Topological Data Analysis of Knowledge Networks
Adam Schroeder, Jingyi Guan, Prof. Lori Ziegelmeier (Macalester College),
Prof. Russell Funk (University of Minnesota), Prof. Jason Owen-Smith (University of Michigan)
Science of Science
• Science of Science involves analyzing big datasets to uncover the mechanisms driving
scientific progress, ranging from selecting research topics to understanding career
trajectories and progress within a specific field.
• Science can be conceptualized as knowledge networks in which the concepts are
nodes, and two concepts get connected with an edge/paper when they appear in the
same paper abstract and are both considered relevant enough to that article. We weigh
the edge with a standardized year of publication of that article.
• In this study, we use the dataset of article publication information in the field of Applied
Mathematics to build knowledge networks with the concepts (that show up 1k to 15k
times* in the field) in order to study how science evolves over time.
*Please note: The frequency cutoff for concepts is not yet optimized and our
proposed optimization algorithm will be discussed in the Future Work section.
Data
• article id — the unique identifier for the article
• year — the year of publication for the article
• concept — the concept
• relevance mean — the “relevance” score of the concept for the article; higher scores
mean more relevant in category (for applied mathematics)
• frequency — how many times the concept appears in the field of the article in total
• number of times cited — number of times this paper has been cited
Topological Data Analysis
• Persistent homology provides a systematic way to study cycles in a knowledge network
• We track cycles through time, characterizing when they first appear (are born) and when
they no longer remain (die)
• These cycles can be inferred as knowledge gaps.
Goals
- Identify holes of varying complexity (dimensionality)
- Identify their opening, closing, and duration
- Characterize the papers and concepts that participate in the formation and closure of
them with OAT*
*OAT (Open Applied Topology) is a computational toolset developed under the
ExHACT project supported by the NSF (DMS-1854703), leveraging sparse and
lazy computational methods to directly analyze high-dimensional data's
topological structure, enabling the study and localization of geometric patterns
within datasets.
Visualization of the Closure of a 1D Hole in
Applied Mathematics
A cycle
formed
Mean Citations by Paper Categories
- To investigate the importance of papers contributing to distinct topological features in the field of
applied mathematics and discern if papers involved in these features receive more citations, we
categorized all papers within the dataset into the following five categories: (as illustrated below)
Building Papers: Papers/edges on the boundary of the hole in the network.
Destroying Papers: Papers/edges not on the boundary of the hole.
Tentpole Papers: Papers/edges where at least one end involves a concept/node not on the
boundary of the hole.
Opening Papers: The most recent paper among the building papers.
Closing Papers: The most recent paper among the destroying papers.
- We found that the mean citation is the highest for papers that build at least one hole and destroy at
least one other hole among all paper categories. More notably, the papers that are involved in
topological holes have a much higher mean citation than those that are not.
- 2,3,4,5: Building papers
- 1,6,7,8: Destroying papers
- 1,6,7: Tentpole papers
- 5: Opening paper
- 8: Closing paper
Survival Analysis of Knowledge Gaps
We conducted a survival analysis among all knowledge gaps (topological holes) in the
network up to dimension 4. As illustrated by the Kaplan-Meier curves above, we found
that holes of higher dimensions were born later in time, and at any given year, the
proportion of the holes that are still alive is higher for higher dimensions.
BCS-2318171
DMS-1854703
Hole Opening and Closure Over Time
Future Work
A critical task is to set an optimal threshold for concept frequency, which will
define the selection of concepts to be included within the knowledge networks.
To do this, we aim to identify the network with high stability and a good amount
of topological features with linear programming. Specifically, we
- Constructed multiple knowledge networks based on different
concept frequency cutoffs determined by different quantiles of
all frequencies
- Conducted persistent homology analysis for each network to
produce a space of different persistence diagrams
- Filtered out networks lacking sufficient amount of topological
features
- Will select the most stable network which has the lowest
average Euclidean distance between its persistence diagram's
persistence image (PI) and its adjacent diagrams’ PI
Implications
• The growth and dynamics of scientific fields can be understood in
topological terms and analyzed with topological tools like persistent
homology.
• Knowledge gaps with greater complexity or scope take longer to form.
• Papers that are involved in the formation or the closure of knowledge gaps
may exhibit higher importance in the field.