Making the website

README.md

@@ -454,3 +454,4 @@ Our most active contributors are welcome to join the maintainers team. If you ar
 The theme is available as open source under the terms of the [MIT License](https://github.com/alshedivat/al-folio/blob/master/LICENSE).
 
 Originally, **al-folio** was based on the [\*folio theme](https://github.com/bogoli/-folio) (published by [Lia Bogoev](https://liabogoev.com) and under the MIT license). Since then, it got a full re-write of the styles and many additional cool features.
+

_bibliography/papers.bib

@@ -1,113 +1,76 @@
 ---
 ---
 
-@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}
+@inproceedings{haviv2024wasserstein,
+  title={Wasserstein Wormhole: Scalable Optimal Transport Distance with Transformers},
+  author={Haviv, Doron and Kunes, Russell Zhang and Dougherty, Thomas and Burdziak, Cassandra and Nawy, Tal and Gilbert, Anna and Pe'er, Dana},
+  booktitle={International conference on machine learning},
+  year={2024},
+  organization={PMLR}
 }
 
-@book{einstein1956investigations,
-  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{haviv2024covariance,
+  title={The covariance environment defines cellular niches for spatial inference},
+  author={Haviv, Doron and Rem{\v{s}}{\'\i}k, J{\'a}n and Gatie, Mohamed and Snopkowski, Catherine and Takizawa, Meril and Pereira, Nathan and Bashkin, John and Jovanovich, Stevan and Nawy, Tal and Chaligne, Ronan and others},
+  journal={Nature Biotechnology},
+  pages={1--12},
+  year={2024},
+  publisher={Nature Publishing Group US New York}
 }
 
-@article{einstein1950meaning,
-  abbr={AJP},
-  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}
+@inproceedings{kunes2023gradient,
+  title={Gradient estimation for binary latent variables via gradient variance clipping},
+  author={Kunes, Russell Z and Yin, Mingzhang and Land, Max and Haviv, Doron and Pe'er, Dana and Tavar{\'e}, Simon},
+  booktitle={Proceedings of the AAAI Conference on Artificial Intelligence},
+  volume={37},
+  number={7},
+  pages={8405--8412},
+  year={2023}
 }
 
-@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/)},
-  selected={true}
+@article{burdziak2023sckinetics,
+  title={scKINETICS: inference of regulatory velocity with single-cell transcriptomics data},
+  author={Burdziak, Cassandra and Zhao, Chujun Julia and Haviv, Doron and Alonso-Curbelo, Direna and Lowe, Scott W and Pe’er, Dana},
+  journal={Bioinformatics},
+  volume={39},
+  number={Supplement\_1},
+  pages={i394--i403},
+  year={2023},
+  publisher={Oxford University Press}
 }
 
-@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}
+@inproceedings{mani2022spot,
+  title={SPOT: Spatial Optimal Transport for Analyzing Cellular Microenvironments},
+  author={Mani, Shouvik and Haviv, Doron and Kunes, Russell and Pe'er, Dana},
+  booktitle={NeurIPS 2022 Workshop on Learning Meaningful Representations of Life},
+  year={2022}
 }
 
-@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{raayoni2021generating,
+  title={Generating conjectures on fundamental constants with the Ramanujan Machine},
+  author={Raayoni, Gal and Gottlieb, Shahar and Manor, Yahel and Pisha, George and Harris, Yoav and Mendlovic, Uri and Haviv, Doron and Hadad, Yaron and Kaminer, Ido},
+  journal={Nature},
+  volume={590},
+  number={7844},
+  pages={67--73},
+  year={2021},
+  publisher={Nature Publishing Group UK London}
 }
 
-@article{einstein1905electrodynamics,
-  title={On the electrodynamics of moving bodies},
-  author={Einstein, A.},
-  year={1905}
+@inproceedings{haviv2019understanding,
+  title={Understanding and controlling memory in recurrent neural networks},
+  author={Haviv, Doron and Rivkind, Alexander and Barak, Omri},
+  booktitle={International conference on machine learning},
+  pages={2663--2671},
+  year={2019},
+  organization={PMLR}
 }
 
-@Article{einstein1905photoelectriceffect,
-  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}
+@inproceedings{elad2019direct,
+  title={Direct validation of the information bottleneck principle for deep nets},
+  author={Elad, Adar and Haviv, Doron and Blau, Yochai and Michaeli, Tomer},
+  booktitle={Proceedings of the IEEE/CVF International Conference on Computer Vision Workshops},
+  pages={0--0},
+  year={2019}
 }
 
-@book{przibram1967letters,
-  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}
-}

_config.yml

@@ -2,11 +2,10 @@
 # Site settings
 # -----------------------------------------------------------------------------
 
-title: blank # the website title (if blank, full name will be used instead)
-first_name: You
-middle_name: R.
-last_name: Name
-email: [email protected]
+title: Doron Haviv's Personal Website # the website title (if blank, full name will be used instead)
+first_name: Doron
+last_name: Haviv
+email: [email protected]
 description: > # the ">" symbol means to ignore newlines until "footer_text:"
   A simple, whitespace theme for academics. Based on [*folio](https://github.com/bogoli/-folio) design.
 footer_text: >

_data/cv.yml

@@ -1,97 +0,0 @@
-- title: General Information
-  type: map
-  contents:
-    - name: Full Name
-      value: Albert Einstein
-    - name: Date of Birth
-      value: 14th March 1879
-    - name: Languages
-      value: English, German
-
-- title: Education
-  type: time_table
-  contents:
-    - title: PhD
-      institution: University of Zurich, Zurich, Switzerland
-      year: 1905
-      description:
-        - Description 1.
-        - Description 2.
-        - title: Description 3.
-          contents:
-            - Sub-description 1.
-            - Sub-description 2.
-    - title: Federal teaching diploma
-      institution: Eidgenössische Technische Hochschule, Zurich, Switzerland
-      year: 1900
-      description:
-        - Description 1.
-        - Description 2.
-
-- title: Experience
-  type: time_table
-  contents:
-    - title: Professor of Theoretical Physics
-      institution: Institute for Advanced Study, Princeton University
-      year: 1933 - 1955
-      description:
-        - Description 1.
-        - Description 2.
-        - title: Description 3.
-          contents:
-            - Sub-description 1.
-            - Sub-description 2.
-    - title: Visiting Professor
-      institution: California Institute of Technology, Pasadena, California, US
-      year: 1933
-      description:
-        - Description 1.
-        - Description 2.
-
-    - title: Director
-      institution: Kaiser Wilhelm Institute for Physics, Berlin, Germany.
-      year: 1917-1933
-
-    - title: Professor of Theoretical Physics
-      institution: Karl-Ferdinand University, Prague, Czechoslovakia
-      year: 1911 - 1917
-      description:
-
-    - title: Associate Professor of Theoretical Physics
-      institution: University of Zurich, Zurich, Switzerland
-      year: 1909 - 1911
-
-- title: Open Source Projects
-  type: time_table
-  contents:
-    - title: <a href="https://github.com/alshedivat/al-folio">al-folio</a>
-      year: 2015-now
-      description: A beautiful, simple, clean, and responsive Jekyll theme for academics.
-
-- title: Honors and Awards
-  type: time_table
-  contents:
-    - year: 1921
-      items:
-        - Nobel Prize in Physics
-        - Matteucci Medal
-    - year: 2029
-      items:
-        - Max Planck Medal
-
-- title: Academic Interests
-  type: nested_list
-  contents:
-    - title: Topic 1.
-      items:
-        - Description 1.
-        - Description 2.
-    - title: Topic 2.
-      items:
-        - Description 1.
-        - Description 2.
-
-- title: Other Interests
-  type: list
-  contents:
-    - <u>Hobbies:</u> Hobby 1, Hobby 2, etc.

_data/repositories.yml

@@ -1,12 +1,6 @@
 github_users:
-  - torvalds
-  - alshedivat
+  - DoronHav
 
 github_repos:
-  - alshedivat/al-folio
-  - twbs/bootstrap
-  - jekyll/jekyll
-  - jquery/jquery
-  - FortAwesome/Font-Awesome
-  - jpswalsh/academicons
-  - mathjax/MathJax
+  - dpeerlab/ENVI
+  - dpeerlab/WassersteinWormhole

_news/announcement_envi.md

@@ -0,0 +1,8 @@
+---
+layout: post
+date: 2024-04-02 07:59:00-0400
+inline: true
+related_posts: false
+---
+
+ENVI is now published in [Nature Biotechnology](https://www.nature.com/articles/s41587-024-02193-4)

_news/announcement_wormhole.md

@@ -0,0 +1,8 @@
+---
+layout: post
+date: 2024-05-01 07:59:00-0400
+inline: true
+related_posts: false
+---
+
+[Wasserstein Wormhole](https://arxiv.org/pdf/2404.09411) was accepted to ICML2024!