Python software for the Biological Expression Language, integrating biomedical knowledge, and systems biology
Germany
Joined December 2019
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Home: pybel.github.io
GitHub: github.com/pybel
Docs: pybel.readthedocs.org
Paper: academic.oup.com/bioinformat…
PyBEL retweeted
We're happy to announce that Gilda has been published in @BioinfoAdv - read it at
doi.org/10.1093/bioadv/vbac0… and try it at github.com/indralab/gilda
Next, we’ll use it for ontology alignment in @OBOFoundry and to make plugins in programs like Google Docs for dataset annotation 🚀
PyBEL retweeted
Our @benjamingyori is presenting today on automated hypothesis generation and human-machine collaboration at the 1st Workshop on Nobel Turing Challenge: groups.oist.jp/obu/event/wor…
PyBEL retweeted
🚨 We're happy to share one of our submissions to @GLB_Workshop outlining new, more comparable link prediction metrics than MR, MRR, and Hits@K including the zMR, zMRR, and zHits@K
Thanks to authors @cthoyt @BerrendorfMax @michael_galkin @vtresp @benjamingyori
#arXiv #machinelearning [csLG] A Unified Framework for Rank-based Evaluation Metrics for Link Prediction in Knowledge Graphs. (arXiv:2203.07544v1 [cs.LG]) bit.ly/3qb4Mxs #mw
The link prediction task on knowledge graphs without explicit negative triples in the training…
PyBEL retweeted
Happy to release #pyABC 0.12! 👶 github.com/icb-dcm/pyabc
🧵Featuring a bunch of new features:
PyBEL retweeted
🚨 Our @Bioregistry project imports and standardizes prefixes/metadata for biomedical nomenclatures from 15 external registries (e.g. @OBOFoundry @IdentifiersOrg @bioportal) and allows for community 👪 extension using an open data model at github.com/biopragmatics/bio….
PyBEL retweeted
Our speaker's list for our @cecamEvents workshop (/w @JoshuaSchrier @BenBlaiszik @petermurrayrust @helsoeste @cthoyt) is now finalized! Consider registering if you're interested in making chemical data machine-actionable! @EPFLOpenScience #chemtwitter
We are happy to announce MADICES 2022 (Machine-Actionable Data Interoperability for Chemical Sciences), an upcoming (Feb 7–9) virtual @cecamEvents workshop for which more information and registration details can be found on madices.github.io/.
PyBEL retweeted
We’re so excited to see @BerrendorfMax pass his defense magna cum laude!
We already updated our team page 💪
PyBEL retweeted
Our @benjamingyori gave the first @cosi_sysmod webinar for @iscb Academy describing our team's work.
📽️ Full recording: youtube.com/watch?v=v_XC_JUA…
🔗 More about what we do: indralab.github.io/
PyBEL retweeted
🚨 PyKEEN 1.7.0 is out! 🚨
New: 7 models, 3 encoders, 2 trackers, keras-style training callbacks, uncertainty estimation, and more
📖 Full Release Notes: github.com/pykeen/pykeen/rel…
💪 Huge S/O to external contributors @dobraczka @michael_galkin @SBonner0 @Ralph_Abb and others
PyBEL retweeted
ISB2022 Biocuration Conference first session 🎉
🗓️ 29 March 2022
➡️ Panel: Promotion and dissemination of biocuration efforts
➡️ Invited Speakers Talks
Submit your abstracts: forms.gle/iaXGAQFqFCdW5oit9
More info: biocuration.org/15th-annual-…
PyBEL retweeted
📣The first SysMod Webinar is coming up. Dr. Gyori (@benjamingyori from @HavardUnivers) will talk about “Accelerating biomedical discovery with large-scale knowledge assembly and human-machine collaboration” – join us on January 18, 2022, at 11:00 AM EST: iscb.org/iscbacademy-upcomin…
Welcome BioPAX to the Python scientific ecosystem :))
We've been developing PyBioPAX, a native Python object model for BioPAX Level 3 with parsing, serializing, and traversal of BioPAX models.
🚀 Install: pip install pybiopax
🖥️ Code: github.com/indralab/pybiopax
📖 Docs: pybiopax.rtfd.io
PyBEL retweeted
We’re still actively maintaining FamPlex, a resource for text mining and reasoning over human protein families/complexes. Here's some links to learn more and a thread on a few improvements we made recently:
🖥️Code/data: github.com/sorgerlab/famplex
📜Paper: bmcbioinformatics.biomedcent…
PyBEL retweeted
PyKEEN 1.6.0 is out, now with batteries from PyTorch 1.9 built in!
🎁 It’s got new models, new datasets, new loss functions, bug fixes, and improvements.
🙏 Huge s/o to our many external contributors for this release
📖 Release notes: github.com/pykeen/pykeen/rel…
PyBEL retweeted
Cool use of @indrasysbio to integrate text-mining systems and assemble models of cardiomyopathy mechanisms from literature. I'm proud that INDRA is increasingly picked up and applied (and in this case also carefully evaluated) by independent groups! @glavaski_mila @LazarVelicki
#biocuration ift.tt/3D0N1VM Humans and machines in biomedical knowledge curation: hypertrophic cardiomyopathy molecular mechanisms' representation
PyBEL retweeted
PyKEEN 1.3 is out, with new datasets, new trackers, faster and more elegant code, improved support for big datasets, and a better interface for running predictions on your trained models.
Full changelog at github.com/pykeen/pykeen/rel…
P.S. Happy Rosenmontag! Kölle alaaf 🤡
Useful for biologists making the transition to AI/ML - this is written for newcomers
Are you new to knowledge graph embedding models? Are you confused about loss functions?
We wrote a nice introduction for you: pykeen.readthedocs.io/en/lat…
PyBEL retweeted
Today, we added @earthling91’s Common Sense Knowledge Graph (CSKG) as a benchmark dataset.
Train your KGE model with:
>>> from pykeen.pipeline import pipeline
>>> results = pipeline(dataset=‘cskg’, model=‘RotatE’)
See how we did it: github.com/pykeen/pykeen/pul…
For BEL users who are embedding their networks for drug repositioning, disease-target prioritization, etc should get excited!