Related papers: Extracting Biological Pathway Models From NLP Even…
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…
Event-driven genetic programming representations have been shown to outperform traditional imperative representations on interaction-intensive problems. The event-driven approach organizes genome content into modules that are triggered in…
Understanding the mechanisms of interactions within cells, tissues, and organisms is crucial to driving developments across biology and medicine. Mathematical modeling is an essential tool for simulating biological systems and revealing…
With accurate and timely traffic forecasting, the impacted traffic conditions can be predicted in advance to guide agencies and residents to respond to changes in traffic patterns appropriately. However, existing works on traffic…
Large systems biology projects can encompass several workgroups often located in different countries. An overview about existing data standards in systems biology and the management, storage, exchange and integration of the generated data…
Determining the different conformational states of a protein and the transition paths between them is key to fully understanding the relationship between biomolecular structure and function. This can be accomplished by sampling protein…
OLAF (Open Life Science Analysis Framework) is an open-source platform that enables researchers to perform bioinformatics analyses using natural language. By combining large language models (LLMs) with a modular agent-pipe-router…
NLP Workbench is a web-based platform for text mining that allows non-expert users to obtain semantic understanding of large-scale corpora using state-of-the-art text mining models. The platform is built upon latest pre-trained models and…
Spectroscopy is a central pillar of materials characterization, providing useful information on properties like structure, composition, or excited state dynamics of a system. However, many spectroscopic techniques present challenges in…
Composition is a powerful principle for systems biology, focused on the interfaces, interconnections, and orchestration of distributed processes to enable integrative multiscale simulations. Whereas traditional models focus on the structure…
Recent advances in Generative Artificial Intelligence, particularly Large Language Models (LLMs), have stimulated growing interest in automating or assisting Business Process Modeling tasks using natural language. Several approaches have…
Dialogue systems is an increasingly popular task of natural language processing. However, the dialogue paths tend to be deterministic, restricted to the system rails, regardless of the given request or input text. Recent advances in program…
Generative models have been showing potential for producing data in mass. This study explores the enhancement of clinical natural language processing performance by utilizing synthetic data generated from advanced language models. Promising…
To coordinate with other agents in its environment, an agent needs models of what the other agents are trying to do. When communication is impossible or expensive, this information must be acquired indirectly via plan recognition. Typical…
We suggest to employ techniques from Natural Language Processing (NLP) and Knowledge Representation (KR) to transform existing documents into documents amenable for the Semantic Web. Semantic Web documents have at least part of their…
Computational synthesis planning approaches have achieved recent success in organic chemistry, where tabulated synthesis procedures are readily available for supervised learning. The syntheses of inorganic materials, however, exist…
Many real-world systems studied are governed by complex, nonlinear dynamics. By modeling these dynamics, we can gain insight into how these systems work, make predictions about how they will behave, and develop strategies for controlling…
I give an overview of rare event simulation techniques to generate dynamical pathways across high free energy barriers. The methods on which I will concentrate are the reactive flux approach, transition path sampling, (replica-exchange)…
A model is a simplified representation of portion of reality that hides a system s nonessential characteristics. It provides a means for reducing complexity as well as visualization and communication and a basis for building it. Most models…
Linguistic typology aims to capture structural and semantic variation across the world's languages. A large-scale typology could provide excellent guidance for multilingual Natural Language Processing (NLP), particularly for languages that…