updated website

_bibliography/papers.bib

@@ -1,115 +1,123 @@
 ---
 ---
-
-@string{aps = {American Physical Society,}}
-
-@book{einstein1920relativity,
-  title={Relativity: the Special and General Theory},
-  author={Einstein, Albert},
-  year={1920},
-  publisher={Methuen & Co Ltd},
-  html={relativity.html}
-}
-
-@book{einstein1956investigations,
+@article{yoonDowker,
+      title={Dowker duality, profunctors, and spectral sequences}, 
+      author={Iris H. R. Yoon},
+      year={2024},
+        publisher = {arXiv},
+      abbr={preprint},
+  doi = {10.48550/arXiv.2408.13136},
+  html  ={https://doi.org/10.48550/arXiv.2408.13136},
   bibtex_show={true},
-  title={Investigations on the Theory of the Brownian Movement},
-  author={Einstein, Albert},
-  year={1956},
-  publisher={Courier Corporation},
-  preview={brownian-motion.gif}
 }
 
-@article{einstein1950meaning,
-  abbr={AJP},
+@article{stolz2023relational,
+      title={Relational persistent homology for multispecies data with application to the tumor microenvironment}, 
+      author={Bernadette J. Stolz and Jagdeep Dhesi and Joshua A. Bull and Heather A. Harrington and Helen M. Byrne and Iris H. R. Yoon},
+      year={2024},
+	abbr={Bull Math Biol},
+  doi = {10.1007/s11538-024-01353-6},
+  html  ={https://doi.org/10.1007/s11538-024-01353-6},
   bibtex_show={true},
-  title={The meaning of relativity},
-  author={Einstein, Albert and Taub, AH},
-  journal={American Journal of Physics},
-  volume={18},
-  number={6},
-  pages={403--404},
-  year={1950},
-  publisher={American Association of Physics Teachers}
 }
 
-@article{PhysRev.47.777,
-  abbr={PhysRev},
-  title={Can Quantum-Mechanical Description of Physical Reality Be Considered Complete?},
-  author={Einstein*†, A. and Podolsky*, B. and Rosen*, N.},
-  abstract={In a complete theory there is an element corresponding to each element of reality. A sufficient condition for the reality of a physical quantity is the possibility of predicting it with certainty, without disturbing the system. In quantum mechanics in the case of two physical quantities described by non-commuting operators, the knowledge of one precludes the knowledge of the other. Then either (1) the description of reality given by the wave function in quantum mechanics is not complete or (2) these two quantities cannot have simultaneous reality. Consideration of the problem of making predictions concerning a system on the basis of measurements made on another system that had previously interacted with it leads to the result that if (1) is false then (2) is also false. One is thus led to conclude that the description of reality as given by a wave function is not complete.},
-  journal={Phys. Rev.},
-  location={New Jersey},
-  volume={47},
-  issue={10},
-  pages={777--780},
-  numpages={0},
-  year={1935},
-  month={May},
-  publisher=aps,
-  doi={10.1103/PhysRev.47.777},
-  url={http://link.aps.org/doi/10.1103/PhysRev.47.777},
-  html={https://journals.aps.org/pr/abstract/10.1103/PhysRev.47.777},
-  pdf={example_pdf.pdf},
-  altmetric={248277},
-  dimensions={true},
-  google_scholar_id={qyhmnyLat1gC},
-  video={https://www.youtube-nocookie.com/embed/aqz-KE-bpKQ},
-  additional_info={. *More Information* can be [found here](https://github.com/alshedivat/al-folio/)},
-  annotation={* Example use of superscripts<br>† Albert Einstein},
-  selected={true},
-  inspirehep_id = {3255}
-}
-
-@article{einstein1905molekularkinetischen,
-  title={{\"U}ber die von der molekularkinetischen Theorie der W{\"a}rme geforderte Bewegung von in ruhenden Fl{\"u}ssigkeiten suspendierten Teilchen},
-  author={Einstein, A.},
-  journal={Annalen der physik},
-  volume={322},
-  number={8},
-  pages={549--560},
-  year={1905},
-  publisher={Wiley Online Library}
+@article{yoonLungTDA,
+      title={Deciphering the diversity and sequence of extracellular matrix and cellular spatial patterns in lung adenocarcinoma using topological data analysis}, 
+      author={Iris H.R. Yoon, Robert Jenkins,  Emma Colliver, Hanyun Zhang, David Novo, David Moore, Zoe Ramsden, Antonio Rullan, Xiao Fu, Yinyin Yuan, Heather A. Harrington, Charles Swanton,  Helen M. Byrne, Erik Sahai},
+      year={2024},
+        publisher = {bioRXiv},
+      abbr={preprint},
+  doi = {10.1101/2024.01.05.574362},
+  html  ={https://doi.org/10.1101/2024.01.05.574362},
+  bibtex_show={true},
 }
 
-@article{einstein1905movement,
-  abbr={Ann. Phys.},
-  title={Un the movement of small particles suspended in statiunary liquids required by the molecular-kinetic theory 0f heat},
-  author={Einstein, A.},
-  journal={Ann. Phys.},
-  volume={17},
-  pages={549--560},
-  year={1905}
-}
 
-@article{einstein1905electrodynamics,
-  title={On the electrodynamics of moving bodies},
-  author={Einstein, A.},
-  year={1905}
-}
 
-@Article{einstein1905photoelectriceffect,
+@article{yang2023topological,
+      title={Topological classification of tumour-immune interactions and dynamics}, 
+      author={Jingjie Yang and Heidi Fang and Jagdeep Dhesi and Iris H. R. Yoon and Joshua A. Bull and Helen M. Byrne and Heather A. Harrington and Gillian Grindstaff},
+      year={2023},
+  abbr={preprint},
+  doi = {10.48550/arXiv.2308.05294},
+  html  ={https://arxiv.org/abs/2308.05294},
   bibtex_show={true},
-  abbr={Ann. Phys.},
-  title="{{\"U}ber einen die Erzeugung und Verwandlung des Lichtes betreffenden heuristischen Gesichtspunkt}",
-  author={Albert Einstein},
-  abstract={This is the abstract text.},
-  journal={Ann. Phys.},
-  volume={322},
-  number={6},
-  pages={132--148},
-  year={1905},
-  doi={10.1002/andp.19053220607},
-  award={Albert Einstein receveid the **Nobel Prize in Physics** 1921 *for his services to Theoretical Physics, and especially for his discovery of the law of the photoelectric effect*},
-  award_name={Nobel Prize}
+  copyright = {arXiv.org perpetual, non-exclusive license}
 }
 
-@book{przibram1967letters,
+@article{hyperTDA,
+  doi = {10.48550/ARXIV.2210.07545},
+  url = {https://arxiv.org/abs/2210.07545},
+  author = {Barbensi, Agnese and Yoon, Hee Rhang and Madsen, Christian Degnbol and Ajayi, Deborah O. and Stumpf, Michael P. H. and Harrington, Heather A.},
+  title = {Hypergraphs for multiscale cycles in structured data},
+  publisher = {arXiv},
+  year = {2022},
+  abbr={preprint},
+  html  ={https://arxiv.org/abs/2210.07545},
   bibtex_show={true},
-  title={Letters on wave mechanics},
-  author={Einstein, Albert and Schrödinger, Erwin and Planck, Max and Lorentz, Hendrik Antoon and Przibram, Karl},
-  year={1967},
-  publisher={Vision},
-  preview={wave-mechanics.gif},
-  abbr={Vision}
+  copyright = {arXiv.org perpetual, non-exclusive license}
+  }
+@article{analogous_bars,
+  doi = {10.1007/s41468-023-00115-y},
+  url = {https://link.springer.com/article/10.1007/s41468-023-00115-y},
+  author = {Yoon, Hee Rhang and Ghrist, Robert and Giusti, Chad},
+  journal= {Journal of Applied and Computational Topology},
+  title = {Persistent Extension and Analogous Bars: Data-Induced Relations Between Persistence Barcodes},
+  publisher = {Springer},
+  abbr={JACT},
+  html={https://rdcu.be/c9Z4e},
+  bibtex_show={true},
+  year = {2023},
+}
+@article{YoonCoriaLaederachHeitsch,
+author = {Hee Rhang Yoon and Aaztli Coria and Alain Laederach and Christine Heitsch},
+doi = {doi:10.1515/cmb-2019-0004},
+url = {https://doi.org/10.1515/cmb-2019-0004},
+title = {Towards an understanding of RNA structural modalities: a riboswitch case study},
+journal = {Computational and Mathematical Biophysics},
+abbr={CMB},
+number = {1},
+volume = {7},
+year = {2019},
+html={https://www.degruyter.com/document/doi/10.1515/cmb-2019-0004/html},
+bibtex_show = {true},
+pages = {48--63}
+}
+@phdthesis{Yoon_dissertation,
+    title    = {Cellular Sheaves and Cosheaves For Distributed Topological Data Analysis},
+    abbr={Ph.D. thesis},
+     bibtex_show={true},
+    school   = {University of Pennsylvania},
+    author   = {Hee Rhang Yoon},
+    html={https://repository.upenn.edu/dissertations/AAI10810230/},
+    bibtex_show={true},
+    year     = {2018},
+}
+@misc{yoon2020persistence,
+      title={Persistence by Parts: Multiscale Feature Detection via Distributed Persistent Homology}, 
+      author={Hee Rhang Yoon and Robert Ghrist},
+      abbr={preprint},
+      year={2020},
+      eprint={2001.01623},
+      archivePrefix={arXiv},
+      html= {https://arxiv.org/abs/2001.01623},
+      bibtex_show = {true},
+      primaryClass={math.AT}
 }
+@article{Mancala,
+author = {L. Taalman and A. Tongen and B. Warren and F. Wyrick-Flax and I. Yoon},
+title = {Mancala Matrices},
+journal = {The College Mathematics Journal},
+abbr={Coll. Math},
+volume = {44},
+number = {4},
+pages = {273-283},
+year  = {2013},
+publisher = {Taylor & Francis},
+doi = {10.4169/college.math.j.44.4.273},
+html = {https://doi.org/10.4169/college.math.j.44.4.273},
+eprint = {https://doi.org/10.4169/college.math.j.44.4.273}
+}
+
+
+

_config.yml

@@ -135,9 +135,9 @@ bing_site_verification: # out your bing-site-verification ID (Bing Webmaster)
 # permalink: /blog/:year/:title/
 # lsi: false # produce an index for related posts
 
-# # Pagination
-# pagination:
-#   enabled: true
+# Pagination
+pagination:
+  enabled: true
 
 # related_blog_posts:
   enabled: true
@@ -195,6 +195,10 @@ collections:
   projects:
     output: true
     permalink: /:collection/:title/
+  data science:
+    output: true
+    permalink: /:collection/:title/
+
 
 # announcements:
 #   enabled: true

_pages/projects.md

@@ -1,6 +1,6 @@
 ---
 layout: page
-title: projects
+title: research
 permalink: /projects/
 description: A summary of my research projects.
 nav: true

_projects/covid.md

@@ -0,0 +1,26 @@
+---
+layout: page
+title: hospital bed shortage prediction
+description: Predicting hospital bed shortage due to COVID-19
+img: assets/img/covid.png
+importance: 4
+category: data science
+---
+
+Check out this <a href="https://covid19-hospital.herokuapp.com/">COVID-19 hospital app</a> I built!  
+
+The app predicts the dates during which hospitals in the US are expected to experience bed shortage due to COVID-19. 
+
+<p align="center">
+  <img width="350" src="https://irisyoon.com/assets/img/app_imag.png">
+</p>
+
+
+The app uses COVID-19 data from the <a href="https://github.com/CSSEGISandData/COVID-19">Johns Hopkins CSSE repository</a> to fit a SIR model. It also uses state-level demographic information and hospital capacity to predict the number of COVID-19 patients that will require hospital and ICU beds. 
+
+For details on the model, please read this <a href="https://medium.com/@irishryoon/predicting-hospital-bed-shortage-in-the-us-due-to-covid-19-2d860ecdaba2">medium post.</a> 
+
+You can play around with the <a href="https://gist.github.com/irishryoon/fe2c769ccca1028dbda2e4a5f060fb7e"> code</a> on Google Colab.
+
+
+*Note: The app uses data that was available on March 26, 2020*

_projects/musicians.md

@@ -4,7 +4,7 @@ title: classical musicians recommender
 description: 
 img: assets/img/smallgraph.png
 importance: 1
-category: data science
+category: data science #data science
 ---
 
 I built a recommendation system for classical music performers. The recommender is based on the idea that musicians with frequent collaborations likely have similar performance styles. It first creates a graph of classical musicians and their collaborations and uses node2vec embeddings to find vector representations of the musicians. Given a list of users' favorite artists, the recommender uses similarity of the vector representations to recommend artists that a user may enjoy.