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Large language models (LLMs) have become important tools in solving biological problems, offering improvements in accuracy and adaptability over conventional methods. Several benchmarks have been proposed to evaluate the performance of…
Property-based testing (PBT) is a popular software testing methodology and is effective in validating the functionality of mobile applications (apps for short). However, its adoption in practice remains limited, largely due to the manual…
We present ESPnet-SpeechLM, an open toolkit designed to democratize the development of speech language models (SpeechLMs) and voice-driven agentic applications. The toolkit standardizes speech processing tasks by framing them as universal…
The application of deep learning methods, particularly foundation models, in biological research has surged in recent years. These models can be text-based or trained on underlying biological data, especially omics data of various types.…
Instance segmentation is an important task for biomedical and biological image analysis. Due to the complicated background components, the high variability of object appearances, numerous overlapping objects, and ambiguous object…
Motivation: Biomedical named-entity normalization involves connecting biomedical entities with distinct database identifiers in order to facilitate data integration across various fields of biology. Existing systems for biomedical named…
Evaluating early design concepts is crucial as it impacts quality and cost. This process is often hindered by vague and uncertain design information. This article introduces the SysML-based Simulated-Physical Systems Modelling Language…
Machine learning (ML) offers a collection of powerful approaches for detecting and modeling associations, often applied to data having a large number of features and/or complex associations. Currently, there are many tools to facilitate…
Among the main features of biological intelligence are energy efficiency, capacity for continual adaptation, and risk management via uncertainty quantification. Neuromorphic engineering has been thus far mostly driven by the goal of…
Proteins, as essential biomolecules, play a central role in biological processes, including metabolic reactions and DNA replication. Accurate prediction of their properties and functions is crucial in biological applications. Recent…
BioNetGen is an open-source software package for rule-based modeling of complex biochemical systems. Version 2.2 of the software introduces numerous new features for both model specification and simulation. Here, we report on these…
Recent advances in Language Models have enabled the protein modeling community with a powerful tool since protein sequences can be represented as text. Specifically, by taking advantage of Transformers, sequence-to-property prediction will…
Large Language Models (LLMs) have demonstrated remarkable capabilities across various domains, including software development, education, and technical assistance. Among these, software development is one of the key areas where LLMs are…
Climate models play a critical role in understanding and projecting climate change. Due to their complexity, their horizontal resolution of about 40-100 km remains too coarse to resolve processes such as clouds and convection, which need to…
The diagnosis of cyber-physical systems aims to detect faulty behaviour, its root cause and a mitigation or even prevention policy. Therefore, diagnosis relies on a representation of the system's functional and faulty behaviour combined…
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…
Background: Simulated nucleotide or amino acid sequences are frequently used to assess the performance of phylogenetic reconstruction methods. BEAST, a Bayesian statistical framework that focuses on reconstructing time-calibrated molecular…
Large language models (LLMs) trained on internet-scale corpora can exhibit systematic biases that increase the probability of unwanted behavior. In this study, we examined potential biases towards synthetic vs. biological technological…
Mathematical formulas serve as the means of communication between humans and nature, encapsulating the operational laws governing natural phenomena. The concise formulation of these laws is a crucial objective in scientific research and an…
Large language models (LLMs) are increasingly applied to materials science questions, including literature comprehension, property prediction, materials discovery and alloy design. At the same time, a wide range of physics-based…