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The vast majority of scientific contributions in the field of computational systems biology are based on mathematical models. These models can be broadly classified as either dynamic (kinetic) models or steady-state (constraint-based)…

其他定量生物学 · 定量生物学 2025-04-17 Moritz E. Beber

We consider open domain event extraction, the task of extracting unconstraint types of events from news clusters. A novel latent variable neural model is constructed, which is scalable to very large corpus. A dataset is collected and…

计算与语言 · 计算机科学 2022-12-19 Xiao Liu , Heyan Huang , Yue Zhang

Generating synthetic datasets that accurately reflect real-world observational data is critical for evaluating causal estimators, but it remains a challenging task. Existing generative methods offer a solution by producing synthetic…

机器学习 · 计算机科学 2026-04-07 Pracheta Amaranath , Vinitra Muralikrishnan , Amit Sharma , David Jensen

We tackle the task of adapting event extractors to new domains without labeled data, by aligning the marginal distributions of source and target domains. As a testbed, we create two new event extraction datasets using English texts from two…

计算与语言 · 计算机科学 2020-08-24 Aakanksha Naik , Jill Lehman , Carolyn Rose

Claims are a fundamental unit of scientific discourse. The exponential growth in the number of scientific publications makes automatic claim extraction an important problem for researchers who are overwhelmed by this information overload.…

计算与语言 · 计算机科学 2020-01-20 Titipat Achakulvisut , Chandra Bhagavatula , Daniel Acuna , Konrad Kording

Nested Event Extraction (NEE) aims to extract complex event structures where an event contains other events as its arguments recursively. Nested events involve a kind of Pivot Elements (PEs) that simultaneously act as arguments of…

计算与语言 · 计算机科学 2024-04-09 Weicheng Ren , Zixuan Li , Xiaolong Jin , Long Bai , Miao Su , Yantao Liu , Saiping Guan , Jiafeng Guo , Xueqi Cheng

Missing data is a widespread problem in many domains, creating challenges in data analysis and decision making. Traditional techniques for dealing with missing data, such as excluding incomplete records or imputing simple estimates (e.g.,…

数据库 · 计算机科学 2024-01-09 Massimo Perini , Milos Nikolic

Event Extraction (EE), aiming to identify and classify event triggers and arguments from event mentions, has benefited from pre-trained language models (PLMs). However, existing PLM-based methods ignore the information of trigger/argument…

计算与语言 · 计算机科学 2023-05-22 Xingyu Bai , Taiqiang Wu , Han Guo , Zhe Zhao , Xuefeng Yang , Jiayi Li , Weijie Liu , Qi Ju , Weigang Guo , Yujiu Yang

Generative document retrieval, an emerging paradigm in information retrieval, learns to build connections between documents and identifiers within a single model, garnering significant attention. However, there are still two challenges: (1)…

信息检索 · 计算机科学 2024-05-14 Yong Guan , Dingxiao Liu , Jinchen Ma , Hao Peng , Xiaozhi Wang , Lei Hou , Ru Li

Document-level biomedical concept extraction is the task of identifying biomedical concepts mentioned in a given document. Recent advancements have adapted pre-trained language models for this task. However, the scarcity of domain-specific…

计算与语言 · 计算机科学 2024-07-04 Qiwei Shao , Fengran Mo , Jian-Yun Nie

The diverse relationships among real-world events, including coreference, temporal, causal, and subevent relations, are fundamental to understanding natural languages. However, two drawbacks of existing datasets limit event relation…

计算与语言 · 计算机科学 2022-11-15 Xiaozhi Wang , Yulin Chen , Ning Ding , Hao Peng , Zimu Wang , Yankai Lin , Xu Han , Lei Hou , Juanzi Li , Zhiyuan Liu , Peng Li , Jie Zhou

Event argument extraction (EAE) is an important task for information extraction to discover specific argument roles. In this study, we cast EAE as a question-based cloze task and empirically analyze fixed discrete token template…

计算与语言 · 计算机科学 2023-01-26 Hongbin Ye , Ningyu Zhang , Zhen Bi , Shumin Deng , Chuanqi Tan , Hui Chen , Fei Huang , Huajun Chen

Event relation extraction (ERE) is a critical and fundamental challenge for natural language processing. Existing work mainly focuses on directly modeling the entire document, which cannot effectively handle long-range dependencies and…

计算与语言 · 计算机科学 2024-05-14 Yong Guan , Xiaozhi Wang , Lei Hou , Juanzi Li , Jeff Pan , Jiaoyan Chen , Freddy Lecue

Adverse reaction caused by drugs is a potentially dangerous problem which may lead to mortality and morbidity in patients. Adverse Drug Event (ADE) extraction is a significant problem in biomedical research. We model ADE extraction as a…

计算与语言 · 计算机科学 2018-01-03 Suriyadeepan Ramamoorthy , Selvakumar Murugan

Most existing event extraction (EE) methods merely extract event arguments within the sentence scope. However, such sentence-level EE methods struggle to handle soaring amounts of documents from emerging applications, such as finance,…

计算与语言 · 计算机科学 2019-09-24 Shun Zheng , Wei Cao , Wei Xu , Jiang Bian

Recently, numerous efforts have continued to push up performance boundaries of document-level relation extraction (DocRE) and have claimed significant progress in DocRE. In this paper, we do not aim at proposing a novel model for DocRE.…

计算与语言 · 计算机科学 2023-06-16 Jing Li , Yequan Wang , Shuai Zhang , Min Zhang

We revisit the classic problem of document-level role-filler entity extraction (REE) for template filling. We argue that sentence-level approaches are ill-suited to the task and introduce a generative transformer-based encoder-decoder…

计算与语言 · 计算机科学 2021-02-01 Xinya Du , Alexander M. Rush , Claire Cardie

Event extraction (EE), which acquires structural event knowledge from texts, can be divided into two sub-tasks: event type classification and element extraction (namely identifying triggers and arguments under different role patterns). As…

计算与语言 · 计算机科学 2022-08-19 Qian Li , Shu Guo , Jia Wu , Jianxin Li , Jiawei Sheng , Lihong Wang , Xiaohan Dong , Hao Peng

Predictive process analytics often apply machine learning to predict the future states of a running business~process. However, the internal mechanisms of many existing predictive algorithms are opaque and a human decision-maker is unable to…

机器学习 · 计算机科学 2021-10-01 Chihcheng Hsieh , Catarina Moreira , Chun Ouyang

Document-level Event Argument Extraction (EAE) requires the model to extract arguments of multiple events from a single document. Considering the underlying dependencies between these events, recent efforts leverage the idea of "memory",…

计算与语言 · 计算机科学 2023-10-26 Quzhe Huang , Yanxi Zhang , Dongyan Zhao