Related papers: Extracting Biological Pathway Models From NLP Even…

In this paper, we introduce HugNLP, a unified and comprehensive library for natural language processing (NLP) with the prevalent backend of HuggingFace Transformers, which is designed for NLP researchers to easily utilize off-the-shelf…

Current-generation Large Language Models (LLMs) have stirred enormous interest in recent months, yielding great potential for accessibility and automation, while simultaneously posing significant challenges and risk of misuse. To facilitate…

Language is the medium for many political activities, from campaigns to news reports. Natural language processing (NLP) uses computational tools to parse text into key information that is needed for policymaking. In this chapter, we…

Here we describe an "information based exchange" model of brain function that ascribes to neocortex, basal ganglia, and thalamus distinct network functions. The model allows us to analyze whole brain system set point measures, such as the…

Understanding large molecular networks consisting of entities such as genes, proteins or RNAs that interact in complex ways to drive the cellular machinery has been an active focus of systems biology. Computational approaches have played a…

In the realm of Business Process Management (BPM), process modeling plays a crucial role in translating complex process dynamics into comprehensible visual representations, facilitating the understanding, analysis, improvement, and…

Biological signaling pathways based upon proteins binding to one another to relay a signal for genetic expression, such as the Bone Morphogenetic Protein (BMP) signaling pathway, can be modeled by mass action kinetics and conservation laws…

When applying machine learning to problems in NLP, there are many choices to make about how to represent input texts. These choices can have a big effect on performance, but they are often uninteresting to researchers or practitioners who…

Models of complicated systems can be represented in different ways - in scientific papers, they are represented using natural language text as well as equations. But to be of real use, they must also be implemented as software, thus making…

In this paper, we present two techniques for use in context-aware systems: Semantic Decomposition, which sequentially decomposes input prompts into a structured and hierarchal information schema in which systems can parse and process…

This paper discusses SYNTAGMA, a rule based NLP system addressing the tricky issues of syntactic ambiguity reduction and word sense disambiguation as well as providing innovative and original solutions for constituent generation and…

Transformer-based language models have revolutionized the field of natural language processing (NLP). However, using these models often involves navigating multiple frameworks and tools, as well as writing repetitive boilerplate code. This…

Background: Qualitative frameworks, especially those based on the logical discrete formalism, are increasingly used to model regulatory and signalling networks. A major advantage of these frameworks is that they do not require precise…

We classify and review current approaches to software infrastructure for research, development and delivery of NLP systems. The task is motivated by a discussion of current trends in the field of NLP and Language Engineering. We describe a…

The advance in machine learning (ML)-driven natural language process (NLP) points a promising direction for automatic bug fixing for software programs, as fixing a buggy program can be transformed to a translation task. While software…

Large language models (LLMs) have unlocked new capabilities of task planning from human instructions. However, prior attempts to apply LLMs to real-world robotic tasks are limited by the lack of grounding in the surrounding scene. In this…

Encoding legislative text in a formal representation is an important prerequisite to different tasks in the field of AI & Law. For example, rule-based expert systems focused on legislation can support laypeople in understanding how…

Software ecosystems have had a tremendous impact on computing and society, capturing the attention of businesses, researchers, and policy makers alike. Massive ecosystems like the JavaScript node package manager (npm) is evidence of how…

Excitable neuromorphic circuits are physical models of event behaviors: their continuous-time trajectories consist of sequences of discrete events. This paper explores the possibility of extracting a discrete-event model out of the physical…

Using different sources of information to support automated extracting of relations between biomedical concepts contributes to the development of our understanding of biological systems. The primary comprehensive source of these relations…