Building networks of shared research interests by embedding words into a representation space
Fuente:
arXiv
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| Natura: | Preprint |
| Pubblicazione: |
2025
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| _version_ | 1866915145422209024 |
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| author | Poon, Art |
| author_facet | Poon, Art |
| contents | Departments within a university are not only administrative units, but also an effort to gather investigators around common fields of academic study. A pervasive challenge is connecting members with shared research interests both within and between departments. Here I describe a workflow that adapts methods from natural language processing to generate a network connecting $n=79$ members of a university department, or multiple departments within a faculty ($n=278$), based on common topics in their research publications. After extracting and processing terms from $n=16,901$ abstracts in the PubMed database, the co-occurrence of terms is encoded in a sparse document-term matrix. Based on the angular distances between the presence-absence vectors for every pair of terms, I use the uniform manifold approximation and projection (UMAP) method to embed the terms into a representational space such that terms that tend to appear in the same documents are closer together. Each author's corpus defines a probability distribution over terms in this space. Using the Wasserstein distance to quantify the similarity between these distributions, I generate a distance matrix among authors that can be analyzed and visualized as a graph. I demonstrate that this nonparametric method produces clusters with distinct themes that are consistent with some academic divisions, while identifying untapped connections among members. A documented workflow comprising Python and R scripts is available under the MIT license at https://github.com/PoonLab/tragula. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2502_07042 |
| institution | arXiv |
| publishDate | 2025 |
| record_format | arxiv |
| spellingShingle | Building networks of shared research interests by embedding words into a representation space Poon, Art Social and Information Networks Departments within a university are not only administrative units, but also an effort to gather investigators around common fields of academic study. A pervasive challenge is connecting members with shared research interests both within and between departments. Here I describe a workflow that adapts methods from natural language processing to generate a network connecting $n=79$ members of a university department, or multiple departments within a faculty ($n=278$), based on common topics in their research publications. After extracting and processing terms from $n=16,901$ abstracts in the PubMed database, the co-occurrence of terms is encoded in a sparse document-term matrix. Based on the angular distances between the presence-absence vectors for every pair of terms, I use the uniform manifold approximation and projection (UMAP) method to embed the terms into a representational space such that terms that tend to appear in the same documents are closer together. Each author's corpus defines a probability distribution over terms in this space. Using the Wasserstein distance to quantify the similarity between these distributions, I generate a distance matrix among authors that can be analyzed and visualized as a graph. I demonstrate that this nonparametric method produces clusters with distinct themes that are consistent with some academic divisions, while identifying untapped connections among members. A documented workflow comprising Python and R scripts is available under the MIT license at https://github.com/PoonLab/tragula. |
| title | Building networks of shared research interests by embedding words into a representation space |
| topic | Social and Information Networks |
| url | https://arxiv.org/abs/2502.07042 |