-level…
Over the last decade, 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 this topic, few…
When addressing professional questions in the biomedical domain, humans typically acquire multiple pieces of information as evidence and engage in multifaceted analysis to provide high-quality answers. Current LLM-based question answering…
Dynamical systems modeling, particularly via systems of ordinary differential equations, has been used to effectively capture the temporal behavior of different biochemical components in signal transduction networks. Despite the recent…
Mathematical modelling and numerical simulations of interaction populations are crucial topics in systems biology. The interactions of ecological models may occur among individuals of the same species or individuals of different species.…
This paper presents the PyEB tool, a Python implementation of the Event-B refinement calculus. The PyEB tool takes a Python program and generates several proof obligations that are then passed into the Z3 solver for verification purposes.…
Patent claims define the scope of protection for an invention. If there are ambiguities in a claim, it is rejected by the patent office. In the US, this is referred to as indefiniteness (35 U.S.C {\S} 112(b)) and is among the most frequent…