zh:notes:topic_linkages2
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zh:notes:topic_linkages2 [2018/11/12 08:55] pzczxs 创建 |
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| - | ====== A Novel Method for Topic Linkages between the Scientific Publications and Patents ====== | + | ====== Topic Linkages between Scientific Publications and Patents ====== |
| + | ===== Citation Information ===== | ||
| + | Shuo Xu, Dongsheng Zhai, Feifei Wang, Xin An, Hongshen Pang, and Yirong Sun, 2019. [[https://doi.org/10.1002/asi.24175|A Novel Method for Topic Linkages between Scientific Publications and Patens]]. //Journal of the Association for Information Science and Technology//, Vol. 70, No. 9, pp. 1026-1042. | ||
| + | |||
| + | ===== Corpora ===== | ||
| + | *[[http://www.biocreative.org/tasks/biocreative-iv/chemdner/|CHEMDNER corpus]] | ||
| + | *[[http://www.biocreative.org/tasks/biocreative-v/track-2-chemdner/|CHEMDNER-patents corpus]] | ||
| + | |||
| + | ===== Convert test set ===== | ||
| + | The format of the test set in the CHEMDNER corpus is inconsistent with the other sets. Therefore, the test set needs to be converted in advance. | ||
| + | ===== Convert the dataset to the Brat format ===== | ||
| + | In order to visualize the annotated entities, these two corpora need to be converted to the Brat format. | ||
| + | |||
| + | http://54xushuo.net:8001/index.xhtml | ||
| + | ===== Topic Extraction ===== | ||
| + | To run <color red>CCorrLDA2.java</color> and <color red>CorrLDA2.java</color> for the CCorrLDA2 and CorrLDA2 model, respectively. | ||
| + | |||
| + | ===== Brown Clustering ===== | ||
| + | <code bash run_brown.sh> | ||
| + | > cd brown-cluster | ||
| + | > cat papers.words.txt patents.words.txt > words.txt | ||
| + | > cat papers.entities.txt patents.entities.txt > entities.txt | ||
| + | > ./wcluster --text words.txt --c 1000 | ||
| + | > ./wcluster --text entities.txt --c 500 | ||
| + | </code> | ||
| + | |||
| + | ===== Perplexities of the CCorrLDA2 and CorrLDA2 models ===== | ||
| + | <code matlab> | ||
| + | > load perplexities | ||
| + | > plotPerplexity(papers_CCorrLDA2, papers_CorrLDA2) | ||
| + | > plotPerplexity(patents_CCorrLDA2, patents_CorrLDA2) | ||
| + | </code> | ||
| + | |||
| + | ===== Negative log likelihood ===== | ||
| + | <code matlab> | ||
| + | > load exchange | ||
| + | > plotExchangeLikelihood(paper_likelihoods) | ||
| + | > plotExchangeLikelihood(patent_likelihoods) | ||
| + | </code> | ||
| + | |||
| + | ===== Optimal Transportation Distance ===== | ||
| + | <code matlab> | ||
| + | > mex -setup C++ | ||
| + | > mex ot_mex.c | ||
| + | > topic_linkage('../data/linkage/', 'sym_KL_divergence', 'CCorrLDA2', 1, 10000, 1/3, 1/3, 90); | ||
| + | > load strength | ||
| + | > convert_strength('../data/linkage/', 'CCorrLDA2', ot_CCorrLDA2_cluster); | ||
| + | </code> | ||
| + | |||
| + | ===== Strength Map ===== | ||
| + | <code bash> | ||
| + | > python strength_map.py ../data/linkage/s2t.CCorrLDA2.txt ../data/linkage/mask.cluster.CCorrLDA2.txt | ||
| + | > python strength_map.py ../data/linkage/t2s.CCorrLDA2.txt ../data/linkage/mask.cluster.CCorrLDA2.txt | ||
| + | </code> | ||
| + | |||
| + | ~~DISCUSSION:closed~~ | ||
zh/notes/topic_linkages2.1541984106.txt.gz · 最后更改: 2018/11/12 08:55 由 pzczxs