相关论文: BactInt: A domain driven transfer learning approac…

Transfer entropy (TE) is a powerful tool for measuring causal relationships within interaction networks. Traditionally, TE and its conditional variants are applied pairwise between dynamic variables to infer these causal relationships.…

Motivation: Protein-protein interactions (PPI) are critical to the function of proteins in both normal and diseased cells, and many critical protein functions are mediated by interactions.Knowledge of the nature of these interactions is…

There is a growing awareness of the important roles that microbial communities play in complex biological processes. Modern investigation of these often uses next generation sequencing of metagenomic samples to determine community…

Networks effectively capture interactions among components of complex systems, and have thus become a mainstay in many scientific disciplines. Growing evidence, especially from biology, suggest that networks undergo changes over time, and…

In an attempt to improve overall translation quality, there has been an increasing focus on integrating more linguistic elements into Machine Translation (MT). While significant progress has been achieved, especially recently with neural…

The aim of this paper is to report on a novel text reduction technique, called Text Denoising, that highlights information-rich content when processing a large volume of text data, especially from the biomedical domain. The core feature of…

We introduce a biomedical information extraction (IE) pipeline that extracts biological relationships from text and demonstrate that its components, such as named entity recognition (NER) and relation extraction (RE), outperform…

Objective: Text mining of clinical notes embedded in electronic medical records is increasingly used to extract patient characteristics otherwise not or only partly available, to assess their association with relevant health outcomes. As…

Background: In the information extraction and natural language processing domain, accessible datasets are crucial to reproduce and compare results. Publicly available implementations and tools can serve as benchmark and facilitate the…

Citation plays a pivotal role in determining the associations among research articles. It portrays essential information in indicative, supportive, or contrastive studies. The task of inline citation classification aids in extrapolating…

The overwhelming amount of available scholarly literature in the life sciences poses significant challenges to scientists wishing to keep up with important developments related to their research, but also provides a useful resource for the…

Understanding the dependence and interplay between architecture and function in biological networks has great relevance to disease progression, biological fabrication and biological systems in general. We propose methods to assess the…

The advancement of science relies on the exchange of ideas across disciplines and the integration of diverse knowledge domains. However, tracking knowledge flows and interdisciplinary integration in rapidly evolving, multidisciplinary…

BERT is a widely used pre-trained model in natural language processing. However, since BERT is quadratic to the text length, the BERT model is difficult to be used directly on the long-text corpus. In some fields, the collected text data…

The growing demand for structured knowledge has led to great interest in relation extraction, especially in cases with limited supervision. However, existing distance supervision approaches only extract relations expressed in single…

Biomedical relation extraction (RE) is the task of automatically identifying and characterizing relations between biomedical concepts from free text. RE is a central task in biomedical natural language processing (NLP) research and plays a…

Multi-task learning (MTL) has achieved remarkable success in natural language processing applications. In this work, we study a multi-task learning model with multiple decoders on varieties of biomedical and clinical natural language…

The standard task-oriented dialogue pipeline uses intent classification and slot-filling to interpret user utterances. While this approach can handle a wide range of queries, it does not extract the information needed to handle more complex…

The built environment provides an excellent setting for interdisciplinary research on the dynamics of microbial communities. The system is simplified compared to many natural settings, and to some extent the entire environment can be…

Rapidly assaying the diversity of a bacterial species present in a sample obtained from a hospital patient or an evironmental source has become possible after recent technological advances in DNA sequencing. For several applications it is…