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leonickson

26 karmajoined 4 bulan yang lalu

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Show HN: I mapped 8.5M research papers into an interactive atlas

tomesphere.com
79 points·by leonickson·kemarin dulu·24 comments

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1 points·by leonickson·2 bulan yang lalu·0 comments

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1 points·by leonickson·4 bulan yang lalu·0 comments

Show HN: ModelSweep - Open-Source Benchmarking for Local LLMs

github.com
2 points·by leonickson·4 bulan yang lalu·0 comments

comments

leonickson
·kemarin dulu·discuss
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leonickson
·kemarin dulu·discuss
I really like your work with the gradients.
leonickson
·kemarin dulu·discuss
Thank you so much! I'd genuinely like to hear more, you can email me here - [email protected]
leonickson
·kemarin dulu·discuss
Hello,

1. Yes, I am working on it, I will soon release it for Firefox and Safari (by this weekend). 2. For now I am just trying to see what people want, may be the business model is more focused on mcp for higher limits for labs, lets see where is goes. 3. The paper/article search already has author search, I can add the university search soon in both the paper/article and altas/map search.

Thank you for all the questions and suggestions.
leonickson
·kemarin dulu·discuss
I am sorry, it should have taken you to the paper page/article, I will investigate it, but I did the same search and clicked on the first link, it to me to this - https://tomesphere.com/paper/2301.01365

Thanks for letting me know.
leonickson
·kemarin dulu·discuss
Will check it, it will be really useful. Thanks
leonickson
·kemarin dulu·discuss
It is all open, bulk-downloadable sources. Here are some links.

  - arXiv: bulk on S3 (https://info.arxiv.org/help/bulk_data_s3.html)
  - PubMed Central Open Access: AWS Open Data (s3://pmc-oa-opendata).
  - bioRxiv / medRxiv: their monthly S3 dumps
  - OpenAlex: for citations, metadata, abstracts (https://developers.openalex.org/download/download-to-machine) 
  - AlphaFold — structures (https://alphafold.ebi.ac.uk/download)
Thanks for the question.
leonickson
·kemarin dulu·discuss
The project has four parts, and I think you may have used the search in the navigation bar. That search is for the paper page (detailed information about that specific paper). When you search, you get a list of results, and if you click one of them, it takes you to a paper page with all the in-depth details about that paper. I should have made the map UX better.

To highlight things in the atlas or map, you might want to go to the filter panel on the left side and scroll down a bit. You will see a search area that helps you search for genes, diseases, and proteins. However it might not highlight any dot for the “ribosome” because filter search for now is only connected to genes, diseases and protein. I noted this, and I will improve it. I may also move that filter search to a different place. Thank you so much.

Tomesphere includes web pages and a browser extension overlays all of this directly on the arXiv, PMC, bioRxiv, Google Scholar, and medRxiv pages you are already reading. I had noticed the Paperclip MCP before, and from what I can see, they have very good data. In some cases, they may even have better data. We also have some additional sources, such as peer review from OpenReview, video links from YouTube and SlidesLive, GitHub links, AlphaFold protein entities, citations, and semantic neighbors.

Thank you for the questions. Will improve the project more.
leonickson
·kemarin dulu·discuss
Hi, I love the genre too. Cosmograph is wonderful, I did try it, but because of its license restriction I could not use it for this project. I do agree that beyond an initial "that's cool" this map may not contribute much, "and that's why I didn't make it the main product. I already had the data as I was building other things (extension, paper page) and wanted a bit of a cool factor so people would take a look at the project. The value is what's under each dot, the enriched page (TLDR, genes/drugs/diseases, trials, 3D structures, code, datasets, full text), extension and the MCP for agents.
leonickson
·kemarin dulu·discuss
Hello, I agree with you, viz are just cool and might not really have a usecase. In this project map is not the product, it is 1 of 4 parts and to be honest the least important. The value is what is under each dot, the enriched page (TLDR, genes/drugs/diseases, trials, protein structures, code, datasets, full text, images, reviews, etc) and the MCP for agents. You are welcome to use whichever part of the project is most useful to you (whether that is the map, paper pages, browser extension, or MCP).
leonickson
·kemarin dulu·discuss
When I read papers, I have to jump between multiple tabs to find the dataset, code, videos, peer reviews, and so on. I tried to fix this with this project.

It started as a project just for papers on arXiv, but after its initial success on Twitter (got like 1.9k views: the most I have gotten for a post), I have now expanded it to include other openly available papers from PubMed Central, bioRxiv, medRxiv, and eLife. These papers have been linked with their genes, proteins, diseases, drugs, clinical trials, 3D protein structures, code, and cited and similar papers.

This project now has four parts:

First, a map. I embedded nearly 8.5M papers (with SPECTER2), ran UMAP for 2D representation, and rendered them as a scatterplot. The dots can be clicked to see brief information about the papers, like an LLM TLDR, key findings, peer reviews, linked entities, and more. The clusters are also labeled, though you might have to zoom in.

Second, I built a detailed paper page for each paper. They give you the paper's full text, images, videos, peer reviews (from OpenReview), GitHub links, Hugging Face dataset/model links, clinical trials, genes, diseases, 3D protein structures, cited papers, and similar papers. You can also copy the whole page, including the full paper text and image URLs, as markdown for your LLM.

Third, I have released an extension so you can read all this information in your sidebar by clicking "open in Tomesphere" that shows up in arXiv, PMC, bioRxiv, Google Scholar, or medRxiv. I have tried to provide as much information as possible in the extension, though for things like viewing all the images or a 3D protein structure, you might still have to go to the paper page using the link provided in the extension.

Fourth, all this data is available for your LLM via MCP. The MCP does have a 50-query free limit (this jumps 10x with signup).

Note: this project is still in beta, so papers might have some mismatched information. I am rolling out feedback forms soon to improve the data quality. Thank you so much for taking the time to read this.
leonickson
·4 bulan yang lalu·discuss
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