CN111581339A - 基于树状lstm对生物医学文献的基因事件的抽取方法 - Google Patents
基于树状lstm对生物医学文献的基因事件的抽取方法 Download PDFInfo
- Publication number
- CN111581339A CN111581339A CN202010276382.6A CN202010276382A CN111581339A CN 111581339 A CN111581339 A CN 111581339A CN 202010276382 A CN202010276382 A CN 202010276382A CN 111581339 A CN111581339 A CN 111581339A
- Authority
- CN
- China
- Prior art keywords
- event
- node
- information
- tree
- word
- Prior art date
- Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
- Granted
Links
- 108090000623 proteins and genes Proteins 0.000 title claims abstract description 28
- 238000000034 method Methods 0.000 title claims description 10
- 238000012549 training Methods 0.000 claims abstract description 20
- 239000013598 vector Substances 0.000 claims abstract description 17
- 238000000605 extraction Methods 0.000 claims abstract description 14
- 230000001419 dependent effect Effects 0.000 claims abstract description 8
- 238000012360 testing method Methods 0.000 claims abstract description 5
- 238000012795 verification Methods 0.000 claims abstract description 4
- 238000013507 mapping Methods 0.000 claims abstract description 3
- 230000006870 function Effects 0.000 claims description 22
- 239000011159 matrix material Substances 0.000 claims description 18
- 230000011218 segmentation Effects 0.000 claims description 7
- 230000004913 activation Effects 0.000 claims description 6
- 230000002068 genetic effect Effects 0.000 claims description 4
- 238000007781 pre-processing Methods 0.000 claims description 4
- 230000001186 cumulative effect Effects 0.000 claims description 3
- 230000001537 neural effect Effects 0.000 claims description 2
- 238000012545 processing Methods 0.000 abstract description 3
- 210000004027 cell Anatomy 0.000 description 19
- 102000004169 proteins and genes Human genes 0.000 description 14
- 238000010586 diagram Methods 0.000 description 8
- 238000003062 neural network model Methods 0.000 description 6
- 230000000694 effects Effects 0.000 description 4
- 238000010200 validation analysis Methods 0.000 description 4
- 238000013135 deep learning Methods 0.000 description 3
- 238000011156 evaluation Methods 0.000 description 3
- ORILYTVJVMAKLC-UHFFFAOYSA-N Adamantane Natural products C1C(C2)CC3CC1CC2C3 ORILYTVJVMAKLC-UHFFFAOYSA-N 0.000 description 2
- 238000013528 artificial neural network Methods 0.000 description 2
- 230000008901 benefit Effects 0.000 description 2
- 238000010801 machine learning Methods 0.000 description 2
- 210000000822 natural killer cell Anatomy 0.000 description 2
- 210000001744 T-lymphocyte Anatomy 0.000 description 1
- 238000013473 artificial intelligence Methods 0.000 description 1
- 230000009286 beneficial effect Effects 0.000 description 1
- 230000033228 biological regulation Effects 0.000 description 1
- 230000015556 catabolic process Effects 0.000 description 1
- 230000001364 causal effect Effects 0.000 description 1
- 238000013136 deep learning model Methods 0.000 description 1
- 230000007547 defect Effects 0.000 description 1
- 230000003828 downregulation Effects 0.000 description 1
- 230000014509 gene expression Effects 0.000 description 1
- 238000002372 labelling Methods 0.000 description 1
- 230000004807 localization Effects 0.000 description 1
- 238000012986 modification Methods 0.000 description 1
- 230000004048 modification Effects 0.000 description 1
- 238000003058 natural language processing Methods 0.000 description 1
- 210000005036 nerve Anatomy 0.000 description 1
- 230000026731 phosphorylation Effects 0.000 description 1
- 238000006366 phosphorylation reaction Methods 0.000 description 1
- 230000008569 process Effects 0.000 description 1
- 238000011160 research Methods 0.000 description 1
- 238000012706 support-vector machine Methods 0.000 description 1
- 238000013518 transcription Methods 0.000 description 1
- 230000035897 transcription Effects 0.000 description 1
- 230000003827 upregulation Effects 0.000 description 1
Images
Classifications
-
- G—PHYSICS
- G06—COMPUTING; CALCULATING OR COUNTING
- G06F—ELECTRIC DIGITAL DATA PROCESSING
- G06F16/00—Information retrieval; Database structures therefor; File system structures therefor
- G06F16/30—Information retrieval; Database structures therefor; File system structures therefor of unstructured textual data
- G06F16/33—Querying
- G06F16/3331—Query processing
- G06F16/334—Query execution
- G06F16/3344—Query execution using natural language analysis
-
- G—PHYSICS
- G06—COMPUTING; CALCULATING OR COUNTING
- G06F—ELECTRIC DIGITAL DATA PROCESSING
- G06F16/00—Information retrieval; Database structures therefor; File system structures therefor
- G06F16/30—Information retrieval; Database structures therefor; File system structures therefor of unstructured textual data
- G06F16/35—Clustering; Classification
-
- G—PHYSICS
- G06—COMPUTING; CALCULATING OR COUNTING
- G06F—ELECTRIC DIGITAL DATA PROCESSING
- G06F40/00—Handling natural language data
- G06F40/20—Natural language analysis
- G06F40/205—Parsing
- G06F40/211—Syntactic parsing, e.g. based on context-free grammar [CFG] or unification grammars
-
- G—PHYSICS
- G06—COMPUTING; CALCULATING OR COUNTING
- G06F—ELECTRIC DIGITAL DATA PROCESSING
- G06F40/00—Handling natural language data
- G06F40/20—Natural language analysis
- G06F40/279—Recognition of textual entities
- G06F40/284—Lexical analysis, e.g. tokenisation or collocates
-
- G—PHYSICS
- G06—COMPUTING; CALCULATING OR COUNTING
- G06N—COMPUTING ARRANGEMENTS BASED ON SPECIFIC COMPUTATIONAL MODELS
- G06N3/00—Computing arrangements based on biological models
- G06N3/02—Neural networks
- G06N3/04—Architecture, e.g. interconnection topology
- G06N3/044—Recurrent networks, e.g. Hopfield networks
-
- G—PHYSICS
- G06—COMPUTING; CALCULATING OR COUNTING
- G06N—COMPUTING ARRANGEMENTS BASED ON SPECIFIC COMPUTATIONAL MODELS
- G06N3/00—Computing arrangements based on biological models
- G06N3/02—Neural networks
- G06N3/04—Architecture, e.g. interconnection topology
- G06N3/045—Combinations of networks
Landscapes
- Engineering & Computer Science (AREA)
- Theoretical Computer Science (AREA)
- Physics & Mathematics (AREA)
- General Physics & Mathematics (AREA)
- General Engineering & Computer Science (AREA)
- Artificial Intelligence (AREA)
- Computational Linguistics (AREA)
- General Health & Medical Sciences (AREA)
- Health & Medical Sciences (AREA)
- Data Mining & Analysis (AREA)
- Biomedical Technology (AREA)
- Molecular Biology (AREA)
- Computing Systems (AREA)
- Evolutionary Computation (AREA)
- Biophysics (AREA)
- Mathematical Physics (AREA)
- Software Systems (AREA)
- Life Sciences & Earth Sciences (AREA)
- Databases & Information Systems (AREA)
- Audiology, Speech & Language Pathology (AREA)
- Machine Translation (AREA)
Abstract
Description
Event Type | Core arguments |
Gene expression | Theme(Protein) |
Transcription | Theme(Protein) |
Protein catabolism | Theme(Protein) |
Phosphorylation | Theme(Protein) |
Localization | Theme(Protein) |
Binding | Theme(Protein)+ |
Regulation | Theme(Protein/Event),Cause(Protein/Event) |
Positive regulation | Theme(Protein/Event),Cause(Protein/Event) |
Negative regulation | Theme(Protein/Event),Cause(Protein/Event) |
Parameter | Value |
Word embedding size | 200 |
Tree-LSTM hidden size | 100 |
Learning rate | 0.001 |
Weight decay | 0.001 |
Batch size | 64 |
Epoch size | 30 |
Dropout rate | 0.3 |
Initial embedding learning rate | 0.01 |
Optimizer | Adam |
Claims (2)
Priority Applications (1)
Application Number | Priority Date | Filing Date | Title |
---|---|---|---|
CN202010276382.6A CN111581339B (zh) | 2020-04-09 | 2020-04-09 | 基于树状lstm对生物医学文献的基因事件的抽取方法 |
Applications Claiming Priority (1)
Application Number | Priority Date | Filing Date | Title |
---|---|---|---|
CN202010276382.6A CN111581339B (zh) | 2020-04-09 | 2020-04-09 | 基于树状lstm对生物医学文献的基因事件的抽取方法 |
Publications (2)
Publication Number | Publication Date |
---|---|
CN111581339A true CN111581339A (zh) | 2020-08-25 |
CN111581339B CN111581339B (zh) | 2021-11-12 |
Family
ID=72124330
Family Applications (1)
Application Number | Title | Priority Date | Filing Date |
---|---|---|---|
CN202010276382.6A Active CN111581339B (zh) | 2020-04-09 | 2020-04-09 | 基于树状lstm对生物医学文献的基因事件的抽取方法 |
Country Status (1)
Country | Link |
---|---|
CN (1) | CN111581339B (zh) |
Cited By (1)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
CN112967816A (zh) * | 2021-04-26 | 2021-06-15 | 四川大学华西医院 | 一种用于急性胰腺炎器官衰竭预测的计算机设备和系统 |
Citations (3)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
CN108628970A (zh) * | 2018-04-17 | 2018-10-09 | 大连理工大学 | 一种基于新标记模式的生物医学事件联合抽取方法 |
CN109615116A (zh) * | 2018-11-20 | 2019-04-12 | 中国科学院计算技术研究所 | 一种电信诈骗事件检测方法和检测系统 |
CN109857990A (zh) * | 2018-12-18 | 2019-06-07 | 重庆邮电大学 | 一种基于文档结构与深度学习的金融类公告信息抽取方法 |
-
2020
- 2020-04-09 CN CN202010276382.6A patent/CN111581339B/zh active Active
Patent Citations (3)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
CN108628970A (zh) * | 2018-04-17 | 2018-10-09 | 大连理工大学 | 一种基于新标记模式的生物医学事件联合抽取方法 |
CN109615116A (zh) * | 2018-11-20 | 2019-04-12 | 中国科学院计算技术研究所 | 一种电信诈骗事件检测方法和检测系统 |
CN109857990A (zh) * | 2018-12-18 | 2019-06-07 | 重庆邮电大学 | 一种基于文档结构与深度学习的金融类公告信息抽取方法 |
Non-Patent Citations (3)
Title |
---|
DIYA LI等: "Biomedical Event Extraction based on Knowledge-driven Tree-LSTM", 《HTTPS://BLENDER.CS.ILLINOIS.EDU/PAPER/BIOEVENT2019.PDF》 * |
沈兰奔等: "结合注意力机制与双向LSTM的中文事件检测方法", 《中文信息学报》 * |
王安然: "基于事件框架的生物信息抽取的研究", 《万方数据》 * |
Cited By (2)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
CN112967816A (zh) * | 2021-04-26 | 2021-06-15 | 四川大学华西医院 | 一种用于急性胰腺炎器官衰竭预测的计算机设备和系统 |
CN112967816B (zh) * | 2021-04-26 | 2023-08-15 | 四川大学华西医院 | 一种急性胰腺炎器官衰竭预测方法、计算机设备和系统 |
Also Published As
Publication number | Publication date |
---|---|
CN111581339B (zh) | 2021-11-12 |
Similar Documents
Publication | Publication Date | Title |
---|---|---|
CN113011533B (zh) | 文本分类方法、装置、计算机设备和存储介质 | |
CN107992597B (zh) | 一种面向电网故障案例的文本结构化方法 | |
CN111737496A (zh) | 一种电力设备故障知识图谱构建方法 | |
CN110321563B (zh) | 基于混合监督模型的文本情感分析方法 | |
CN107273913B (zh) | 一种基于多特征融合的短文本相似度计算方法 | |
CN112395393B (zh) | 一种基于多任务多示例的远程监督关系抽取方法 | |
CN111966812B (zh) | 一种基于动态词向量的自动问答方法和存储介质 | |
CN112784532B (zh) | 用于短文本情感分类的多头注意力记忆系统 | |
CN112306494A (zh) | 一种基于卷积和循环神经网络的代码分类及聚类方法 | |
CN111680494A (zh) | 相似文本的生成方法及装置 | |
CN112232087A (zh) | 一种基于Transformer的多粒度注意力模型的特定方面情感分析方法 | |
CN116521882A (zh) | 基于知识图谱的领域长文本分类方法及系统 | |
CN113705237A (zh) | 融合关系短语知识的关系抽取方法、装置和电子设备 | |
CN112836051A (zh) | 一种在线自学习的法院电子卷宗文本分类方法 | |
CN113535897A (zh) | 一种基于句法关系和意见词分布的细粒度情感分析方法 | |
CN114254645A (zh) | 一种人工智能辅助写作系统 | |
CN115437626A (zh) | 一种基于自然语言的ocl语句自动生成方法和装置 | |
CN114841353A (zh) | 一种融合句法信息的量子语言模型建模系统及其应用 | |
CN111581339B (zh) | 基于树状lstm对生物医学文献的基因事件的抽取方法 | |
CN115204143B (zh) | 一种基于prompt的文本相似度计算方法及系统 | |
CN115840815A (zh) | 基于指针关键信息的自动摘要生成方法 | |
CN115906818A (zh) | 语法知识预测方法、装置、电子设备和存储介质 | |
CN115510230A (zh) | 一种基于多维特征融合与比较增强学习机制的蒙古语情感分析方法 | |
CN115600595A (zh) | 一种实体关系抽取方法、系统、设备及可读存储介质 | |
CN114372138A (zh) | 一种基于最短依存路径和bert的电力领域关系抽取的方法 |
Legal Events
Date | Code | Title | Description |
---|---|---|---|
PB01 | Publication | ||
PB01 | Publication | ||
SE01 | Entry into force of request for substantive examination | ||
SE01 | Entry into force of request for substantive examination | ||
GR01 | Patent grant | ||
GR01 | Patent grant | ||
TR01 | Transfer of patent right |
Effective date of registration: 20220623 Address after: 300461 room 214, building 3, No. 48, Jialingjiang Road, Lingang Economic Zone, Binhai New Area, Tianjin Patentee after: TJU BINHAI INDUSTRIAL RESEARCH INSTITUTE CO.,LTD. Address before: 300072 Tianjin City, Nankai District Wei Jin Road No. 92 Patentee before: Tianjin University |
|
TR01 | Transfer of patent right | ||
EE01 | Entry into force of recordation of patent licensing contract | ||
EE01 | Entry into force of recordation of patent licensing contract |
Application publication date: 20200825 Assignee: Tianjin Green Agriculture Technology Co.,Ltd. Assignor: TJU BINHAI INDUSTRIAL RESEARCH INSTITUTE CO.,LTD. Contract record no.: X2022980027017 Denomination of invention: Extraction of gene events from biomedical literature based on tree LSTM Granted publication date: 20211112 License type: Common License Record date: 20230104 |
|
EC01 | Cancellation of recordation of patent licensing contract | ||
EC01 | Cancellation of recordation of patent licensing contract |
Assignee: Tianjin Green Agriculture Technology Co.,Ltd. Assignor: TJU BINHAI INDUSTRIAL RESEARCH INSTITUTE CO.,LTD. Contract record no.: X2022980027017 Date of cancellation: 20231018 |
|
OL01 | Intention to license declared |