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.
https://blog.scottlogic.com/2021/10/15/efficiently-loading-m...
Never got any idea on any use case that would be covered by such visualizations, apart from looking cool.
https://www.researchrabbit.ai/
ConnectedPapers also has this but they started to limit unless you pay:
https://www.connectedpapers.com/
A few other ones I know of:
https://paper-explorer.aziis98.com/ (also on github https://github.com/aziis98/paper-explorer)
This uses OpenAlex as a source of articles and to let you explore the citation graph of papers. This is still a prototype mostly made to test out how far I could go with vibecoding (well I still checked the code now and then) something without a js framework. Someday I think I will add more features to it, but now there is already a somewhat working version of import/export so I'm fine with it.
That said, I've never had a client or stakeholder show any interest in using one, beyond an initial "that's cool".
And UMAP etc., is just as much an art as a science. You'll go mad trying to get the perfect layout.
Great toy if you're into that sort of thing, but yeah, fiddly and overwhelming for most.
1) Is there a way to filter the visual atlas by the search term? For instance, I searched "ribosome" and it gave me a list, but I couldn't seem to visualize the list
2) I notice there's an MCP tool. I've used https://paperclip.gxl.ai/ in the past to good effect, curious if there are any standout features from tomesphere?
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.
1. I see there is a Chrome extension, but I have not used Chrome since their adblocker blocker announcement. Is a Firefox extension planned?
2. What is the business model? Is this an open beta of a paid product? If this is not a product, will the code be released at some point?
3. It would be helpful to be able to filter papers by institution or author. Is this planned or out of scope?
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.
Thanks for letting me know.
- 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)