Torchcell

None

* exclude dubious ([`cdbd9ad`](https://github.com/Mjvolk3/torchcell/commit/cdbd9ade17538720e1bcde0fc74dff9038878f6f))

* exclude dubious ([`86b07b8`](https://github.com/Mjvolk3/torchcell/commit/86b07b82ad7b0ca83c8c86f465cf244f17da6a16))

Unknown

* update toml ([`0f37659`](https://github.com/Mjvolk3/torchcell/commit/0f37659b62df4095afd1bfd179b77fb9e700de80))

* update toml ([`757ddcc`](https://github.com/Mjvolk3/torchcell/commit/757ddccc82fc60429c7e66711216c26c50453f9e))

* fix: comment ([`23f02a9`](https://github.com/Mjvolk3/torchcell/commit/23f02a99315a49c26d369bdd7076f6678bd1e91b))

* fix: added semantic versioning ([`12ad010`](https://github.com/Mjvolk3/torchcell/commit/12ad0104e0150343b2fe0717b6e09cd137cc0335))

* source update - dump to docker community works -> enterprise ([`ca28679`](https://github.com/Mjvolk3/torchcell/commit/ca28679c478aea7e04c1fc27eea9b192ef79ac1d))

* added chunk size arg ([`fbbe551`](https://github.com/Mjvolk3/torchcell/commit/fbbe55139f8962bd57df27a05bfeea8390c86b70))

* update costanzo adapter ([`61eac91`](https://github.com/Mjvolk3/torchcell/commit/61eac91d049d87e60e6bab71cbd0f328b2daa394))

* config move and update ([`1ec5fa7`](https://github.com/Mjvolk3/torchcell/commit/1ec5fa760de836c22a99d6703a64cb21aab0c8ed))

* reqs update ([`7a00145`](https://github.com/Mjvolk3/torchcell/commit/7a00145388bbb6a97fef5a9aa2d040faad89110c))

* small note clean up ([`5055e12`](https://github.com/Mjvolk3/torchcell/commit/5055e1263a4ad70fedc7e1751693771fb373b7ed))

* revert to pip install. ([`bf4b2fe`](https://github.com/Mjvolk3/torchcell/commit/bf4b2fe49f67cbcaa2001596e109624c1fd43264))

* change in src check docker image build. ([`3ac133a`](https://github.com/Mjvolk3/torchcell/commit/3ac133a1c0866f4cfe7ebe3b420ac69275f756bb))

* Merge remote-tracking branch &39;refs/remotes/torchcell/main&39; ([`b0addc4`](https://github.com/Mjvolk3/torchcell/commit/b0addc4b0ce09a425743566b3d7f58d060623eb8))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`fddccf6`](https://github.com/Mjvolk3/torchcell/commit/fddccf60e21d14a052dc52dd6b63d43404abec6a))

* simplify query ([`c75e0c8`](https://github.com/Mjvolk3/torchcell/commit/c75e0c846d0606c0275008c21d38e30c361d1744))

* docker name change ([`faf1b18`](https://github.com/Mjvolk3/torchcell/commit/faf1b188daae4a1d3a7307b236cf2db45a8404be))

* docker image working ([`43936ea`](https://github.com/Mjvolk3/torchcell/commit/43936ea27b78e51a04919973460b6e737f9bae80))

* Merge remote-tracking branch &39;refs/remotes/torchcell/main&39; ([`e25e49c`](https://github.com/Mjvolk3/torchcell/commit/e25e49cc1ba6a1c1281ffea1cf2a0b8ebfcbfeb3))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`82b61d7`](https://github.com/Mjvolk3/torchcell/commit/82b61d71c6d35885c5d2d5d910c77b1614279a12))

* biocypher config ([`75575d1`](https://github.com/Mjvolk3/torchcell/commit/75575d1d5aa38230f0b36f87ae16a85985b0e399))

* added docker file for neo4j community ([`688c3ee`](https://github.com/Mjvolk3/torchcell/commit/688c3ee06c093086d2d6f0e5af063c3537d4eb93))

* neo4j_fitness_query ([`33d9180`](https://github.com/Mjvolk3/torchcell/commit/33d91807324e5f797c62b7fe50b1f2aac919471d))

* update fitness query ([`41b04e2`](https://github.com/Mjvolk3/torchcell/commit/41b04e2d814ae904ee9935a8479c5a03a393b7fe))

* Merge remote-tracking branch &39;refs/remotes/torchcell/main&39; ([`863a704`](https://github.com/Mjvolk3/torchcell/commit/863a70428b217f99df41988a9b9b2ba5ce71d19a))

* biocypher_config ([`c64e99b`](https://github.com/Mjvolk3/torchcell/commit/c64e99bf83ac3a71236888a3dee3081c20d9f299))

* first db build working on delta ([`391c198`](https://github.com/Mjvolk3/torchcell/commit/391c198e4a55f044298b5800e819e560011c4abc))

* removed dataset import bug ([`cfb8e00`](https://github.com/Mjvolk3/torchcell/commit/cfb8e00da59774e67ffdb26fa824ee6f288520ec))

* notes ([`1d38da0`](https://github.com/Mjvolk3/torchcell/commit/1d38da0b51ca9640ee1f55e8c5c97daa704954d5))

* Merge remote-tracking branch &39;refs/remotes/torchcell/main&39; ([`4099c57`](https://github.com/Mjvolk3/torchcell/commit/4099c5719bc142cd7dd93081504de3d6304e33fb))

* build db slurm ([`ea32dbd`](https://github.com/Mjvolk3/torchcell/commit/ea32dbd8be49ff80d198daa7ebebe8898e429fff))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`0a66446`](https://github.com/Mjvolk3/torchcell/commit/0a664461866c53cc9a29a7339b137620d775f279))

* tc wrk space update ([`f9738f5`](https://github.com/Mjvolk3/torchcell/commit/f9738f50f78c7f5f3b42a01fb9b6441e7c436d18))

* adapters fixed by adding biocypher config ([`d2e4f89`](https://github.com/Mjvolk3/torchcell/commit/d2e4f89b2df283aa7d1a4666513e5e9b42f56201))

* create_kg_small prototype for delta neo4j ([`af628a1`](https://github.com/Mjvolk3/torchcell/commit/af628a1168bd8c735fd1a78688ec5ecf6c153fe9))

* first successful query and deserialization ([`38bfa43`](https://github.com/Mjvolk3/torchcell/commit/38bfa437c5e3d1b87132546c75a9d8766fc31f4e))

* Merge remote-tracking branch &39;refs/remotes/torchcell/main&39; ([`4fa4749`](https://github.com/Mjvolk3/torchcell/commit/4fa47495ad1e455881d4a2b876f405b90728bf9e))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`f1900e8`](https://github.com/Mjvolk3/torchcell/commit/f1900e88c3908ea03d0df2a367678817959ab7c6))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`f44adb8`](https://github.com/Mjvolk3/torchcell/commit/f44adb8aff38c3a29567815a2d1817123230b412))

* remote update ([`6345796`](https://github.com/Mjvolk3/torchcell/commit/63457960b48c91441055de84b822dc0fb0529f36))

* first dmf adapter bulk import to neo4j ([`97bc33c`](https://github.com/Mjvolk3/torchcell/commit/97bc33c7b452e33a27c28df027a8fa781e943bd3))

* pypy updates both runing ok. not perfect. moving to delta db. ([`3b58f42`](https://github.com/Mjvolk3/torchcell/commit/3b58f429578c3f5ddefdd2deb8bffb718704ac4f))

* pypy doesn&39;t seem to work for speed up ([`1f90eff`](https://github.com/Mjvolk3/torchcell/commit/1f90eff153afdfbd1a9d6f51197f22286e69acc4))

* build kuzmin2018 with pypy3.10 works ([`8714045`](https://github.com/Mjvolk3/torchcell/commit/87140454badf1164df44a96e18071e03a19714f0))

* pypy3.10 env working for kuzmin smf db build ([`429f78c`](https://github.com/Mjvolk3/torchcell/commit/429f78c3c8652fa332f0b02ac172546ad9ab5592))

* updated graph run small and big test. ([`1da6891`](https://github.com/Mjvolk3/torchcell/commit/1da6891c5df657baf85ce836423f52dd8cbef57a))

* versioning ([`57de6fa`](https://github.com/Mjvolk3/torchcell/commit/57de6fad9b4d15b755ea5c553802608e90e318bb))

* delta and apostropher replace ([`208cb2f`](https://github.com/Mjvolk3/torchcell/commit/208cb2fe7d6939d30813ffdc1ac83325c72f104f))

* nan to None in SmfKuzmin2018 ([`3aea9fa`](https://github.com/Mjvolk3/torchcell/commit/3aea9fad09c8c6186e1e48a0c194a501285c9be6))

* DmfKuzmin2018Adapter works ([`c1eefc0`](https://github.com/Mjvolk3/torchcell/commit/c1eefc0f382a1058ee2b067e579d34f33b256b63))

* smf costanzo adapter works. ([`26eb83c`](https://github.com/Mjvolk3/torchcell/commit/26eb83caae83e4ff823bd2225951342c20f6f222))

* costanzo adapter working but need finalization ([`0a60d40`](https://github.com/Mjvolk3/torchcell/commit/0a60d40f308ac15b1eddd4d1aea4c09868967b54))

* reorganize naming ([`09f81e9`](https://github.com/Mjvolk3/torchcell/commit/09f81e9700b1242c788b4284fcc29adecf4deff1))

* fix isort, autoflake ([`39d46d1`](https://github.com/Mjvolk3/torchcell/commit/39d46d1a59657a9e9818fc04db4e9bef48366e30))

* organize imports ([`b96f7eb`](https://github.com/Mjvolk3/torchcell/commit/b96f7eb3caa1e28d072ef7f91c46e923cbe3a41e))

* data organize ([`2c719ab`](https://github.com/Mjvolk3/torchcell/commit/2c719ab3cccec702e481f682d3a6cf82f16aa165))

* experiment reference index dmf ([`9aa797c`](https://github.com/Mjvolk3/torchcell/commit/9aa797c2c8d3fc2f4874cef12d779ddae6ac562a))

* Experiment Reference Index ([`e1d1b74`](https://github.com/Mjvolk3/torchcell/commit/e1d1b7464190990369f770437b0c465a51d927b9))

* notes ([`4538222`](https://github.com/Mjvolk3/torchcell/commit/4538222a3842c6fd58191ac7ef5a24ae17a7a0ae))

* ignore specific data ([`afb9482`](https://github.com/Mjvolk3/torchcell/commit/afb9482c1c8c9b1b76c12f6d528594291249fe93))

* dmf Kuzmin works ([`b74a92b`](https://github.com/Mjvolk3/torchcell/commit/b74a92b6f9ac12fe461b8e31464fc86c32fe16f8))

* hosting data ([`e28fc5b`](https://github.com/Mjvolk3/torchcell/commit/e28fc5b4602dfbc678d34221347bf2868a18791a))

* dmf updated ([`863b745`](https://github.com/Mjvolk3/torchcell/commit/863b7455775166237102b73b33a3b9c300696418))

* smf working ([`e257186`](https://github.com/Mjvolk3/torchcell/commit/e257186c9dd6b7dd8359acf55aa9843913d46b92))

* pre strain id check point ([`7af5afb`](https://github.com/Mjvolk3/torchcell/commit/7af5afbb149bede6c493df764d5fc5922f6ae669))

* dataset with lmdb and pydantic ([`b94f0e8`](https://github.com/Mjvolk3/torchcell/commit/b94f0e8993ff39018bf66fc277bbbd482502e651))

* dmf neo costanzo with issues ([`e933788`](https://github.com/Mjvolk3/torchcell/commit/e9337884bc85871a793632fcfec48665af664e8b))

* bumped version ([`23d72d4`](https://github.com/Mjvolk3/torchcell/commit/23d72d4308627cb85e30db518321e7b84656fbdd))

* prime to _prime for biocypher import ([`7b12ceb`](https://github.com/Mjvolk3/torchcell/commit/7b12ceb694ed1092e078439a107738f851e90cba))

* no polars ([`f0cf3fc`](https://github.com/Mjvolk3/torchcell/commit/f0cf3fc16e2da8283ed4f2498ed2bd33f1674338))

* update mplstyle dir ([`ed0f630`](https://github.com/Mjvolk3/torchcell/commit/ed0f630baa363825c6bb2f9209d6f06cb7d64746))

* build works ([`e72076a`](https://github.com/Mjvolk3/torchcell/commit/e72076a3b93cafdeb829629e8e0097482b7938fc))

* need to check docker graph ([`b55a0b2`](https://github.com/Mjvolk3/torchcell/commit/b55a0b282199e049e7cb1c08f8ca2136b61bdaeb))

* graph progress - added subclasssed nodes ([`61c6d59`](https://github.com/Mjvolk3/torchcell/commit/61c6d59cd95fec9d4f7c0a8c45b5846c4c60bad9))

* working model for neo costanzo ([`b2b6756`](https://github.com/Mjvolk3/torchcell/commit/b2b6756245e79391b4d19678a0632b8d109a0315))

* frontmatter refactor ([`73c4595`](https://github.com/Mjvolk3/torchcell/commit/73c459597ea83f23b9c8166dd6e419cf0937a5e5))

* fixed file moving, broken from before ([`ea46275`](https://github.com/Mjvolk3/torchcell/commit/ea46275197b85c5996cac16a0927cdf4f643228e))

* python refactor last of them ([`df63f29`](https://github.com/Mjvolk3/torchcell/commit/df63f297b2f7f1806c1a4155c175915339c293b3))

* note and python refactor ([`3abee77`](https://github.com/Mjvolk3/torchcell/commit/3abee774b32a65cfeb5f18679f3fce812a1d98b5))

* refactor ([`7f339eb`](https://github.com/Mjvolk3/torchcell/commit/7f339eb96eaf5c6b21c9b8c1cebc57f16d8d7805))

* biocypher added ([`6e712b5`](https://github.com/Mjvolk3/torchcell/commit/6e712b57e6810e63b000e6d53a113ffa592a83ce))

* clean up root ([`3d772d9`](https://github.com/Mjvolk3/torchcell/commit/3d772d9590c69dbe8872a3ba5e5b43245f893bf3))

* Merge remote-tracking branch &39;refs/remotes/torchcell/main&39; ([`3435d82`](https://github.com/Mjvolk3/torchcell/commit/3435d828624189b7a5b28a4257215456347ceb0e))

* update req... not sure why not updating ([`6153e13`](https://github.com/Mjvolk3/torchcell/commit/6153e13c49c74c152e5116e7ff3618f79ad1bc3b))

* pydant ([`c1f7b44`](https://github.com/Mjvolk3/torchcell/commit/c1f7b44f885f28dcad29502cd761ef7d21fd3e7b))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`389bf9c`](https://github.com/Mjvolk3/torchcell/commit/389bf9cd2b4dcca17f46ae99603c1e55b7524742))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`ff382dd`](https://github.com/Mjvolk3/torchcell/commit/ff382ddf33dae5ffebf808217654dc85331bc8bc))

* l2 weight decay duplicate ([`e3cf35b`](https://github.com/Mjvolk3/torchcell/commit/e3cf35bd23027d75e1269b04565a4c871618ee87))

* dcell update for slimming model ([`ca05466`](https://github.com/Mjvolk3/torchcell/commit/ca0546609b68d358dcd19b8fd1d21bf1d7ac2afd))

* json schema test ([`1726aee`](https://github.com/Mjvolk3/torchcell/commit/1726aee594cdd4d6e59dec38356e38a33e2614f8))

* rdf update ([`7f828c3`](https://github.com/Mjvolk3/torchcell/commit/7f828c3c0b1cb029349473e8948502affe1344e4))

* update tc rdf ([`cd1d29a`](https://github.com/Mjvolk3/torchcell/commit/cd1d29a168bb1caf81185deafa17d3da17fc962c))

* torchcell.rdf ([`0e8d97b`](https://github.com/Mjvolk3/torchcell/commit/0e8d97b1d2adce1f7d751c22838b4e83952853bf))

* onto update ([`9d17af7`](https://github.com/Mjvolk3/torchcell/commit/9d17af734eb560f2c164de51faaca2056852f807))

* updated onto ([`47670e5`](https://github.com/Mjvolk3/torchcell/commit/47670e5e544a87c412d0b0a4d1e8fffb33bf3240))

* simple onto ([`dd06731`](https://github.com/Mjvolk3/torchcell/commit/dd067313e7367fd8e7a0324fe8da3de2358b1f61))

* owl in owl ([`c33cadd`](https://github.com/Mjvolk3/torchcell/commit/c33cadd3de199f8196d62a041c174e143c2fd3cc))

* del my owl ([`a011aa6`](https://github.com/Mjvolk3/torchcell/commit/a011aa699c14c6744bc519fb57179b400971cb1b))

* my_ontology robot converted ([`09373e9`](https://github.com/Mjvolk3/torchcell/commit/09373e9191d907bb4c02e53e6f620114de02ad00))

* try rdf ([`4ea32a4`](https://github.com/Mjvolk3/torchcell/commit/4ea32a42f0d2074730001ea37fde09b67e1f61f4))

* tasks and owl ([`f846edd`](https://github.com/Mjvolk3/torchcell/commit/f846edd59f266d433d47632fa65648421dd50eae))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`c1956f8`](https://github.com/Mjvolk3/torchcell/commit/c1956f8c9df16297ea9e8d55883ca4b7e5a27afc))

* moving logging metrics ([`879c4b1`](https://github.com/Mjvolk3/torchcell/commit/879c4b1ad66dff7826702bb7bafd8f2c65ed9b22))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`2603b51`](https://github.com/Mjvolk3/torchcell/commit/2603b518d932227c08835fee2a00ecfbec53c317))

* 32 b, 6 wrks ([`dc382dd`](https://github.com/Mjvolk3/torchcell/commit/dc382dd21512ab368805d4dc9cddcfe52253c93a))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`5c1d344`](https://github.com/Mjvolk3/torchcell/commit/5c1d344602664e1a2d66f9f57e1139105143fcd2))

* dcell slim yaml ([`5e2a3ec`](https://github.com/Mjvolk3/torchcell/commit/5e2a3ec5e11d5f1b5a771867767d3505151a96fc))

* profiling ([`0f0674a`](https://github.com/Mjvolk3/torchcell/commit/0f0674a0be0c79129b7e4aa341d25816268a4252))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`6b6f521`](https://github.com/Mjvolk3/torchcell/commit/6b6f521598b5298c1cfa872734a3949d53951cc6))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`f3ba05f`](https://github.com/Mjvolk3/torchcell/commit/f3ba05f542b00367cd451a0edbf7a2ff94b3224f))

* slim ([`67d4262`](https://github.com/Mjvolk3/torchcell/commit/67d426233539b942b2e6875fab4be1347eb46ceb))

* dcell ([`c5ebf52`](https://github.com/Mjvolk3/torchcell/commit/c5ebf5266ebc8d777d8a4f94cd07aa98a5cf4c3f))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`18ae9ff`](https://github.com/Mjvolk3/torchcell/commit/18ae9ff69b696e3144fc13a16f26f1ec2369b944))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`28ba45c`](https://github.com/Mjvolk3/torchcell/commit/28ba45cf47bb118d30103c78eb53c49d79193d97))

* dcell yaml ([`be5fdfc`](https://github.com/Mjvolk3/torchcell/commit/be5fdfc8c0335d3ace815305b0dcc033cba58520))

* delta dmf yaml ([`174951c`](https://github.com/Mjvolk3/torchcell/commit/174951c67c7f77736193eab027cae5a414f78f35))

* slim ([`89468e1`](https://github.com/Mjvolk3/torchcell/commit/89468e14d2a4cc27766bf4c4b515ff1dc5b6055b))

* lambda reg slim ([`159d793`](https://github.com/Mjvolk3/torchcell/commit/159d793f339913e9c9b77811a992864a8df405d5))

* dcell slim ([`0a202ee`](https://github.com/Mjvolk3/torchcell/commit/0a202eec6a2787914b7f4961b3ed5d1410be92a6))

* lightning refactor, preds to gpu ([`eca0e7d`](https://github.com/Mjvolk3/torchcell/commit/eca0e7d87d0ed979e17ebc92f78e7c69e7e25380))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`5aa9c2b`](https://github.com/Mjvolk3/torchcell/commit/5aa9c2bda294af9ea296b62da27a4bdd9725fe96))

* investigating failed ddp dcell ([`a769ff9`](https://github.com/Mjvolk3/torchcell/commit/a769ff982fe7073c1a69d6b13ea7fbe3927d85d1))

* profile ([`d1fbabd`](https://github.com/Mjvolk3/torchcell/commit/d1fbabdc2ff49ce8945c1e24b74f02f6829c06b2))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`a3f0ce8`](https://github.com/Mjvolk3/torchcell/commit/a3f0ce8a55a2ab3d753a90d6692dcb9e8eb0207a))

* increase epochs ([`ee673e1`](https://github.com/Mjvolk3/torchcell/commit/ee673e1bd035947e019aeff117e0fad152d391ff))

* fixed logging ([`aa8a785`](https://github.com/Mjvolk3/torchcell/commit/aa8a785dfd46621aa7894e5f344926f1cefd0899))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`a9fb882`](https://github.com/Mjvolk3/torchcell/commit/a9fb8826960e9aa10a0f9050c860c7135d4cfa8b))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`270299b`](https://github.com/Mjvolk3/torchcell/commit/270299b5e1d9b1a76c131a4e1ce8ca9d8eee090b))

* dmf delta configs ([`e7b5611`](https://github.com/Mjvolk3/torchcell/commit/e7b56118193d2ea51bfc9cd24b3a034f9e5d1a79))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`b28c475`](https://github.com/Mjvolk3/torchcell/commit/b28c4750063268df803049970b05cd4574d59c17))

* dcell delta ([`6f641ac`](https://github.com/Mjvolk3/torchcell/commit/6f641ac8b6a417a42dbb2bd4a1ed484962b8ccaa))

* device dcell and loss fix ([`dd377af`](https://github.com/Mjvolk3/torchcell/commit/dd377afed5912014807b9ae0ccb406855157f20e))

* dmf loss update ([`07e423c`](https://github.com/Mjvolk3/torchcell/commit/07e423c87711998f656c0fd910b352123cf3bdeb))

* dcell update ([`bb63fc0`](https://github.com/Mjvolk3/torchcell/commit/bb63fc040c343924b91a5946e44b7fb42855cddd))

* notes on Dcell bool state ([`a43619a`](https://github.com/Mjvolk3/torchcell/commit/a43619afe578a05c68687fe40d2860ee21543bfc))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`cc7591a`](https://github.com/Mjvolk3/torchcell/commit/cc7591afc5c6b6877a0559d85d19b5102da88a90))

* launch dcell ([`b70b7d8`](https://github.com/Mjvolk3/torchcell/commit/b70b7d834c3b15f35ca0bac5544396a26d6f25f3))

* task update, fonts ([`9c0f921`](https://github.com/Mjvolk3/torchcell/commit/9c0f9215b1adf45e86307cd6af139e09e4cc35d0))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`e3ffc31`](https://github.com/Mjvolk3/torchcell/commit/e3ffc3136fce17aee09f6798d2ee869f00d3fc3e))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`58df118`](https://github.com/Mjvolk3/torchcell/commit/58df118761a28cb8fc2b0204dfda914ddc27a319))

* dcell dump ([`16f76ab`](https://github.com/Mjvolk3/torchcell/commit/16f76aba9e15dd2f1973148a934e4ff9296d9e7c))

* dmf_costanzo_graph_convolution ([`8689d91`](https://github.com/Mjvolk3/torchcell/commit/8689d910cc5ba7933c8549cdaa7bf74672d0c9b3))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`d33f1e6`](https://github.com/Mjvolk3/torchcell/commit/d33f1e6f85b3c344e348d2c9a3061084ba2f5c3d))

* std same scale hack ([`2bd1bf3`](https://github.com/Mjvolk3/torchcell/commit/2bd1bf3015e49f28fd7457a266624f3d32b99c9a))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`91862c8`](https://github.com/Mjvolk3/torchcell/commit/91862c8b775748d70df3edf36d2acf40e0934375))

* std hack on fitness ([`4049a0c`](https://github.com/Mjvolk3/torchcell/commit/4049a0cfa8a12d38d0c290aa2f54fdbf7b9431f5))

* dmf graph update ([`3182adf`](https://github.com/Mjvolk3/torchcell/commit/3182adfcd0ed828ecaee66ac38821af8e25636c3))

* train on two target ([`6bf3dd7`](https://github.com/Mjvolk3/torchcell/commit/6bf3dd7777b2aad512470592bb0d6bd0a18e106a))

* zero pert ([`2863641`](https://github.com/Mjvolk3/torchcell/commit/2863641ac98c0ff5a6f1f8cf44157bf674222eee))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`adcb6ee`](https://github.com/Mjvolk3/torchcell/commit/adcb6ee4007f17cb5ee630d66e8a509163b29602))

* added zero pert ([`bbc7faf`](https://github.com/Mjvolk3/torchcell/commit/bbc7fafeda672f417fcdff3aed7a2814c1e86806))

* conv slurm ([`860e4d7`](https://github.com/Mjvolk3/torchcell/commit/860e4d7021669ede7e72b9d4b43899a028907998))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`a05e8dc`](https://github.com/Mjvolk3/torchcell/commit/a05e8dc6507414384f9a783d310356d40dd79893))

* hacks on hacks on hacks ppi ([`7ea911a`](https://github.com/Mjvolk3/torchcell/commit/7ea911a9b862df2e0b863d3ef9109cb3e576f634))

* ddp costanzo conv ([`d91e5a5`](https://github.com/Mjvolk3/torchcell/commit/d91e5a5dcd4edfe213f37d0f58cbde0a717ca9f3))

* num_workers >0 slow 🧹notes and config ([`64cb7a0`](https://github.com/Mjvolk3/torchcell/commit/64cb7a0ea38c614a1bfb3adb64f3c0a073d2ca5f))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`bdd8a1c`](https://github.com/Mjvolk3/torchcell/commit/bdd8a1c2e426f000866468aaa07446db9c4b39ad))

* weird embedding hack these clases are confusing ([`9b26204`](https://github.com/Mjvolk3/torchcell/commit/9b26204860fa2dcd83639d9dc60f29da68e66200))

* dubious ([`167da2b`](https://github.com/Mjvolk3/torchcell/commit/167da2bce1553fcc930018c8e4df3c61900ebfba))

* 1 k hop ppi ([`90f3a1a`](https://github.com/Mjvolk3/torchcell/commit/90f3a1af5d7396f02a52145c99792f0c158666a0))

* first graph ([`91ae125`](https://github.com/Mjvolk3/torchcell/commit/91ae1254f6b9fb22c7d903250ced5f4bbc76541f))

* dmf costanzo deepset protein ([`2ea54be`](https://github.com/Mjvolk3/torchcell/commit/2ea54be4ddd8d76cfd025cc5dc869f3a8f8ceed8))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`a07405b`](https://github.com/Mjvolk3/torchcell/commit/a07405b298f6851c5cb55b6d52d4642d2053299a))

* minimal protT5 ([`ae556ae`](https://github.com/Mjvolk3/torchcell/commit/ae556ae1a42dac0ddc81f6716f847dcd53e2ff48))

* fix model init ([`37b8594`](https://github.com/Mjvolk3/torchcell/commit/37b85945a4917cfbcd988a71b1a638c498286a0a))

* dna_windows ([`a21b991`](https://github.com/Mjvolk3/torchcell/commit/a21b991ee0690b9bc3be59b601c50f174a123a99))

* t5 embeddings ([`4466416`](https://github.com/Mjvolk3/torchcell/commit/4466416ad6abfa4912435d26a0faa48a30d0fb09))

* llm ([`dcc85e1`](https://github.com/Mjvolk3/torchcell/commit/dcc85e1c530f89bb135f8dad58ceaf3d50c88fb3))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`08ec860`](https://github.com/Mjvolk3/torchcell/commit/08ec860b05dc2e60c8a7ef6ae150936a0faa4e20))

* added ddp ([`18cfad6`](https://github.com/Mjvolk3/torchcell/commit/18cfad6db58afeb34cbe471694e9e334932491b9))

* rename slurm linear ([`4bdd60b`](https://github.com/Mjvolk3/torchcell/commit/4bdd60b10b3df4273405afede2e7fab3c785d6fb))

* prot T5 ([`6002778`](https://github.com/Mjvolk3/torchcell/commit/600277806f15b2f3a2e626a1fe5b14297f34063a))

* test out gpu embeddings ([`392741d`](https://github.com/Mjvolk3/torchcell/commit/392741ddcadab57e494b737fa3ed7016ea727f3f))

* linear models tasks ([`24688cd`](https://github.com/Mjvolk3/torchcell/commit/24688cd40144403bd92df5d4a7d75ce8d41bf652))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`e9564c8`](https://github.com/Mjvolk3/torchcell/commit/e9564c82425c19ae2ba87773c1d7fb1dea8c60ff))

* slurm update ([`d506a27`](https://github.com/Mjvolk3/torchcell/commit/d506a27be3b07340ecb14a46bd7f7251326ae957))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`fb91161`](https://github.com/Mjvolk3/torchcell/commit/fb911614831271bed891b7ec18c4b272f6a0dcc0))

* one_hot_node ([`679fcd4`](https://github.com/Mjvolk3/torchcell/commit/679fcd4d945cb56a6ea9a1855ab40d45696b415c))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`4a97993`](https://github.com/Mjvolk3/torchcell/commit/4a97993c5aee6bf5b06558939cb59e4c4d3e4282))

* 1e6 ([`b766c84`](https://github.com/Mjvolk3/torchcell/commit/b766c84d13bd8c25619f561276ca3e5ce36e7551))

* notes on why SGD linear ([`778b764`](https://github.com/Mjvolk3/torchcell/commit/778b7643f6f86f60d44ff6206a0bcadfd1e94316))

* simple linear SGD ([`e17ba59`](https://github.com/Mjvolk3/torchcell/commit/e17ba594cfb69e072965fdccfcc2f0ef8b54f4c6))

* regression spacing ([`3c40f30`](https://github.com/Mjvolk3/torchcell/commit/3c40f306f14504cd4738b145e9e4b69d46f51c04))

* linear ([`79cc322`](https://github.com/Mjvolk3/torchcell/commit/79cc322bdc63b0860a044c9d103aea69b9333c62))

* Helvetica font ([`646ea66`](https://github.com/Mjvolk3/torchcell/commit/646ea662249dce74e16c980f386c2b55f4149ba5))

* combining new embeddings fails, run one hot ([`a18222f`](https://github.com/Mjvolk3/torchcell/commit/a18222f934211b5d468cee3b6343ba6c6037ec06))

* one_hot_gene dataset ([`9eaa85f`](https://github.com/Mjvolk3/torchcell/commit/9eaa85f40e2703e5dc7df517276bb171e7a08e87))

* box plot in regression ([`78097d9`](https://github.com/Mjvolk3/torchcell/commit/78097d9ebaf84d2d0bbdfbdd93e63c65bf9975db))

* genetic_interaction_score box plot ([`d6df26d`](https://github.com/Mjvolk3/torchcell/commit/d6df26dd40b719f7000d0862f2e5696cd5afbe0f))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`af2d6c2`](https://github.com/Mjvolk3/torchcell/commit/af2d6c2701b55e5c16762b3164a0a49fb301a8f6))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`e308fe1`](https://github.com/Mjvolk3/torchcell/commit/e308fe167566e916b004ef668ee5f7a1521fb200))

* full train ([`a9f5f66`](https://github.com/Mjvolk3/torchcell/commit/a9f5f665bc4d0dec2b27587f8a9e59869c84812e))

* MergedExperiment ([`798104c`](https://github.com/Mjvolk3/torchcell/commit/798104ce535375de6f780d760cb9f26eeb1236b9))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`8655064`](https://github.com/Mjvolk3/torchcell/commit/8655064f66901685d96562bf58fa33f5d05d18fa))

* made large model ([`8f3a361`](https://github.com/Mjvolk3/torchcell/commit/8f3a3611bd7e5c4af691bbfc07e23453060b8b11))

* no verbose ([`af33b99`](https://github.com/Mjvolk3/torchcell/commit/af33b997e183c479a68b67df28b36ffc8986795e))

* notes update ([`e8fb1e0`](https://github.com/Mjvolk3/torchcell/commit/e8fb1e07f0ba07f3844bb84ea3d46935e9581749))

* log artifacts ([`6057c1f`](https://github.com/Mjvolk3/torchcell/commit/6057c1ff397da02fe2f791e434c81ffa7d6a5dce))

* callbacks ([`dcc8d57`](https://github.com/Mjvolk3/torchcell/commit/dcc8d57b4150d2ff70a33ab9a304772ff5635c31))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`1ce5217`](https://github.com/Mjvolk3/torchcell/commit/1ce52177016741e8f7979c5189fc99c949f632ce))

* delete plotnine ([`1f852c1`](https://github.com/Mjvolk3/torchcell/commit/1f852c120810a67463b9e3dfcde747877d6d04d4))

* box plot ([`1050766`](https://github.com/Mjvolk3/torchcell/commit/1050766791332838a1e41a381f0a340b47797925))

* ddp update time ([`dcaf232`](https://github.com/Mjvolk3/torchcell/commit/dcaf23282f1400abd0e607a30900c8f07f766c70))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`124e7f2`](https://github.com/Mjvolk3/torchcell/commit/124e7f2151b35625bbd5f30ed4edb855f5ea16ed))

* add upstream sequence to training dmf ([`344c7ee`](https://github.com/Mjvolk3/torchcell/commit/344c7ee3358f9f5b865234537b591c6a54a208ce))

* plot ([`c0a6d52`](https://github.com/Mjvolk3/torchcell/commit/c0a6d529e975d5a03eb6437188841eb4856800ea))

* dataset add ([`fbc7317`](https://github.com/Mjvolk3/torchcell/commit/fbc7317cb36b1a41675edc8b8f15f009ec9c98b8))

* note update ([`1888a4f`](https://github.com/Mjvolk3/torchcell/commit/1888a4f7bf115bd43b066dc44ffca2bb278776ff))

* remove depreacted GO comment bug ([`4da821e`](https://github.com/Mjvolk3/torchcell/commit/4da821e791f79ca70150b0123f28c28077dd6626))

* dmf ([`71d4697`](https://github.com/Mjvolk3/torchcell/commit/71d46971352df160ba17285ca8bde27feb66b8ea))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`e7c7b23`](https://github.com/Mjvolk3/torchcell/commit/e7c7b23b774d8a3b96c125be6878e426b393c788))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`4b10802`](https://github.com/Mjvolk3/torchcell/commit/4b10802d9ca5d19524a95cb5c0030e0613348249))

* dmf delta ([`fbdfc8d`](https://github.com/Mjvolk3/torchcell/commit/fbdfc8deb3fd3f324d01ea53f2f6564ce2c83043))

* x and x pert ([`8876b21`](https://github.com/Mjvolk3/torchcell/commit/8876b2142bd2d61bd268c7ede63c10fd14b9d369))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`6fd793a`](https://github.com/Mjvolk3/torchcell/commit/6fd793af4721a7fd8bf36b48171fce0bdcbe77e9))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`c1730b6`](https://github.com/Mjvolk3/torchcell/commit/c1730b6d83abd7c0e2bdcfcbd49eeb5608248584))

* dmf yaml slurm ([`1b7cbb4`](https://github.com/Mjvolk3/torchcell/commit/1b7cbb4258bf84769d1e3991372461204333f9f1))

* fix in place operator for tanh ([`8e5370e`](https://github.com/Mjvolk3/torchcell/commit/8e5370edbea07f4dca626381c577bf4b1249a561))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`f953636`](https://github.com/Mjvolk3/torchcell/commit/f953636dd1a9ffc5da2816987d59c816051d43e4))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`335250e`](https://github.com/Mjvolk3/torchcell/commit/335250eca672ef93e96f9c6c0b7c918984f62843))

* dmf delta ([`5ef6776`](https://github.com/Mjvolk3/torchcell/commit/5ef6776dbca00ad07f694718c62c365a6c2460ee))

* wt_train_per_epoch ([`52f53ad`](https://github.com/Mjvolk3/torchcell/commit/52f53ad4c4a824a7e2585279d75c114eb14e5e6f))

* notes ([`913e93f`](https://github.com/Mjvolk3/torchcell/commit/913e93f8abd461b060884a912963ed17cad96e83))

* dmf at position for sweeping ([`e6bc1c2`](https://github.com/Mjvolk3/torchcell/commit/e6bc1c2ee4ebba4d52ee122ea47603131c352af3))

* removed extra batch size ([`7dac4bc`](https://github.com/Mjvolk3/torchcell/commit/7dac4bca75cc06d4904899f3020b76b1e12f0398))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`3124afb`](https://github.com/Mjvolk3/torchcell/commit/3124afb4a3e13e3a55f9c2197e989da4b0b4d0b3))

* regression ([`0d51546`](https://github.com/Mjvolk3/torchcell/commit/0d51546afd68d5bf3b806a141a47c0bc0e1c6686))

* dmf delta ([`2437691`](https://github.com/Mjvolk3/torchcell/commit/2437691ce3de6aa5057921113682ec371ff4d0bf))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`5e390ac`](https://github.com/Mjvolk3/torchcell/commit/5e390ac2a4654e77a9fa6640916a3ede67d9b6aa))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`5c46cd3`](https://github.com/Mjvolk3/torchcell/commit/5c46cd30e4c6ce08b0f685226c6603f5d5bd0289))

* dmf delta deep set ([`00841ba`](https://github.com/Mjvolk3/torchcell/commit/00841badc86f18526f7e93248a7f9e09e0d1dcdf))

* weighted rmse ([`17d4722`](https://github.com/Mjvolk3/torchcell/commit/17d472217852f0b5528136daaf8767fc8362830e))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`6fca4ea`](https://github.com/Mjvolk3/torchcell/commit/6fca4ea865ff734bab900287db347cbc997b1b2a))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`11269ac`](https://github.com/Mjvolk3/torchcell/commit/11269ac45b068d2b5897aff5f9889761dd89fff6))

* 1e5 ddp issues ([`bd1f5be`](https://github.com/Mjvolk3/torchcell/commit/bd1f5be20b96deb473e53d4fe09fac7a70289a5a))

* dmf deep set with more regularization ([`e4149b6`](https://github.com/Mjvolk3/torchcell/commit/e4149b6b0160b5681c9e8907fcaac00f7d406624))

* starting training robustness ([`593ee8b`](https://github.com/Mjvolk3/torchcell/commit/593ee8b0bcaedeecc15284d74c5d2dd7727a5590))

* fungal up down corrected embedding ([`dded486`](https://github.com/Mjvolk3/torchcell/commit/dded486392c01c0d803611620820d61936720a69))

* ddp issues notes ([`516e933`](https://github.com/Mjvolk3/torchcell/commit/516e93301294c087f2cea103064818eea0fc6d90))

* configured lr and wd ([`69b6ce1`](https://github.com/Mjvolk3/torchcell/commit/69b6ce15824a4f86aa87f67ec3d93b7a2d679783))

* update parse genome - black magic ([`74182ae`](https://github.com/Mjvolk3/torchcell/commit/74182ae9c3f64f0dcb409eb596bef71fe07ff88b))

* notes ([`35c27ff`](https://github.com/Mjvolk3/torchcell/commit/35c27ffaeb71ae9236bad9310ba27443315bfdcb))

* parse genome, ddp problems on delta, need debug local ([`6d087ed`](https://github.com/Mjvolk3/torchcell/commit/6d087ed5eda668bc2761d12cc637dc25ac7f6d1c))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`f6d8341`](https://github.com/Mjvolk3/torchcell/commit/f6d834140945ad3343826bc7df056841b939b405))

* box plot parameterized ([`f0802ac`](https://github.com/Mjvolk3/torchcell/commit/f0802acd072468f04609939fab6d31c958bee21e))

* delta refresh ([`489ab51`](https://github.com/Mjvolk3/torchcell/commit/489ab51f3bd6c86a530aaca95babc7b6edac27a9))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`9f58a0d`](https://github.com/Mjvolk3/torchcell/commit/9f58a0d10419a0c485b156e7edad4b924fd2fd25))

* wt freq ([`7bdf6a7`](https://github.com/Mjvolk3/torchcell/commit/7bdf6a7ebbae62f0983c2ff8fdbb5af873c2bc21))

* delta exp update ([`e0f34d4`](https://github.com/Mjvolk3/torchcell/commit/e0f34d4f00388c34e6f01b57c1d595aae3381aef))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`4240d8e`](https://github.com/Mjvolk3/torchcell/commit/4240d8e90ed2da01a5bbbc95412d3151d5e84d32))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`4a9c834`](https://github.com/Mjvolk3/torchcell/commit/4a9c834f7576ccaa7be98a99e269808fe1779b4c))

* delta exp ([`f43d870`](https://github.com/Mjvolk3/torchcell/commit/f43d87079337fa61f08b85f530cd1c3ebaed034c))

* dmf logging wt time to launch ([`f28d439`](https://github.com/Mjvolk3/torchcell/commit/f28d439bfb84032fe284ebc09ceb870dc80aea57))

* has group ([`a059bf0`](https://github.com/Mjvolk3/torchcell/commit/a059bf0996c0205ad00531c8dfdbed906acc91a5))

* fungal embeddings model ([`b18e57f`](https://github.com/Mjvolk3/torchcell/commit/b18e57f13dfc9711b018aefce02eb09e33d5b755))

* dump, fungal_up_down, wt difference ([`0c6b947`](https://github.com/Mjvolk3/torchcell/commit/0c6b9472db5ed86287d807bf119cac6c365805a5))

* git rm docs build ([`982015b`](https://github.com/Mjvolk3/torchcell/commit/982015bdfdc6ab1b00cd5930a74746834ce60f69))

* SpeciesLM model, notes ([`d4b8b95`](https://github.com/Mjvolk3/torchcell/commit/d4b8b95585addcce5db51557bf48f9ff940f8169))

* tests ([`d0c5c63`](https://github.com/Mjvolk3/torchcell/commit/d0c5c63755ac11281dc0d8d4881c70b87187058f))

* test genome ([`754fa55`](https://github.com/Mjvolk3/torchcell/commit/754fa55f13849740e89841501e958383347b33b4))

* updated docs ([`beca614`](https://github.com/Mjvolk3/torchcell/commit/beca6140a1c66fe8cbfaed6a37da4e475f4b388a))

* update actions ([`7643b06`](https://github.com/Mjvolk3/torchcell/commit/7643b06c49d64f96b17a02c14ff382fdd33759ed))

* updated reqs worked locally ([`63bc91d`](https://github.com/Mjvolk3/torchcell/commit/63bc91d2cb9bcf7e56fabaf64f4941312624023b))

* updated reqs ([`d44d1eb`](https://github.com/Mjvolk3/torchcell/commit/d44d1eb5c80b29b901fee4beb1a81c6446cd1a62))

* reqs remove torch vision, audio ([`fbdd7d8`](https://github.com/Mjvolk3/torchcell/commit/fbdd7d8d749e65fdd0518d9b4b843f527650ff62))

* removed graphviz ([`6c3a740`](https://github.com/Mjvolk3/torchcell/commit/6c3a7404167ad62965dbb192520c54db58b37cf0))

* test ([`cf67681`](https://github.com/Mjvolk3/torchcell/commit/cf67681d9137c0985ad36f026a27a00a033a7205))

* logo update ([`49ccf54`](https://github.com/Mjvolk3/torchcell/commit/49ccf543b1fe1ac0a1052b0e3d6d716034ec0552))

* update logo ([`0d32075`](https://github.com/Mjvolk3/torchcell/commit/0d32075ae473a3902d8dc20bd69d9338d9f5512a))

* logo ([`cc71950`](https://github.com/Mjvolk3/torchcell/commit/cc71950b92b674bb02ac92eb73552195d7087789))

* req reorder for scatter ([`4e23b3e`](https://github.com/Mjvolk3/torchcell/commit/4e23b3e97679b92b92b4c5d894b31232885685e1))

* pandas pin ([`8d108c6`](https://github.com/Mjvolk3/torchcell/commit/8d108c62050406c928d7cfd72255be9417946cd4))

* zoom ([`07c9bdb`](https://github.com/Mjvolk3/torchcell/commit/07c9bdbc3153b7220a8141fe1329f0d501fff441))

* reqs torch scatter issue ([`c0a8676`](https://github.com/Mjvolk3/torchcell/commit/c0a867657a793ec94f153ca7aa18856b4e5e7a11))

* logo ([`49c903c`](https://github.com/Mjvolk3/torchcell/commit/49c903ca7e8f90e58eceb23b70a072017b276fc5))

* req update, move gene set ([`7367a3b`](https://github.com/Mjvolk3/torchcell/commit/7367a3bad12be17b435e792a22bdc545c8edfc9a))

* testing ([`9951815`](https://github.com/Mjvolk3/torchcell/commit/9951815d3962b6127b74436f935163ebae357828))

* test seq data ([`00225fa`](https://github.com/Mjvolk3/torchcell/commit/00225fa7d5daa8d4a386f1a717e0b6554665ff6c))

* tasks ([`02a9336`](https://github.com/Mjvolk3/torchcell/commit/02a93362742fac39d328c6a88db2699a2cc12766))

* env coverage ([`bd73fbb`](https://github.com/Mjvolk3/torchcell/commit/bd73fbb0f312df620d230ad06d889c42e15abf21))

* src dump... in the middle of major rewrites ([`b8a434d`](https://github.com/Mjvolk3/torchcell/commit/b8a434d2b795f0ef1fbb7fd10bcaf7baf4f356b0))

* notes, images, drawings ([`3a4c151`](https://github.com/Mjvolk3/torchcell/commit/3a4c151209caa9fcf26343d5dce7e0293a92702c))

* dmf demo update for clarity ([`7f9a340`](https://github.com/Mjvolk3/torchcell/commit/7f9a34008f784f50be0ba0df23be849edc6e99b4))

* deep set ([`eee1db0`](https://github.com/Mjvolk3/torchcell/commit/eee1db0a6ce44a451417091f32715cb504d3253e))

* genome ([`f43e3af`](https://github.com/Mjvolk3/torchcell/commit/f43e3afe1538417ffd983c47283d7644ecd35920))

* dcell model start ([`3864b06`](https://github.com/Mjvolk3/torchcell/commit/3864b069b3022687bcfe2d906d5ce0f58d9b6d1b))

* cached df for easy stats ([`9cf468f`](https://github.com/Mjvolk3/torchcell/commit/9cf468ff030ebc3ab4715ee3e9cb1a5056f85548))

* comments on issues ([`e29580f`](https://github.com/Mjvolk3/torchcell/commit/e29580f2adcee69a2c2e36e7a29d969b6ed0e863))

* notes ([`7e32a05`](https://github.com/Mjvolk3/torchcell/commit/7e32a05691d40b2f7b08c08fd1c515f5ab767509))

* dmf nt projection viz ([`cf2ad64`](https://github.com/Mjvolk3/torchcell/commit/cf2ad64b02c7a049cf3516ca1ee7d41ad5bd9c68))

* umap ([`72da49f`](https://github.com/Mjvolk3/torchcell/commit/72da49fc861e58de6d476620e4c35c925048d76d))

* added perturbation to data ([`a227c21`](https://github.com/Mjvolk3/torchcell/commit/a227c21296db93ac92bbca3ed6f1214b8cc354ae))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`08b5203`](https://github.com/Mjvolk3/torchcell/commit/08b520337e5184ca7b638e14b4c4f841d789bfa1))

* dmf config ([`3e29cea`](https://github.com/Mjvolk3/torchcell/commit/3e29ceafa3935e303f22ca050b7e270f09bca8ff))

* dmf ddp jobs ([`c5f3247`](https://github.com/Mjvolk3/torchcell/commit/c5f3247174521bcd474e2749a25f8563f0152004))

* print data ([`4ea041d`](https://github.com/Mjvolk3/torchcell/commit/4ea041dd451f1fca910e1934567b15365580fea1))

* s288c check for db ([`0d9f398`](https://github.com/Mjvolk3/torchcell/commit/0d9f398824bd7a51af4144a21d54ff7e357c2345))

* dmf deepset do, bnorm ([`570ecaf`](https://github.com/Mjvolk3/torchcell/commit/570ecaf6fe7442dd52b2268b3fcc4a39bd20aaa6))

* workspace delta interactive ([`b8aa68f`](https://github.com/Mjvolk3/torchcell/commit/b8aa68f938e4a1677f921b0bce00c02b2f410a50))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`904919e`](https://github.com/Mjvolk3/torchcell/commit/904919ee3a52fa71ebd7c1f0f1b1b9dcd67179b9))

* slurm ([`7fee426`](https://github.com/Mjvolk3/torchcell/commit/7fee426a91ae61c0b3f19ee7d4bcb92a73ff9225))

* images and notes ([`a1c32fa`](https://github.com/Mjvolk3/torchcell/commit/a1c32fad8e1f79b0a54bb0363508388c9672f3f6))

* data profiling process ([`16996d1`](https://github.com/Mjvolk3/torchcell/commit/16996d1c1d3f5f514886afcbaa117b0acfa3f5c4))

* cell data different data sizes ([`2ac2dbc`](https://github.com/Mjvolk3/torchcell/commit/2ac2dbc74faa6a59535fb889a313f9561c0cd291))

* dataset hack ([`da3a254`](https://github.com/Mjvolk3/torchcell/commit/da3a25441057060fcccf6a9f005825ed786614cf))

* cell revert, costanzo init db ([`4b89202`](https://github.com/Mjvolk3/torchcell/commit/4b892022ef9f3a365861ad2bc53598461a6832d4))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`e148645`](https://github.com/Mjvolk3/torchcell/commit/e148645f225175130a6fdc5f4710196694647171))

* crank the threads 1.0 ([`cfff586`](https://github.com/Mjvolk3/torchcell/commit/cfff58638082f48c2a10643730cfbbb679405329))

* crank the threads ([`f68d2ff`](https://github.com/Mjvolk3/torchcell/commit/f68d2ffecce827d8fceacbe4053345b430379fd3))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`7cdcc5f`](https://github.com/Mjvolk3/torchcell/commit/7cdcc5f9a4327646220befaf3be392b73bd1dd31))

* slurm scripts and exp files ([`78dc0ce`](https://github.com/Mjvolk3/torchcell/commit/78dc0ce1dba2fcf1450cffbea9cda83c0f820df9))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`2c6d626`](https://github.com/Mjvolk3/torchcell/commit/2c6d62677e18ca01f84bfb5f5f5588c81425d644))

* dot env ([`29b80ee`](https://github.com/Mjvolk3/torchcell/commit/29b80eea86019f971378f441386893eaf7db5c8a))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`4a85f8e`](https://github.com/Mjvolk3/torchcell/commit/4a85f8ea03152925dcca800e8f3112f730b0d324))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`7994354`](https://github.com/Mjvolk3/torchcell/commit/7994354d4e1bd53c58b14a17c52982414920d931))

* lmbd delta ([`0df0225`](https://github.com/Mjvolk3/torchcell/commit/0df02252c83d576adcb4b25ece24a1b2fd473fa4))

* prof ([`ce614e5`](https://github.com/Mjvolk3/torchcell/commit/ce614e534d4d6d9f64112db4e16b4f0ebcd18f7c))

* cell mutlithreading for filter speed, same on M1 ([`7ef2a78`](https://github.com/Mjvolk3/torchcell/commit/7ef2a78ca358a6cf3521340a0db56e6ff285ae98))

* process thread pool ([`25312b6`](https://github.com/Mjvolk3/torchcell/commit/25312b6272b2d0ba7ca0da0c9c5b627d50b2b380))

* correct import ([`df09899`](https://github.com/Mjvolk3/torchcell/commit/df098993d8bcbee811f8e5dd6399a48339e4a7ab))

* lmdb, subset graph ([`a73b2a4`](https://github.com/Mjvolk3/torchcell/commit/a73b2a4a4018fcba5c60007f401ffeb60851b149))

* go hist ([`667b763`](https://github.com/Mjvolk3/torchcell/commit/667b7639c0577d76cf995b88214bf1d1ecd43b2c))

* go methods ([`2db73f4`](https://github.com/Mjvolk3/torchcell/commit/2db73f46fbd930dfd477a71d060d3d112ab5b918))

* moved into genome ([`b0a98bf`](https://github.com/Mjvolk3/torchcell/commit/b0a98bf5069839ec545193a74d592d7870e78e81))

* drop_chrmt and drop_empty_go ([`b0c5ee2`](https://github.com/Mjvolk3/torchcell/commit/b0c5ee2083a370334bfa39d72417de2ab6ef5093))

* drop_empty_go, drop_chrmt, remove_deprecated_go ([`b1cc2c9`](https://github.com/Mjvolk3/torchcell/commit/b1cc2c97be8ceaa998103f459ff9b87e0792bed6))

* lmdb ([`d7ad461`](https://github.com/Mjvolk3/torchcell/commit/d7ad461e6fc99f677dbaca37bfd320aac826abcb))

* lmdb mvp dmf deepset ([`c027f7d`](https://github.com/Mjvolk3/torchcell/commit/c027f7d174e285ce2a98d484f62dc6367791fdfa))

* costanzo lmdb ([`d5e7e3f`](https://github.com/Mjvolk3/torchcell/commit/d5e7e3fd64b2a5f33ced976b3889f47898aca923))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`2ba17dd`](https://github.com/Mjvolk3/torchcell/commit/2ba17dda8bf55d95e97921901b2ed9d82cc22684))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`9797a51`](https://github.com/Mjvolk3/torchcell/commit/9797a511f3d0ce8853506003b999f8d9ffb4f1dd))

* cpu run for dataset creation ([`4ec8344`](https://github.com/Mjvolk3/torchcell/commit/4ec8344c81776efca8d6bca407de4487f9749f05))

* req update ([`b6eb9d1`](https://github.com/Mjvolk3/torchcell/commit/b6eb9d1843261b40cba073b6e26ffb501e3901ac))

* delete subset for long deletions of 1e6+ files ([`32e4fb9`](https://github.com/Mjvolk3/torchcell/commit/32e4fb9937175fcfb5e113a29201fd9cf7373611))

* dump ([`0df8f25`](https://github.com/Mjvolk3/torchcell/commit/0df8f25de202f72648291e59dece116f9ddc6d8d))

* notes ([`abb3db1`](https://github.com/Mjvolk3/torchcell/commit/abb3db18c74f41e8d61a3c87f7877d0ae7a270d8))

* dmf poc ([`ba36f34`](https://github.com/Mjvolk3/torchcell/commit/ba36f34ca2e0934f6c46e195a4df853943c44182))

* data ([`41be721`](https://github.com/Mjvolk3/torchcell/commit/41be721f371a484300084f09d0344129b527ed01))

* old pkg info ([`acc7c44`](https://github.com/Mjvolk3/torchcell/commit/acc7c442f3d428dfb0842bbdd63f840df2d68930))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`d5d1a68`](https://github.com/Mjvolk3/torchcell/commit/d5d1a682ab2dbf8e5496c04ad14787eda80b4876))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`cbf12ec`](https://github.com/Mjvolk3/torchcell/commit/cbf12ec03a47cc4c5c8c0c9139ffc2638146c30d))

* slurm scripts ([`f16d474`](https://github.com/Mjvolk3/torchcell/commit/f16d474a7c3da6cb15ade41e1e30e51fd94cd717))

* move file util, works on exps too ([`47f06ad`](https://github.com/Mjvolk3/torchcell/commit/47f06ad2407deeb22526727b11fb4c1a7bd61ccf))

* dmf hydra ([`55a91aa`](https://github.com/Mjvolk3/torchcell/commit/55a91aa16b986d0ce12a9b1ca06a65fc34639e08))

* frontmatter ([`ed4183c`](https://github.com/Mjvolk3/torchcell/commit/ed4183cbe3433a8784e25142325b2325f4da2b08))

* notes ([`5ebf047`](https://github.com/Mjvolk3/torchcell/commit/5ebf0475c329bbfd3c71d6a4526ca736585aa7f1))

* ig up ([`b34256e`](https://github.com/Mjvolk3/torchcell/commit/b34256e87a22e0cea7b2618cc754d2378403d244))

* experiment config ([`e52fddf`](https://github.com/Mjvolk3/torchcell/commit/e52fddf9a683c93962cb34f2cc7f8f1e7ad3d7b2))

* notability update ([`1484278`](https://github.com/Mjvolk3/torchcell/commit/14842781b134652e2a3576701c64ed1bdf8b32ff))

* deleted files ([`67330c5`](https://github.com/Mjvolk3/torchcell/commit/67330c5ab0e6a715136a0b14216fd26721139063))

* git ignore update ([`79c3451`](https://github.com/Mjvolk3/torchcell/commit/79c3451cee9f6d441a1a227eb100e3f28e19db00))

* sorted set ([`8bbacdb`](https://github.com/Mjvolk3/torchcell/commit/8bbacdb6f538d9fa4c8fd780510fcc5d6fdc2789))

* uncommented windowing ([`86b7139`](https://github.com/Mjvolk3/torchcell/commit/86b7139f252dfef349efd3a6b50c659916f42c03))

* GO info, attrs, sorted set, types ([`3b2bb1e`](https://github.com/Mjvolk3/torchcell/commit/3b2bb1e96efc275e3764794bdefbe22e8b0774fb))

* phenotype future ([`a591413`](https://github.com/Mjvolk3/torchcell/commit/a5914139417678aeb032e3e5f83af7e53123fc29))

* profiles ([`63d1f68`](https://github.com/Mjvolk3/torchcell/commit/63d1f68879872cfde56093caf17a5f1531e2f7e6))

* notes ([`1d0bf56`](https://github.com/Mjvolk3/torchcell/commit/1d0bf56394b8f62448df66db69652194b35b8b7f))

* mvp dmf large costanzo ([`da4c981`](https://github.com/Mjvolk3/torchcell/commit/da4c981270eea99fb20c2c4c1f66b213e466d2c7))

* cache len ([`cf7afbc`](https://github.com/Mjvolk3/torchcell/commit/cf7afbc58d311a3cb736f8851b1e1f8099b0e57b))

* dmf still loading all data on second process ([`2def144`](https://github.com/Mjvolk3/torchcell/commit/2def144daa0994e39dcf5fe3260aa3de5a3931e7))

* costanzo ([`7bff55b`](https://github.com/Mjvolk3/torchcell/commit/7bff55b79e04e66b1bc0187bf752c304781b9150))

* io threading speedup ([`d8712c9`](https://github.com/Mjvolk3/torchcell/commit/d8712c9c0780cbd084427db96badfa8f7ab7c123))

* rm data messing rel paths ([`55251ba`](https://github.com/Mjvolk3/torchcell/commit/55251ba676aff584a1f727dcdbc06a0cd709334c))

* reqs hd5 ([`75e2291`](https://github.com/Mjvolk3/torchcell/commit/75e22918e3c2472247ab2cc40ca6b8621cb42128))

* costanzo preprocess ([`fae71f8`](https://github.com/Mjvolk3/torchcell/commit/fae71f8a57cc7b859712098bdf8315a5c8f85bdf))

* thread ckpt ([`42aca65`](https://github.com/Mjvolk3/torchcell/commit/42aca6511919b6f0c2aa790e328fbdb0ca725b50))

* prof ([`1270c89`](https://github.com/Mjvolk3/torchcell/commit/1270c89f89a58b3290697269f5d19e879c1e2179))

* notes ([`07bea43`](https://github.com/Mjvolk3/torchcell/commit/07bea437079a9869a2ebf9b7e5daa1d58cb4c739))

* reqs up ([`29b4d24`](https://github.com/Mjvolk3/torchcell/commit/29b4d240a14c7207d6dde35b44dace4bbc489953))

* init update ([`2562352`](https://github.com/Mjvolk3/torchcell/commit/2562352887ce755f0155f3ec386b504cf233b2ed))

* fitness and regression ([`3ed467d`](https://github.com/Mjvolk3/torchcell/commit/3ed467d10f43d40ebe6445ff0fb74b785b56015a))

* docs ([`c829917`](https://github.com/Mjvolk3/torchcell/commit/c829917977fbc22352277e325bd497bfd769ca54))

* notes ([`d20c497`](https://github.com/Mjvolk3/torchcell/commit/d20c497b96e309d0b9c0e3d2ee16d0f1c14eaaf6))

* ws ([`e5d1ec4`](https://github.com/Mjvolk3/torchcell/commit/e5d1ec4ed99393672b7cbe99fefe75ddb2fe83a3))

* notability sync ([`635c3e6`](https://github.com/Mjvolk3/torchcell/commit/635c3e6b34ad981b47f7b164fe41c7a7b379023a))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`550c905`](https://github.com/Mjvolk3/torchcell/commit/550c9052164143a347824dd6a4b9bfb41a76b6b0))

* costanzo options ([`252293b`](https://github.com/Mjvolk3/torchcell/commit/252293b5e51acf1ba82ea263a92fbfcf8e35bca3))

* future tasks ([`efeead4`](https://github.com/Mjvolk3/torchcell/commit/efeead4afb954ee4e8a9d088666d570af27e020a))

* slurm ([`a15d230`](https://github.com/Mjvolk3/torchcell/commit/a15d230e66a4bcee2a14be8646eb934f0136fe68))

* delta mvp ([`f84318d`](https://github.com/Mjvolk3/torchcell/commit/f84318deb204bb65e6699a0c8e9e62fac0e792ad))

* experiments data root ([`7d0a679`](https://github.com/Mjvolk3/torchcell/commit/7d0a679ea6b3befce96d79e3515772750cf92b75))

* reqs pydantic pin ([`073f61d`](https://github.com/Mjvolk3/torchcell/commit/073f61da984995d2046c770d6b8eedd9462ac88a))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`18c8d8f`](https://github.com/Mjvolk3/torchcell/commit/18c8d8f8cbf0e5346f3e21b782e62297963369f5))

* remote workspace ([`ef659de`](https://github.com/Mjvolk3/torchcell/commit/ef659dea00da021bf20083e1d826aed38c4360a4))

* workspaces ([`706d2e1`](https://github.com/Mjvolk3/torchcell/commit/706d2e1db002b25a11f549294ddd7f2a1f08b350))

* data path for SCerevisiaeGenome ([`0186f8d`](https://github.com/Mjvolk3/torchcell/commit/0186f8da23bc2bee81c777e463888aa63f636e52))

* lightning ([`0b3329a`](https://github.com/Mjvolk3/torchcell/commit/0b3329ab6a720614f338de6e7d3ab6695fcfc580))

* updated dmf with env ([`638b2f9`](https://github.com/Mjvolk3/torchcell/commit/638b2f9b5ca944eef70fdaf37ae96126597e5070))

* first training loop ([`018b203`](https://github.com/Mjvolk3/torchcell/commit/018b20323cd1e20a4deb2de1284bf5aa4edb8211))

* isort black compat ([`9680c2e`](https://github.com/Mjvolk3/torchcell/commit/9680c2eab12b7a5a5e1e4240596a90b4ad6ed1e4))

* add isort ([`68d8503`](https://github.com/Mjvolk3/torchcell/commit/68d8503da7faadb2cdafeb00166e989881e1eae6))

* project toml for config ([`f831756`](https://github.com/Mjvolk3/torchcell/commit/f831756be103571f81c4f8dd9e91219424818543))

* notes ([`13ecbfe`](https://github.com/Mjvolk3/torchcell/commit/13ecbfec40d385b544d6a6c69f2a009a730dd38e))

* precommit install ([`3be0cdd`](https://github.com/Mjvolk3/torchcell/commit/3be0cddc88761fd723cfd257a470ac4a2b533c17))

* reqs update ([`63881d9`](https://github.com/Mjvolk3/torchcell/commit/63881d93a1eb592b78a25dd4b7ee24d8cfb37a56))

* precommit and workspace ([`b0a13d2`](https://github.com/Mjvolk3/torchcell/commit/b0a13d22b159e0a26969c0839bc98db4c68c7c52))

* frontmatter repo reset ([`0f3a72e`](https://github.com/Mjvolk3/torchcell/commit/0f3a72e4b05955803ae98b4da29d906b2410b4e8))

* readme ([`b44f787`](https://github.com/Mjvolk3/torchcell/commit/b44f7875755d07e31f2605639515fea0c079d64a))

* update test cache ([`e998032`](https://github.com/Mjvolk3/torchcell/commit/e99803283c0fa5755e36aaf1f7a7271cca4b2963))

* update cache ([`10e981e`](https://github.com/Mjvolk3/torchcell/commit/10e981eee290db76b40f55bd269b96fc0f1b81e5))

* remove &39;p&39;, pre-commit hook setup ([`62441ed`](https://github.com/Mjvolk3/torchcell/commit/62441edb7c53d8c906c9be35a24769736f93b13a))

* test CI ([`c96d2c2`](https://github.com/Mjvolk3/torchcell/commit/c96d2c2e03d64db3cc94242a85424af644bff979))

* concurrency ([`6dfa5cf`](https://github.com/Mjvolk3/torchcell/commit/6dfa5cf0289a6902f34d6bdff523d73120d42ca2))

* CI ([`3ac0108`](https://github.com/Mjvolk3/torchcell/commit/3ac0108c6a04500865417750c963ca2440ebffc2))

* tranformer datasets ([`5145173`](https://github.com/Mjvolk3/torchcell/commit/514517372c84513ab68b129ae2a6a96e3b36c6f0))

* docs update ([`64bb7ff`](https://github.com/Mjvolk3/torchcell/commit/64bb7ffbea26b54bf27d87bc2c162d4bfcf898c7))

* reqs update ([`bf6a23e`](https://github.com/Mjvolk3/torchcell/commit/bf6a23e3c5d4005ef07e0a2574e57ff3c0450257))

* flake 8 config ([`e09635d`](https://github.com/Mjvolk3/torchcell/commit/e09635d953c8ae5f4fe1c4432316e4d8965caa3f))

* data_models updated for pydantic 1.10 ([`1a24394`](https://github.com/Mjvolk3/torchcell/commit/1a24394623bcae63ca2a15b3300cc60c60572ddc))

* new actions ([`869d443`](https://github.com/Mjvolk3/torchcell/commit/869d4430bdfe0dd7292f14deb55555794f5f0d51))

* docs ([`e15b5b3`](https://github.com/Mjvolk3/torchcell/commit/e15b5b3739cacdf9ee3e415f75ebf7e22f30bf80))

* tutorial ([`a7e2e6a`](https://github.com/Mjvolk3/torchcell/commit/a7e2e6af157e22b47224ce3d606265a4a15c5528))

* llm push ([`471a7d6`](https://github.com/Mjvolk3/torchcell/commit/471a7d6f44b53e955fac5a6fcb95c619d259f921))

* docs move ([`430f406`](https://github.com/Mjvolk3/torchcell/commit/430f406b2c2ec3e000b7250cab966566c30d18ad))

* remove hidden notes ([`f8a28c2`](https://github.com/Mjvolk3/torchcell/commit/f8a28c2818b729b65889ce6d7d27c4a36010f86d))

* readme update ([`5ef93b0`](https://github.com/Mjvolk3/torchcell/commit/5ef93b07b5cc99d34359a17ca55b198669b3115a))

* action update format on push ([`8773585`](https://github.com/Mjvolk3/torchcell/commit/8773585e2adf4a6ce4d6299da4ea294ec7f64d91))

* workspace refactor ([`4ef424d`](https://github.com/Mjvolk3/torchcell/commit/4ef424da130b3758106d738eef6373fcaecc2ea2))

* rm dendron temp files ([`c617d93`](https://github.com/Mjvolk3/torchcell/commit/c617d93aa6581c675ba340745e3dae56f9a2cbed))

* task note ([`f90e52f`](https://github.com/Mjvolk3/torchcell/commit/f90e52fa26bc36aab77ab2134d1bc85fd4e52de8))

* py dump ([`f0e1ee8`](https://github.com/Mjvolk3/torchcell/commit/f0e1ee8b61117cb60556fddb7e4a770fea1b063a))

* delete scrap model lin on nt tformer ([`d828a2d`](https://github.com/Mjvolk3/torchcell/commit/d828a2dfe17fb06cc815004c472da77cccbe4222))

* deep set drawing ([`5c5c3aa`](https://github.com/Mjvolk3/torchcell/commit/5c5c3aa382675d068ff8a7509dd272e88cffc533))

* scrap model, smf fitnes pred lin on nt tformer ([`7fe6334`](https://github.com/Mjvolk3/torchcell/commit/7fe63344402cdebaabd7c04f9dc39f46dd8fec7c))

* s288c feature types ([`a236cd5`](https://github.com/Mjvolk3/torchcell/commit/a236cd5fef528e37e72cf4fa994cf689065d9ca3))

* dmypy json, not sure if needed ([`6ee6c36`](https://github.com/Mjvolk3/torchcell/commit/6ee6c36bb7a055484523623d7d7045cd3b9558ea))

* naming ([`546b14f`](https://github.com/Mjvolk3/torchcell/commit/546b14fb330f162ea9137e698e7142d5ac3cae5d))

* test sequence.py ([`a6501d2`](https://github.com/Mjvolk3/torchcell/commit/a6501d266ee382d592e6ee1eb149b4a8296c637a))

* gene_list property ([`85627bf`](https://github.com/Mjvolk3/torchcell/commit/85627bfa694b16c6349b2e685afcf92fad4a229e))

* correct seq len calc ([`7302852`](https://github.com/Mjvolk3/torchcell/commit/7302852587f38224972b24ece4da0c7a6a7978a0))

* make mito first chr index 0 in contansts ([`1a6e488`](https://github.com/Mjvolk3/torchcell/commit/1a6e4889fce5219fc60cb5a49311c9c9c6a9ebe7))

* fix inequality value error ([`e41d85d`](https://github.com/Mjvolk3/torchcell/commit/e41d85d7a2157f497894089773032497d89a6feb))

* deleted files ([`3bfdccf`](https://github.com/Mjvolk3/torchcell/commit/3bfdccf2e51a9bdfeeeee5784a735b88e2d803a9))

* imports - import trick ([`f63a958`](https://github.com/Mjvolk3/torchcell/commit/f63a95876350c1e0a2109473f18ef6b084f070b8))

* dna window resut works ([`a56678f`](https://github.com/Mjvolk3/torchcell/commit/a56678fb57693d2941028a6b28310c968ba86683))

* DnaWindowResult and dna window helpers ([`ee9a656`](https://github.com/Mjvolk3/torchcell/commit/ee9a6568a2997f6c5ed858becca02d88832c1e46))

* 60kb typo fix ([`04500b9`](https://github.com/Mjvolk3/torchcell/commit/04500b9062a049590661408af4a920a37cf241a1))

* mito to chromosome const ([`da9a845`](https://github.com/Mjvolk3/torchcell/commit/da9a8459c63042d502f2b07222f6eb9ba4316323))

* init import trick ([`758ef13`](https://github.com/Mjvolk3/torchcell/commit/758ef139eac97a4308c5750658c9ceaa562c4831))

* sequence.py sgd yeast ([`9ebe7c4`](https://github.com/Mjvolk3/torchcell/commit/9ebe7c41d26b0897298b92f7287517fa984831ec))

* sequence torch library ([`8e8f1db`](https://github.com/Mjvolk3/torchcell/commit/8e8f1dbdf0aad55713216025b888d78d3719d834))

* workspace config ([`2fafacc`](https://github.com/Mjvolk3/torchcell/commit/2fafacc34f096788f70879674ef736d00a701ff5))

* dendron msc ([`9221f6d`](https://github.com/Mjvolk3/torchcell/commit/9221f6dfefed6019a8ba57c8fa57751f24fc39ee))

* readme update ([`d400f9c`](https://github.com/Mjvolk3/torchcell/commit/d400f9c93f9092f29a7367667558507708833d64))

* src dump ([`e4951e2`](https://github.com/Mjvolk3/torchcell/commit/e4951e23c199a961b42696f13e35e16db23bbd59))

* docs ([`98b86f0`](https://github.com/Mjvolk3/torchcell/commit/98b86f04462cb4f46ed1e29a25a4bb04aea5a221))

* notes ([`c88bcce`](https://github.com/Mjvolk3/torchcell/commit/c88bccedb93ec9dde258b29295d647a73d47c995))

* pipeline image update ([`06f5cbb`](https://github.com/Mjvolk3/torchcell/commit/06f5cbb9201adec3b2dac697745d072b10970d3a))

* locus pydantic check ([`ba80eca`](https://github.com/Mjvolk3/torchcell/commit/ba80eca1482bd7d293c6ee8f3f8806f74e0610ba))

* sgd no async ([`1b4d19d`](https://github.com/Mjvolk3/torchcell/commit/1b4d19d0ed87af917face23e2b9679f8ce0d114b))

* first commit ([`9e97ff1`](https://github.com/Mjvolk3/torchcell/commit/9e97ff14a2af606b743aab256f57bd9796964944))

* Initial commit ([`60a6d35`](https://github.com/Mjvolk3/torchcell/commit/60a6d35ef09f951477bb586a1e66df0924424626))

* dump bc pydant error ([`c7a9edf`](https://github.com/Mjvolk3/torchcell/commit/c7a9edfdd91c3ef9234713fcce2a42d246af9393))

* pydant ([`c653de3`](https://github.com/Mjvolk3/torchcell/commit/c653de30838891dc5ce8deefe1874b30741d6203))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`b488731`](https://github.com/Mjvolk3/torchcell/commit/b488731b3a459f6b1b29e6dd7f8a7eea0a97feef))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`7931675`](https://github.com/Mjvolk3/torchcell/commit/79316757640cd549ea8b070bc84081d5f4b53f98))

* l2 weight decay duplicate ([`6f1fa2b`](https://github.com/Mjvolk3/torchcell/commit/6f1fa2bba636cf99e1aa116028b3c964458a8549))

* dcell update for slimming model ([`22b9ed6`](https://github.com/Mjvolk3/torchcell/commit/22b9ed6fcfa17769f2ffa47d01a3f61735ce9343))

* json schema test ([`c7502eb`](https://github.com/Mjvolk3/torchcell/commit/c7502eb640840259c0f4698cb8d8ba5ff6877028))

* rdf update ([`b79853c`](https://github.com/Mjvolk3/torchcell/commit/b79853c2a1cbb20f987d843274e0dfc9eddb92ca))

* update tc rdf ([`99f7889`](https://github.com/Mjvolk3/torchcell/commit/99f7889f9d8e68225922d829d8d5bb5a4024f210))

* torchcell.rdf ([`0679925`](https://github.com/Mjvolk3/torchcell/commit/06799251967f5d8d6e7fefb3d694937fcaa55ec5))

* onto update ([`630e081`](https://github.com/Mjvolk3/torchcell/commit/630e081e9059f2a43503061c78372b512fb111a8))

* updated onto ([`2d634ca`](https://github.com/Mjvolk3/torchcell/commit/2d634cafef2c883ce5a35a149fba13ec00f9e660))

* simple onto ([`15c3315`](https://github.com/Mjvolk3/torchcell/commit/15c3315fe7ff6ebbb9a1bd6e4ed906ad3d5bd218))

* owl in owl ([`ec4d03c`](https://github.com/Mjvolk3/torchcell/commit/ec4d03c5b3504d960ed7725f616a22f3ad74e4cb))

* del my owl ([`c744f93`](https://github.com/Mjvolk3/torchcell/commit/c744f936de54bbc0ef753450b9510d9880a08801))

* my_ontology robot converted ([`375f5f8`](https://github.com/Mjvolk3/torchcell/commit/375f5f8f3624b2a3f0084bbdf812dbdbc5868fd7))

* try rdf ([`6dc3c29`](https://github.com/Mjvolk3/torchcell/commit/6dc3c2965dc09ccdbe55e7ac54627c079b17ee25))

* tasks and owl ([`b6aec92`](https://github.com/Mjvolk3/torchcell/commit/b6aec926d4b272952ef891b07cbce25528f624f8))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`1fb4974`](https://github.com/Mjvolk3/torchcell/commit/1fb4974f2a69a3b31f25f5c18e9c442415a763f6))

* moving logging metrics ([`0c1ca27`](https://github.com/Mjvolk3/torchcell/commit/0c1ca2741905fd0b13b049d4da24ae09f34cdcd1))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`a265b7e`](https://github.com/Mjvolk3/torchcell/commit/a265b7e3ebf7711ec7f38a1a952a4fe7a71b6f87))

* 32 b, 6 wrks ([`f65159f`](https://github.com/Mjvolk3/torchcell/commit/f65159f0962b1495bb543d0af87958a212a78d28))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`be67aab`](https://github.com/Mjvolk3/torchcell/commit/be67aabb2e681c678f4622bd2528b8082605fef6))

* dcell slim yaml ([`412bcee`](https://github.com/Mjvolk3/torchcell/commit/412bceef3104b062d167dbbbe4a6d624caa5215e))

* profiling ([`497ae54`](https://github.com/Mjvolk3/torchcell/commit/497ae5405eb170205d4b19dfd78b391daa6cf8a4))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`cd6dea2`](https://github.com/Mjvolk3/torchcell/commit/cd6dea22654c0dd4e5185c742ec78cd46f759e11))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`100048c`](https://github.com/Mjvolk3/torchcell/commit/100048c495c1b168ce3d92a9aafa2935d150d137))

* slim ([`8908ee6`](https://github.com/Mjvolk3/torchcell/commit/8908ee6367d06dd578e5efb5b76f5923ceab56c8))

* dcell ([`e7edfa3`](https://github.com/Mjvolk3/torchcell/commit/e7edfa319c860cb3378a83043121f2fb02263aca))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`d26ad74`](https://github.com/Mjvolk3/torchcell/commit/d26ad74b36bb4895e1a4407785f9cc7be20c150e))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`3ef4e95`](https://github.com/Mjvolk3/torchcell/commit/3ef4e950f7a66832e8c227fcfc45d3339585f315))

* dcell yaml ([`e526825`](https://github.com/Mjvolk3/torchcell/commit/e526825c8b9e6477e7386e38a47ce885eb5d6428))

* delta dmf yaml ([`5ad8d90`](https://github.com/Mjvolk3/torchcell/commit/5ad8d9053fdc76c7708c131a33a98e023a1a1baa))

* slim ([`e67ec95`](https://github.com/Mjvolk3/torchcell/commit/e67ec956fe31f357cb9083ccc60ddefec86a1c3b))

* lambda reg slim ([`484cf43`](https://github.com/Mjvolk3/torchcell/commit/484cf43874e86247c4132b457d7c01dae5d8e8d9))

* dcell slim ([`e3464f7`](https://github.com/Mjvolk3/torchcell/commit/e3464f7c6e2b43c06dfff747f54881a6f7664d30))

* lightning refactor, preds to gpu ([`29450b9`](https://github.com/Mjvolk3/torchcell/commit/29450b9be09642ad168aa558469f09903556a11b))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`1448608`](https://github.com/Mjvolk3/torchcell/commit/1448608edd899ea53516f3697c4a078f7b7b3b00))

* investigating failed ddp dcell ([`14380ca`](https://github.com/Mjvolk3/torchcell/commit/14380ca81b210bdaa775c2b765b01ae6f7475221))

* profile ([`b23478b`](https://github.com/Mjvolk3/torchcell/commit/b23478b3e03aa2ed567e622285410b6c542bef0b))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`912f406`](https://github.com/Mjvolk3/torchcell/commit/912f4064371fdb3126bc8d1ad83ee6ea3feca439))

* increase epochs ([`ad74721`](https://github.com/Mjvolk3/torchcell/commit/ad74721fb85415541c224a2a3865c3763324fbf6))

* fixed logging ([`1025c17`](https://github.com/Mjvolk3/torchcell/commit/1025c17daa0c61a30d9f140c5fe52f1608e02f21))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`ec030a8`](https://github.com/Mjvolk3/torchcell/commit/ec030a8636007a604304ee6a7a83366bd8496ae8))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`bbcf946`](https://github.com/Mjvolk3/torchcell/commit/bbcf946d63ba9833a753e138569b1e16186dbdec))

* dmf delta configs ([`db2bc17`](https://github.com/Mjvolk3/torchcell/commit/db2bc17287c296194ab6658a801bf62e9d59054c))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`1623d73`](https://github.com/Mjvolk3/torchcell/commit/1623d73f183329b5d3caa1898c623267e0173e93))

* dcell delta ([`9c86fa1`](https://github.com/Mjvolk3/torchcell/commit/9c86fa1d3e51676bd94fa8e1c314afdda4b2befa))

* device dcell and loss fix ([`cc862ba`](https://github.com/Mjvolk3/torchcell/commit/cc862ba875e210377589204ead19295400508d57))

* dmf loss update ([`741287b`](https://github.com/Mjvolk3/torchcell/commit/741287bd961be9867f6bb3b576889b8494771b8d))

* dcell update ([`a66f5ab`](https://github.com/Mjvolk3/torchcell/commit/a66f5ab8c58f96450639c34f83e41a9d7cb8cdf7))

* notes on Dcell bool state ([`b1d8541`](https://github.com/Mjvolk3/torchcell/commit/b1d85418603e8290c8f1fdceb08f42e5d66e57a8))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`f466554`](https://github.com/Mjvolk3/torchcell/commit/f466554f75b24427facec67ca3e68894e2c39912))

* launch dcell ([`41661e7`](https://github.com/Mjvolk3/torchcell/commit/41661e70b2a006f7fdfb815190b4641e13a2ffaf))

* task update, fonts ([`8db0a1f`](https://github.com/Mjvolk3/torchcell/commit/8db0a1ff979143239a43cb494aa89699607b759c))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`09e9c99`](https://github.com/Mjvolk3/torchcell/commit/09e9c99cbd884ae69fe6d464b3a78087ebabb8fa))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`f62ea77`](https://github.com/Mjvolk3/torchcell/commit/f62ea778310ec05ad7cb28d5f2cf1c3537f6dea7))

* dcell dump ([`25259e8`](https://github.com/Mjvolk3/torchcell/commit/25259e85c13c3852e1a04ea9360021f20b614d1d))

* dmf_costanzo_graph_convolution ([`7bfc0e4`](https://github.com/Mjvolk3/torchcell/commit/7bfc0e4857f87881085c3b2cb7c538b8d3f48411))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`2ac7e9b`](https://github.com/Mjvolk3/torchcell/commit/2ac7e9b0649c585bfa41a6936f665a87f9c1e0e3))

* std same scale hack ([`5199c13`](https://github.com/Mjvolk3/torchcell/commit/5199c13cc316a7217e26aac46fa790ba072b7ab9))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`50300a3`](https://github.com/Mjvolk3/torchcell/commit/50300a39576781a4df0906971159151c67fc7032))

* std hack on fitness ([`0134b4c`](https://github.com/Mjvolk3/torchcell/commit/0134b4c53fb203f2dea1df7f62a0f98f3ab86de9))

* dmf graph update ([`34299c5`](https://github.com/Mjvolk3/torchcell/commit/34299c512a9ac7e8108f464789c771d61a113363))

* train on two target ([`b051e37`](https://github.com/Mjvolk3/torchcell/commit/b051e37982b1cd85ca742175da8e2db6a32b9665))

* zero pert ([`4ba1d0b`](https://github.com/Mjvolk3/torchcell/commit/4ba1d0b14664387199b34a8bf462865714dd1878))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`e07d558`](https://github.com/Mjvolk3/torchcell/commit/e07d558107e4b29f05696af3f30ca5e521d9d941))

* added zero pert ([`bbd5eca`](https://github.com/Mjvolk3/torchcell/commit/bbd5eca9ed7d55e4778b87f9442df09fa4b6324c))

* conv slurm ([`055e758`](https://github.com/Mjvolk3/torchcell/commit/055e758e04e399ff84424b5f295d043551aa209f))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`4bfbb60`](https://github.com/Mjvolk3/torchcell/commit/4bfbb6004241e6b9fa7fe6c508ba5e227e21f7e2))

* hacks on hacks on hacks ppi ([`0f8fe15`](https://github.com/Mjvolk3/torchcell/commit/0f8fe151382c9d62109f44c3ffec01b0675e5468))

* ddp costanzo conv ([`8300812`](https://github.com/Mjvolk3/torchcell/commit/8300812b3cce91683dd6da77833fcfcf5e4e3977))

* num_workers >0 slow 🧹notes and config ([`383f532`](https://github.com/Mjvolk3/torchcell/commit/383f5327d372d8ea2441fd0caa221100c3d9c685))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`929ad7c`](https://github.com/Mjvolk3/torchcell/commit/929ad7c9e05be9d85e02fb0d30b8c42b2e496579))

* weird embedding hack these clases are confusing ([`ab97272`](https://github.com/Mjvolk3/torchcell/commit/ab97272a31479fa371fe5ced5e1540cb96702545))

* dubious ([`a91b1d6`](https://github.com/Mjvolk3/torchcell/commit/a91b1d62b249a511bfd2a6f5eacb314082677c96))

* 1 k hop ppi ([`207594f`](https://github.com/Mjvolk3/torchcell/commit/207594fb1fc1659853b4229acd5b9ded8befd079))

* first graph ([`7decfeb`](https://github.com/Mjvolk3/torchcell/commit/7decfeb57776ac63eca51b6e07eed8573f49a242))

* dmf costanzo deepset protein ([`a7eed87`](https://github.com/Mjvolk3/torchcell/commit/a7eed87bb3b862eb49909182a67a7af6f585b7b9))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`74a718e`](https://github.com/Mjvolk3/torchcell/commit/74a718edb86e652e80850037e084ca92988ff910))

* minimal protT5 ([`fda7f19`](https://github.com/Mjvolk3/torchcell/commit/fda7f198ed0c60043bda5f4bc3538e261b9dd78d))

* fix model init ([`475df23`](https://github.com/Mjvolk3/torchcell/commit/475df23742a3f1ab3eb99a921740a7990f40cd04))

* dna_windows ([`daf5eed`](https://github.com/Mjvolk3/torchcell/commit/daf5eedc611a4bb8d2f29500ecc567bb8015f54c))

* t5 embeddings ([`ca14ee5`](https://github.com/Mjvolk3/torchcell/commit/ca14ee5284e527fb04baf184167c7313b52d8b71))

* llm ([`030bd57`](https://github.com/Mjvolk3/torchcell/commit/030bd5786d6724ea16e7e8dcb9bb816c0187851a))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`7ae9ae0`](https://github.com/Mjvolk3/torchcell/commit/7ae9ae08157c0e6003deca8eaf1b5364d9578eb0))

* added ddp ([`90e358b`](https://github.com/Mjvolk3/torchcell/commit/90e358bbbb8b70d563bb72527bc2a2642ece69e9))

* rename slurm linear ([`0162686`](https://github.com/Mjvolk3/torchcell/commit/01626865506a92c5bb015beed8fc91b2b090c013))

* prot T5 ([`723bc21`](https://github.com/Mjvolk3/torchcell/commit/723bc2161db0a87f5ed99d554ab263e2afbe1fc8))

* test out gpu embeddings ([`210cb54`](https://github.com/Mjvolk3/torchcell/commit/210cb548e29702f2b4957369fdef9406c1ed66ef))

* linear models tasks ([`cfa0e45`](https://github.com/Mjvolk3/torchcell/commit/cfa0e45be07929c161093d68bcef439592ae6685))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`7dafcf8`](https://github.com/Mjvolk3/torchcell/commit/7dafcf8f95402db27b2b4821e63b5cb134f88bef))

* slurm update ([`0297983`](https://github.com/Mjvolk3/torchcell/commit/0297983226998105ad3a04d162d59cabdc131a3d))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`8d1fd26`](https://github.com/Mjvolk3/torchcell/commit/8d1fd264aaef8434c32aa58c38239293c972def6))

* one_hot_node ([`5d2ee1a`](https://github.com/Mjvolk3/torchcell/commit/5d2ee1a2d94fbc26585e010468e61b86715f068c))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`c837271`](https://github.com/Mjvolk3/torchcell/commit/c837271776035072ed6dd74c5c9b9efc07244c8e))

* 1e6 ([`8d35c31`](https://github.com/Mjvolk3/torchcell/commit/8d35c31b207cfdd7ef73cb172509cf225d391a77))

* notes on why SGD linear ([`07f27a1`](https://github.com/Mjvolk3/torchcell/commit/07f27a13430fb9d35707646ed99196695058867e))

* simple linear SGD ([`667ab77`](https://github.com/Mjvolk3/torchcell/commit/667ab77af708d835b3e1ecaa5b8c74ffe4660b37))

* regression spacing ([`bb6a324`](https://github.com/Mjvolk3/torchcell/commit/bb6a3249f04ddee10ceaeb180fe13f39ac4f58de))

* linear ([`6f7f950`](https://github.com/Mjvolk3/torchcell/commit/6f7f9504675235a30f3b7ff49e156ad258c42af3))

* Helvetica font ([`f26fd7d`](https://github.com/Mjvolk3/torchcell/commit/f26fd7d30142030c1f706ac6368943c4605487d1))

* combining new embeddings fails, run one hot ([`358922d`](https://github.com/Mjvolk3/torchcell/commit/358922d9915ec54fc63a9685bfa565a58964e0b5))

* one_hot_gene dataset ([`2ef447e`](https://github.com/Mjvolk3/torchcell/commit/2ef447ed3ce8a6222040361d53851000b357e776))

* box plot in regression ([`74302c5`](https://github.com/Mjvolk3/torchcell/commit/74302c57d3303875172dd272281b9ef0aea52c2f))

* genetic_interaction_score box plot ([`38c4cd3`](https://github.com/Mjvolk3/torchcell/commit/38c4cd337bb182d437c5c3941e3e919ff3954fc8))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`ac3384a`](https://github.com/Mjvolk3/torchcell/commit/ac3384a01ff274d89d85567f194481eb494f4685))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`d5ab1f8`](https://github.com/Mjvolk3/torchcell/commit/d5ab1f83a578535bca1aae4ca3f61d9acd2aad98))

* full train ([`427fd75`](https://github.com/Mjvolk3/torchcell/commit/427fd75d73835314a45e85a05309e5fd11853ba3))

* MergedExperiment ([`d70b291`](https://github.com/Mjvolk3/torchcell/commit/d70b291718a949ff21f24342b7832e620813f2f5))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`541c98a`](https://github.com/Mjvolk3/torchcell/commit/541c98a3fd2a898ac3f98f60e338b79891c4ea32))

* made large model ([`f8a0ab2`](https://github.com/Mjvolk3/torchcell/commit/f8a0ab2e93a3d5b6982ca17f480f2b352ffae07a))

* no verbose ([`030a3e1`](https://github.com/Mjvolk3/torchcell/commit/030a3e191b9be39c553a4f39743f8895144cb29c))

* notes update ([`31f102e`](https://github.com/Mjvolk3/torchcell/commit/31f102eabeac741e9a3eb8f7d811ccab1028ce21))

* log artifacts ([`5989871`](https://github.com/Mjvolk3/torchcell/commit/598987145b3fba419df599fbc9d95ed86ef2096d))

* callbacks ([`849a2c7`](https://github.com/Mjvolk3/torchcell/commit/849a2c77819ba55aa0dc2c82d13a72768e2c942e))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`da77eb8`](https://github.com/Mjvolk3/torchcell/commit/da77eb8f06cba745b3e9d5f8e8907423c757016e))

* delete plotnine ([`c75749a`](https://github.com/Mjvolk3/torchcell/commit/c75749a0a38453a233c02c4f067e19b4b880b6cb))

* box plot ([`db7645c`](https://github.com/Mjvolk3/torchcell/commit/db7645c1ba27aa3489d8c26ae8399becf1c955b3))

* ddp update time ([`c45fd2c`](https://github.com/Mjvolk3/torchcell/commit/c45fd2cdf3137e8e1cc3c944d36940e6a4946ed2))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`1ce8359`](https://github.com/Mjvolk3/torchcell/commit/1ce8359390a670cdabdd1c51dc11e1dcac68abd5))

* add upstream sequence to training dmf ([`542a056`](https://github.com/Mjvolk3/torchcell/commit/542a056b7034055831da95963a36a87d03803bdf))

* plot ([`4ab2b23`](https://github.com/Mjvolk3/torchcell/commit/4ab2b235b17313a857b7ce99054576a2d1bc8851))

* dataset add ([`4bd6e0c`](https://github.com/Mjvolk3/torchcell/commit/4bd6e0cef69a18ed18b38b8b39d60e86ae4d7f72))

* note update ([`f6ce410`](https://github.com/Mjvolk3/torchcell/commit/f6ce4109cb48279dc0a6e3742ca0368444f00b6f))

* remove depreacted GO comment bug ([`6d24b43`](https://github.com/Mjvolk3/torchcell/commit/6d24b439eb08910395905c4d274d8cc5bcacd189))

* dmf ([`d6f653f`](https://github.com/Mjvolk3/torchcell/commit/d6f653fe2d634b7d7806f764c819480701e5d3bc))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`71fda01`](https://github.com/Mjvolk3/torchcell/commit/71fda01e0ec2f097fffc4a9137e22d72a76cd2da))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`0028d51`](https://github.com/Mjvolk3/torchcell/commit/0028d51743ccd46a41ac5315419a3a9fdf1991d6))

* dmf delta ([`698f920`](https://github.com/Mjvolk3/torchcell/commit/698f920053a095107f371d3e6602f721541f7704))

* x and x pert ([`07d987d`](https://github.com/Mjvolk3/torchcell/commit/07d987d9dffc5976f69ef0ac1d1bcf8246ced456))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`914a5bb`](https://github.com/Mjvolk3/torchcell/commit/914a5bb7f5e002120091c68cf19d9f2f5fef7f35))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`a476490`](https://github.com/Mjvolk3/torchcell/commit/a4764905a54940a4cbb9e1eac95bd36b0b527317))

* dmf yaml slurm ([`cff9351`](https://github.com/Mjvolk3/torchcell/commit/cff93511e8efc844bb923fdc6174ce8d7e4503fb))

* fix in place operator for tanh ([`b736271`](https://github.com/Mjvolk3/torchcell/commit/b736271ce607eeb35c807937125fe4b8f10bb6b5))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`b3f4802`](https://github.com/Mjvolk3/torchcell/commit/b3f4802c14e563a70d78ef111c53fbb20f5515bd))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`95d230c`](https://github.com/Mjvolk3/torchcell/commit/95d230c77647d05c09b0cf5e3cd8105317559db5))

* dmf delta ([`49bf717`](https://github.com/Mjvolk3/torchcell/commit/49bf717ce0493bf4127acc473c7a9dc642246e72))

* wt_train_per_epoch ([`447ea83`](https://github.com/Mjvolk3/torchcell/commit/447ea839b00a05a84b453975686cc2c07a8df805))

* notes ([`e41bea5`](https://github.com/Mjvolk3/torchcell/commit/e41bea546d3365ae5bf2a3ff4818b23546695491))

* dmf at position for sweeping ([`cd29d3a`](https://github.com/Mjvolk3/torchcell/commit/cd29d3acba8e150e5e3c25081e8cc2f0c32baa3f))

* removed extra batch size ([`671325e`](https://github.com/Mjvolk3/torchcell/commit/671325ee64842d2460a052eb5d0c02d82adeb616))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`5e5a446`](https://github.com/Mjvolk3/torchcell/commit/5e5a446531ed22a2c3cc8db56c9652fb1c381221))

* regression ([`1d44d22`](https://github.com/Mjvolk3/torchcell/commit/1d44d228a3844bf600890b578b9fc2d97a3c5055))

* dmf delta ([`80ba1b8`](https://github.com/Mjvolk3/torchcell/commit/80ba1b845e31b38ac2a0b6084490f4977096a9c1))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`df6bf62`](https://github.com/Mjvolk3/torchcell/commit/df6bf62bd9240b2f6a2eceb0f2b51e62d08a2170))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`f2908b0`](https://github.com/Mjvolk3/torchcell/commit/f2908b0781d3078c7e6f9313ee769cff730210cd))

* dmf delta deep set ([`9d1b17b`](https://github.com/Mjvolk3/torchcell/commit/9d1b17bd1103e99cd699f5cab30defad00b407c2))

* weighted rmse ([`83e7741`](https://github.com/Mjvolk3/torchcell/commit/83e7741c60007554133c6c50aa9e37b04fb4c003))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`1f6072b`](https://github.com/Mjvolk3/torchcell/commit/1f6072be48099aa8c302071b0d1f0885e496e4e2))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`585710f`](https://github.com/Mjvolk3/torchcell/commit/585710f01e9bda6fb10502467820b0011f3c161e))

* 1e5 ddp issues ([`c6c81e3`](https://github.com/Mjvolk3/torchcell/commit/c6c81e312fe4ac134a39026cb8b10b7a6a36fbd6))

* dmf deep set with more regularization ([`1ee879d`](https://github.com/Mjvolk3/torchcell/commit/1ee879dfc3d37155ed5a791d9a94b372df8c5697))

* starting training robustness ([`d47d0b6`](https://github.com/Mjvolk3/torchcell/commit/d47d0b65108dec80271ce05d2182c3639b35b87c))

* fungal up down corrected embedding ([`f6715c7`](https://github.com/Mjvolk3/torchcell/commit/f6715c7fac2bc6425ffa73d4f61ae2ad3f15bdeb))

* ddp issues notes ([`b97edc3`](https://github.com/Mjvolk3/torchcell/commit/b97edc3024043c275db2e4c08e4dcabe407fdabf))

* configured lr and wd ([`7cb6c2b`](https://github.com/Mjvolk3/torchcell/commit/7cb6c2b8392c44b8caa58aa9455714317acdd023))

* update parse genome - black magic ([`83e3a35`](https://github.com/Mjvolk3/torchcell/commit/83e3a356c2f8a870d9d54c7e677839fcf7c9eb59))

* notes ([`2c252fb`](https://github.com/Mjvolk3/torchcell/commit/2c252fb52dba3e87b34eb6eb10a75007562a8e51))

* parse genome, ddp problems on delta, need debug local ([`1960071`](https://github.com/Mjvolk3/torchcell/commit/196007133af339b6ff303c132461cab61f7ce04e))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`cb1b5c0`](https://github.com/Mjvolk3/torchcell/commit/cb1b5c0e622c770436fb65dc512f9e4aaa0a7346))

* box plot parameterized ([`88d0c63`](https://github.com/Mjvolk3/torchcell/commit/88d0c63230cf039a9e52f8c74b218ad5a8e78632))

* delta refresh ([`3a76ebd`](https://github.com/Mjvolk3/torchcell/commit/3a76ebd5b26c7dfbd953014a6001a5cb7c12e74d))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`c63681e`](https://github.com/Mjvolk3/torchcell/commit/c63681e5a504210f1685f85ce12f6b035d13c55b))

* wt freq ([`a9fe86c`](https://github.com/Mjvolk3/torchcell/commit/a9fe86cd31d52f30866558cc53785bdd6349360e))

* delta exp update ([`e5bba75`](https://github.com/Mjvolk3/torchcell/commit/e5bba75a2aadc8396d5a0fd7011b37584a65a876))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`822e3b8`](https://github.com/Mjvolk3/torchcell/commit/822e3b84c548cdf37f774c6ee837c840d2937041))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`f6a2a10`](https://github.com/Mjvolk3/torchcell/commit/f6a2a109b409044e37f6adabbafc045abf656671))

* delta exp ([`df085f4`](https://github.com/Mjvolk3/torchcell/commit/df085f468a33841bf4313fd0ea283b9d6cb6977d))

* dmf logging wt time to launch ([`404287b`](https://github.com/Mjvolk3/torchcell/commit/404287b841e9d004966a54d40f68168bbe81fed9))

* has group ([`d020ed4`](https://github.com/Mjvolk3/torchcell/commit/d020ed4bfa90ce0b0f0e76ea942bda209745bdc2))

* fungal embeddings model ([`11b84b3`](https://github.com/Mjvolk3/torchcell/commit/11b84b32f44c80fc390aaf2df7d475a92b4713aa))

* dump, fungal_up_down, wt difference ([`17b0d54`](https://github.com/Mjvolk3/torchcell/commit/17b0d5492817423606946e4e489d6787e2dcc2a7))

* git rm docs build ([`bfaeed2`](https://github.com/Mjvolk3/torchcell/commit/bfaeed23979865f961222eb2542a86c24cedc323))

* SpeciesLM model, notes ([`35c5a30`](https://github.com/Mjvolk3/torchcell/commit/35c5a30e97288808cfbde9e30fc76d4f4fa43ccf))

* tests ([`3b08328`](https://github.com/Mjvolk3/torchcell/commit/3b08328b52b1933bc9e5466c0c373b444e6dc747))

* test genome ([`d5809cb`](https://github.com/Mjvolk3/torchcell/commit/d5809cb4c5129529f20658cd7a91d32937de05cf))

* updated docs ([`c96bdb3`](https://github.com/Mjvolk3/torchcell/commit/c96bdb352e920f595114d1333edce673e813f0e4))

* update actions ([`dda2f52`](https://github.com/Mjvolk3/torchcell/commit/dda2f52531af47ff038a89ab34e89dcbaa049988))

* updated reqs worked locally ([`57ebb21`](https://github.com/Mjvolk3/torchcell/commit/57ebb21133c13e4079fd3e1068bee4cec8cb2a98))

* updated reqs ([`b225f8c`](https://github.com/Mjvolk3/torchcell/commit/b225f8c443489f211c9cc0524ce70db9430bc7c6))

* reqs remove torch vision, audio ([`1418ba3`](https://github.com/Mjvolk3/torchcell/commit/1418ba38f49c8da551e3e9d41a130a82779b9145))

* removed graphviz ([`be87627`](https://github.com/Mjvolk3/torchcell/commit/be87627e6c5509ad702a0486d6b9a977a598dcf1))

* test ([`5eb781e`](https://github.com/Mjvolk3/torchcell/commit/5eb781e95d01345188a2d26cb297acba2ae1bd58))

* logo update ([`57f4fc8`](https://github.com/Mjvolk3/torchcell/commit/57f4fc8bd5ee43d1d81ac6d7866895219fb4affc))

* update logo ([`fa40ef9`](https://github.com/Mjvolk3/torchcell/commit/fa40ef991661e83b34b05dc367b6332ff9868100))

* logo ([`4d993ba`](https://github.com/Mjvolk3/torchcell/commit/4d993ba45bff09c8bb2f7d697c165263449b8424))

* req reorder for scatter ([`0cc1979`](https://github.com/Mjvolk3/torchcell/commit/0cc1979a90354d304098fe1d2bd73972c9262be9))

* pandas pin ([`f94d865`](https://github.com/Mjvolk3/torchcell/commit/f94d865200c6d6c18fcbfaef9deb8bfa7baf8af7))

* zoom ([`1be0b09`](https://github.com/Mjvolk3/torchcell/commit/1be0b096f4cec18109bb54a2fcb21a0ef8c70d44))

* reqs torch scatter issue ([`79c28c9`](https://github.com/Mjvolk3/torchcell/commit/79c28c9f43ac17228b4943fcbbf757a69b72c12c))

* logo ([`3b7877b`](https://github.com/Mjvolk3/torchcell/commit/3b7877b67bbe8c45cdc138fa4ff47d46b9e580f0))

* req update, move gene set ([`b3f1934`](https://github.com/Mjvolk3/torchcell/commit/b3f19347f59435ff14d370cc713ab4c28c80c7be))

* testing ([`f00e87d`](https://github.com/Mjvolk3/torchcell/commit/f00e87d7bd0e48e343f656961d8511d6bb6a42ae))

* test seq data ([`420e535`](https://github.com/Mjvolk3/torchcell/commit/420e5350549e111153e4e1b31e9c5465bda5f500))

* tasks ([`3c22bce`](https://github.com/Mjvolk3/torchcell/commit/3c22bce8aa380653986c21f7ee9cec38d5aa8ea0))

* env coverage ([`16079af`](https://github.com/Mjvolk3/torchcell/commit/16079af7dabeef9a6840ef9785159abbc999c9dc))

* src dump... in the middle of major rewrites ([`421289c`](https://github.com/Mjvolk3/torchcell/commit/421289c16b7509695543d34bb8196847b1b9b625))

* notes, images, drawings ([`db9793b`](https://github.com/Mjvolk3/torchcell/commit/db9793b03516d47e91b1f517e316aa6f4e8a8bd4))

* dmf demo update for clarity ([`f1d4876`](https://github.com/Mjvolk3/torchcell/commit/f1d487638d179106d86073e1ed460e3080365e5a))

* deep set ([`b91b1ac`](https://github.com/Mjvolk3/torchcell/commit/b91b1acddd6970729b5d48543012078915e9416a))

* genome ([`1c61816`](https://github.com/Mjvolk3/torchcell/commit/1c6181641298b8ababefa3a75a5d22534045ec6f))

* dcell model start ([`e4a4fa5`](https://github.com/Mjvolk3/torchcell/commit/e4a4fa5d3ad4a833cae66b179b95094d5c50ceb2))

* cached df for easy stats ([`caf962a`](https://github.com/Mjvolk3/torchcell/commit/caf962abcfe5da856a932cbf525f886fe0f189df))

* comments on issues ([`0b29ec4`](https://github.com/Mjvolk3/torchcell/commit/0b29ec4d5d2070d0fc092a993fcf71df7aa7e2cd))

* notes ([`e1a3c62`](https://github.com/Mjvolk3/torchcell/commit/e1a3c6276dce509905d510da9a024c7c9caae05f))

* dmf nt projection viz ([`a82a95d`](https://github.com/Mjvolk3/torchcell/commit/a82a95d71c58522c6fe6d6dce3b5e025aad71fd3))

* umap ([`84565fc`](https://github.com/Mjvolk3/torchcell/commit/84565fc39a3cb9a2887d8820caf92ab81d367747))

* added perturbation to data ([`c457497`](https://github.com/Mjvolk3/torchcell/commit/c4574970d2d7b659e493f5f90eea7454b993ee29))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`31b82e0`](https://github.com/Mjvolk3/torchcell/commit/31b82e098a215a76a22978de89f003de61d855be))

* dmf config ([`01e5aab`](https://github.com/Mjvolk3/torchcell/commit/01e5aab1ad9d25ab64e0866d66a5db752d26fc21))

* dmf ddp jobs ([`7481294`](https://github.com/Mjvolk3/torchcell/commit/7481294892d45e629fd862634cc238e3ce25db49))

* print data ([`eda18f5`](https://github.com/Mjvolk3/torchcell/commit/eda18f5b0fe39ad70192d787bbe53b2fd1674616))

* s288c check for db ([`194d014`](https://github.com/Mjvolk3/torchcell/commit/194d014657e950c9b32a6a9242d7e0a3bce8f3c6))

* dmf deepset do, bnorm ([`43178f7`](https://github.com/Mjvolk3/torchcell/commit/43178f70c95e32715fe42dff7ee28b74d920f228))

* workspace delta interactive ([`ef40fcf`](https://github.com/Mjvolk3/torchcell/commit/ef40fcfa8d105f658c5632854f639cc1cecfa698))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`9b7ab0b`](https://github.com/Mjvolk3/torchcell/commit/9b7ab0b2dc4a4627a163496b77422a11b2b59594))

* slurm ([`d7ee600`](https://github.com/Mjvolk3/torchcell/commit/d7ee60088b57795f332a6e1fa16110328241e654))

* images and notes ([`00e8f47`](https://github.com/Mjvolk3/torchcell/commit/00e8f47b21a96428355d60c808acbbec540c1d66))

* data profiling process ([`db02371`](https://github.com/Mjvolk3/torchcell/commit/db0237196f4532f17e12ba7941092b2964b48572))

* cell data different data sizes ([`445f29a`](https://github.com/Mjvolk3/torchcell/commit/445f29a840ed8728b17fd392b4e50427cfcac5b1))

* dataset hack ([`b60accd`](https://github.com/Mjvolk3/torchcell/commit/b60accd6722f95b8993e8ae0baeb50c8182013bc))

* cell revert, costanzo init db ([`06803b2`](https://github.com/Mjvolk3/torchcell/commit/06803b2d50658fba671f1b07fc5d4f9d8d59bf4e))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`9bdbe4a`](https://github.com/Mjvolk3/torchcell/commit/9bdbe4a32e449dc99062e5b9ad96ee322fc6b534))

* crank the threads 1.0 ([`94ffafd`](https://github.com/Mjvolk3/torchcell/commit/94ffafdba8981aa98011edf1002b1e2138d5ecdc))

* crank the threads ([`cb9213c`](https://github.com/Mjvolk3/torchcell/commit/cb9213c4f173a9b570d1b08a54a961d61f2b0781))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`d85fc92`](https://github.com/Mjvolk3/torchcell/commit/d85fc92ce423114e992f4ff26535492fdaa51ad9))

* slurm scripts and exp files ([`48b32b8`](https://github.com/Mjvolk3/torchcell/commit/48b32b8262f2fd428c5886f1e355c1d616a5dbae))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`e26d7f3`](https://github.com/Mjvolk3/torchcell/commit/e26d7f308751ddee8678189894415b36c75cc682))

* dot env ([`85dc0e3`](https://github.com/Mjvolk3/torchcell/commit/85dc0e3ae7f30e18e7d26328111d9aef12f0069a))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`905fadd`](https://github.com/Mjvolk3/torchcell/commit/905faddc75d3e654c3de658ae84e71a3e33cedc6))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`981fdbd`](https://github.com/Mjvolk3/torchcell/commit/981fdbda4739f8b7159ef1e32b92695202b78569))

* lmbd delta ([`107bd3b`](https://github.com/Mjvolk3/torchcell/commit/107bd3bd79c93b68fe25d13a6acaa8456c766d49))

* prof ([`8c8d9db`](https://github.com/Mjvolk3/torchcell/commit/8c8d9db186d4a0db3913b0eff0f8f5ca4a35c411))

* cell mutlithreading for filter speed, same on M1 ([`1520ff8`](https://github.com/Mjvolk3/torchcell/commit/1520ff86ee59171a2a420e8b6120b447e452d937))

* process thread pool ([`de33de6`](https://github.com/Mjvolk3/torchcell/commit/de33de6e99a324d9a003fbc05345fcf86d93c8b4))

* correct import ([`5f8303a`](https://github.com/Mjvolk3/torchcell/commit/5f8303adacdb5f07edba98c293938d2ffa2afa15))

* lmdb, subset graph ([`30b4564`](https://github.com/Mjvolk3/torchcell/commit/30b45643cc8c61d195dd99cf347237fba2cc91ec))

* go hist ([`43b9af1`](https://github.com/Mjvolk3/torchcell/commit/43b9af13ae0fd7f12ccc5cb10084acfc96fc4324))

* go methods ([`9a2cdfa`](https://github.com/Mjvolk3/torchcell/commit/9a2cdfa7d468a25946efaaf5e3c55fb8d6ca5e09))

* moved into genome ([`08b9e3e`](https://github.com/Mjvolk3/torchcell/commit/08b9e3eddc3ec466e1e4b3873516d83727da518d))

* drop_chrmt and drop_empty_go ([`a4372c3`](https://github.com/Mjvolk3/torchcell/commit/a4372c3493be71ba07eace06dbb2c9848b4c511e))

* drop_empty_go, drop_chrmt, remove_deprecated_go ([`8750df6`](https://github.com/Mjvolk3/torchcell/commit/8750df6f4a90360aedc2f3438db68dd56e98fc35))

* lmdb ([`8e62a41`](https://github.com/Mjvolk3/torchcell/commit/8e62a4182f2023d87013796350c73208ba0e71d8))

* lmdb mvp dmf deepset ([`6750582`](https://github.com/Mjvolk3/torchcell/commit/675058237e14964b9557826e18b0be542c5b36c2))

* costanzo lmdb ([`6d882a9`](https://github.com/Mjvolk3/torchcell/commit/6d882a9e46948a4952a8053e82150dc52d7a4f6f))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`d0d493e`](https://github.com/Mjvolk3/torchcell/commit/d0d493eb3b7f4767d7fd948dc83c7bf87d2a64b1))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`fd21199`](https://github.com/Mjvolk3/torchcell/commit/fd21199b2e1de4ff0b2b0acc538e2fb05fd6981b))

* cpu run for dataset creation ([`ca9e552`](https://github.com/Mjvolk3/torchcell/commit/ca9e55221473fbfc6c094bc0e46943bfde7ad765))

* req update ([`4d58c1c`](https://github.com/Mjvolk3/torchcell/commit/4d58c1c2f0abe348a3cb953d5f08bf9daf6791e6))

* delete subset for long deletions of 1e6+ files ([`3ebe548`](https://github.com/Mjvolk3/torchcell/commit/3ebe5489a71a176fb1b03ab12f4817ec7b97f96d))

* dump ([`1648d4a`](https://github.com/Mjvolk3/torchcell/commit/1648d4a79c9f308acaa810acda73088b2c2642e0))

* notes ([`25b507c`](https://github.com/Mjvolk3/torchcell/commit/25b507c212109f7fee54421b0f722a9b443c2356))

* dmf poc ([`c083e22`](https://github.com/Mjvolk3/torchcell/commit/c083e2213a66df316c22bd26e5ada259810b13d9))

* data ([`40b6650`](https://github.com/Mjvolk3/torchcell/commit/40b665027cad4c21cceb01e47de81e5ea35a801b))

* old pkg info ([`3141b0a`](https://github.com/Mjvolk3/torchcell/commit/3141b0ae224c4e49181a7ca32b880ec15ede2102))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`1bc2a31`](https://github.com/Mjvolk3/torchcell/commit/1bc2a315f3bf9091c4cfd9727c8664853239f12c))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`6dc9589`](https://github.com/Mjvolk3/torchcell/commit/6dc95890318216fa22100ac80c441a00c5c4c309))

* slurm scripts ([`928e6e8`](https://github.com/Mjvolk3/torchcell/commit/928e6e8a9dcdef4758d23423659752c6c7b69fb0))

* move file util, works on exps too ([`11786cc`](https://github.com/Mjvolk3/torchcell/commit/11786cc8a5313749a5514527a00a6b8685158b0b))

* dmf hydra ([`35f3d30`](https://github.com/Mjvolk3/torchcell/commit/35f3d3069fcb2523d8d07295bbf2501d1d4083c4))

* frontmatter ([`373b0cc`](https://github.com/Mjvolk3/torchcell/commit/373b0cc8ccd0f9436cb715eff9d20e19c7643272))

* notes ([`7f142c7`](https://github.com/Mjvolk3/torchcell/commit/7f142c78759596200e07ba8ad040cfac33f14091))

* ig up ([`2e9cc4e`](https://github.com/Mjvolk3/torchcell/commit/2e9cc4ef5d9ccab4a2471859a55245a104b0f26b))

* experiment config ([`06ad854`](https://github.com/Mjvolk3/torchcell/commit/06ad854240f492e4ac98d8d27d09197e6a13b5fb))

* notability update ([`7a81cc3`](https://github.com/Mjvolk3/torchcell/commit/7a81cc3f5f8032b61fff08dcf75274cbda4625b8))

* deleted files ([`2b676c0`](https://github.com/Mjvolk3/torchcell/commit/2b676c02a3987affa3076855c2478d335c94a1b0))

* git ignore update ([`3c80083`](https://github.com/Mjvolk3/torchcell/commit/3c80083e8d0ad9e32f5bbb638d558d772c5bc505))

* sorted set ([`62a06ed`](https://github.com/Mjvolk3/torchcell/commit/62a06eda7207264d6c580029fd92432bc4e528d5))

* uncommented windowing ([`c9249ee`](https://github.com/Mjvolk3/torchcell/commit/c9249eef626378bbee44cbb3e932c2076a50ceec))

* GO info, attrs, sorted set, types ([`ac6f0dd`](https://github.com/Mjvolk3/torchcell/commit/ac6f0ddbcf0672f4a68625bbeb2064ca05cb195e))

* phenotype future ([`7d40b00`](https://github.com/Mjvolk3/torchcell/commit/7d40b00effef8cb2ac5bbee6a65b8caa6d31ead4))

* profiles ([`1e891dc`](https://github.com/Mjvolk3/torchcell/commit/1e891dc4ae228b1d92d6c8dbc18a30e59327b348))

* notes ([`110f553`](https://github.com/Mjvolk3/torchcell/commit/110f553f1f49726a37c6a8a505e183981f6e3cb2))

* mvp dmf large costanzo ([`6f1d251`](https://github.com/Mjvolk3/torchcell/commit/6f1d2511a2f3cf54805e647b4addb89959548f48))

* cache len ([`3f0494a`](https://github.com/Mjvolk3/torchcell/commit/3f0494a35578e189d497e80089c7c026fba3db80))

* dmf still loading all data on second process ([`e1cfeaf`](https://github.com/Mjvolk3/torchcell/commit/e1cfeaf5c232f16f4b06f09e5a278cee7c7b68c5))

* costanzo ([`4e7de4e`](https://github.com/Mjvolk3/torchcell/commit/4e7de4e7f81384e2db05e8d87b60e90bec3600f8))

* io threading speedup ([`27ac1f1`](https://github.com/Mjvolk3/torchcell/commit/27ac1f141b4b1d48de637128c8e5b47adafb246a))

* rm data messing rel paths ([`0bfa262`](https://github.com/Mjvolk3/torchcell/commit/0bfa2625e949d08ef1c5fa45edf12e110c09d77e))

* reqs hd5 ([`c7c6263`](https://github.com/Mjvolk3/torchcell/commit/c7c6263b1a3da2e3edc25170a64eba2b2632d7ed))

* costanzo preprocess ([`c4ad99c`](https://github.com/Mjvolk3/torchcell/commit/c4ad99c5c097ffdff71f9c108a659cd072f61f75))

* thread ckpt ([`598645d`](https://github.com/Mjvolk3/torchcell/commit/598645d168d23a3e2eb6e9439b030d4830e35218))

* prof ([`4af7088`](https://github.com/Mjvolk3/torchcell/commit/4af7088d2ed3090998b1d2d5fc3d1c3acba6ac79))

* notes ([`2940b2c`](https://github.com/Mjvolk3/torchcell/commit/2940b2cdc6a64cb668bfab2b3ce10d437a43fb65))

* reqs up ([`12fae21`](https://github.com/Mjvolk3/torchcell/commit/12fae21e9a14489338ae3ec7415444abdb4ef180))

* init update ([`6b38a1c`](https://github.com/Mjvolk3/torchcell/commit/6b38a1cc9f94cb19a32ac0559a1fc72a45d421dc))

* fitness and regression ([`ef70c61`](https://github.com/Mjvolk3/torchcell/commit/ef70c61c1b4b953570ad794ebf15a7c3f0b50682))

* docs ([`bd0025c`](https://github.com/Mjvolk3/torchcell/commit/bd0025c0f3e6e90d25d6addee409eff075735d77))

* notes ([`5e0d069`](https://github.com/Mjvolk3/torchcell/commit/5e0d0695b1eb147f770620af057f14b23a44f3a3))

* ws ([`d0b8154`](https://github.com/Mjvolk3/torchcell/commit/d0b8154e03efa4a2e91a2ca0f03119d4d3e91f62))

* notability sync ([`947fa81`](https://github.com/Mjvolk3/torchcell/commit/947fa81e46fe717885bd743450e5312bd8fec9a8))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`75ab654`](https://github.com/Mjvolk3/torchcell/commit/75ab6545a66aae681848979b30c7146e8426398a))

* costanzo options ([`eef4c11`](https://github.com/Mjvolk3/torchcell/commit/eef4c1169dddf85e562f941156cc7d96cfd40807))

* future tasks ([`1cea639`](https://github.com/Mjvolk3/torchcell/commit/1cea63957d0b4284d8c8fce5c76800ab73450f5a))

* slurm ([`b27386e`](https://github.com/Mjvolk3/torchcell/commit/b27386ebdd807954f9255b0c6953439860895138))

* delta mvp ([`fe5a768`](https://github.com/Mjvolk3/torchcell/commit/fe5a7680707981a0c89ea330794d1701b43762dd))

* experiments data root ([`064be21`](https://github.com/Mjvolk3/torchcell/commit/064be21fe8306428189fb21ddfea2b139cb586c3))

* reqs pydantic pin ([`a04e12b`](https://github.com/Mjvolk3/torchcell/commit/a04e12be67d25d002c77e10415dac4ce6946aca5))

* Merge remote-tracking branch &39;refs/remotes/origin/main&39; ([`dc8240d`](https://github.com/Mjvolk3/torchcell/commit/dc8240d25e651aa45d8bc15f8f289a068521697f))

* remote workspace ([`6a1e0b6`](https://github.com/Mjvolk3/torchcell/commit/6a1e0b604f6220a17906706a3c35bad9a483ac14))

* workspaces ([`16dccd9`](https://github.com/Mjvolk3/torchcell/commit/16dccd9d891d2b2040c898b17c05a688b6415a21))

* data path for SCerevisiaeGenome ([`1a82617`](https://github.com/Mjvolk3/torchcell/commit/1a8261762072a1f5e3deabfe3f53d3fa683b415c))

* lightning ([`1a534c0`](https://github.com/Mjvolk3/torchcell/commit/1a534c08c2c80bc3b52c070eef09cca6336bae4f))

* updated dmf with env ([`10cb513`](https://github.com/Mjvolk3/torchcell/commit/10cb513a29d1925b1c63550cc15229aad1c309ad))

* first training loop ([`c0011ce`](https://github.com/Mjvolk3/torchcell/commit/c0011ce84f9775ddf147845a9f1e69266cdc6efe))

* isort black compat ([`be19c45`](https://github.com/Mjvolk3/torchcell/commit/be19c453e32ca808ed9bbda7c35282a4323ae45c))

* add isort ([`ee30ef7`](https://github.com/Mjvolk3/torchcell/commit/ee30ef76e4ad10c07c875a743ca40a40361e06b3))

* project toml for config ([`96e76eb`](https://github.com/Mjvolk3/torchcell/commit/96e76eb16b824d6c219ce1a7ddf9d693ba18d9b7))

* notes ([`7a62e22`](https://github.com/Mjvolk3/torchcell/commit/7a62e22de4531c4403df58f2484fa53737279c2a))

* precommit install ([`798c9da`](https://github.com/Mjvolk3/torchcell/commit/798c9dac066dd8dc5bc279422aaa56352992f952))

* reqs update ([`0693f3e`](https://github.com/Mjvolk3/torchcell/commit/0693f3eed10200c55bd1fed83e6413bc0dbacb9a))

* precommit and workspace ([`d79d289`](https://github.com/Mjvolk3/torchcell/commit/d79d289e199152d841ec7caf55cc32d37cd6219a))

* frontmatter repo reset ([`2b43be1`](https://github.com/Mjvolk3/torchcell/commit/2b43be12890738ae56254310a139bc4aa12b9b6e))

* readme ([`25d80c0`](https://github.com/Mjvolk3/torchcell/commit/25d80c0e59adbac577e06be5e1523341039d6fa6))

* update test cache ([`bbd2494`](https://github.com/Mjvolk3/torchcell/commit/bbd2494b078bcb3b32111493a44890f91e2dbbf2))

* update cache ([`9134c74`](https://github.com/Mjvolk3/torchcell/commit/9134c742c58edc1f140a2a98e235608ff4fdd9f7))

* remove &39;p&39;, pre-commit hook setup ([`225e265`](https://github.com/Mjvolk3/torchcell/commit/225e26525730a63bc03145c9b3c8a5e2bafd65fa))

* test CI ([`e4a6f5f`](https://github.com/Mjvolk3/torchcell/commit/e4a6f5f809886beaf6bdc7163d4d9655e9cb716b))

* concurrency ([`82844aa`](https://github.com/Mjvolk3/torchcell/commit/82844aa12ea16740801b2fea21d5e1f9c49bfcfb))

* CI ([`4fc97d9`](https://github.com/Mjvolk3/torchcell/commit/4fc97d9e21d391af1496a7b0a04569d630932f13))

* tranformer datasets ([`451e784`](https://github.com/Mjvolk3/torchcell/commit/451e784aa134a5ec5f9f642c2ae360a5b3faa786))

* docs update ([`49378bc`](https://github.com/Mjvolk3/torchcell/commit/49378bc484848dc008291dc191e6b96d43559801))

* reqs update ([`2e0f92e`](https://github.com/Mjvolk3/torchcell/commit/2e0f92e54796fb0a6605c7385e9aab439da816e3))

* flake 8 config ([`62464a7`](https://github.com/Mjvolk3/torchcell/commit/62464a7d63812018b28dc72ae53cc47b78f38367))

* data_models updated for pydantic 1.10 ([`4e525ae`](https://github.com/Mjvolk3/torchcell/commit/4e525aebe923147f1cf9f2800cf7726b10ffbae8))

* new actions ([`20f00c7`](https://github.com/Mjvolk3/torchcell/commit/20f00c7af1933c655cbb4f59e09943201d9664c0))

* docs ([`7d1cfc3`](https://github.com/Mjvolk3/torchcell/commit/7d1cfc3693ef81e6c2b8e2541b16eeb8b1306554))

* tutorial ([`3660bd3`](https://github.com/Mjvolk3/torchcell/commit/3660bd33680d61cc45d30812e2ad2b053a06348e))

* llm push ([`14eff9b`](https://github.com/Mjvolk3/torchcell/commit/14eff9bbdf1fce0e76c0107a1c7afe82552c6ee5))

* docs move ([`ec42b9a`](https://github.com/Mjvolk3/torchcell/commit/ec42b9a2bac96ca345e5ea3ddfe20d78215c5374))

* remove hidden notes ([`4252172`](https://github.com/Mjvolk3/torchcell/commit/42521722229c7c6518f3b42c6ff9dd7ff9a27057))

* readme update ([`4cc7ed9`](https://github.com/Mjvolk3/torchcell/commit/4cc7ed9499fb9b188b2367887c005b12213a7004))

* action update format on push ([`2e200e5`](https://github.com/Mjvolk3/torchcell/commit/2e200e5b10b3254ea3ebd95edce26df6d64c7d9b))

* workspace refactor ([`5a8a9d8`](https://github.com/Mjvolk3/torchcell/commit/5a8a9d8025ea47ae74105d159c220e92150cf31d))

* rm dendron temp files ([`deb3782`](https://github.com/Mjvolk3/torchcell/commit/deb37821177b8da9a8495d33556534e25ffb0f83))

* task note ([`67485a1`](https://github.com/Mjvolk3/torchcell/commit/67485a1d2fe1e9509bc0c9cf86fe2e68cf95b375))

* py dump ([`ec4256a`](https://github.com/Mjvolk3/torchcell/commit/ec4256af14424dd619b3c64beca77327bff76a79))

* delete scrap model lin on nt tformer ([`8d602bd`](https://github.com/Mjvolk3/torchcell/commit/8d602bdad9f34c875b638218efa94afad100b70b))

* deep set drawing ([`f8a5ddc`](https://github.com/Mjvolk3/torchcell/commit/f8a5ddc488bfcfaf28207a2ea401d0ee2eac995e))

* scrap model, smf fitnes pred lin on nt tformer ([`a6d833f`](https://github.com/Mjvolk3/torchcell/commit/a6d833fbd1fd374dd4ffb357c32af7a7b5b1398d))

* s288c feature types ([`c770f28`](https://github.com/Mjvolk3/torchcell/commit/c770f2886560520c321f160e1e60cae430d09057))

* dmypy json, not sure if needed ([`29278d3`](https://github.com/Mjvolk3/torchcell/commit/29278d3df52ca7c23f9d553fa0a7008297642fce))

* naming ([`f9d40ed`](https://github.com/Mjvolk3/torchcell/commit/f9d40ed07506e6f94189ea47962017d8c2103bb6))

* test sequence.py ([`df9b04b`](https://github.com/Mjvolk3/torchcell/commit/df9b04b7e586c9dac7a01115ec8375055f757daa))

* gene_list property ([`05d92ce`](https://github.com/Mjvolk3/torchcell/commit/05d92ceec5eb3d3fa293288f33640354ac4cbb60))

* correct seq len calc ([`3241317`](https://github.com/Mjvolk3/torchcell/commit/3241317a42510df2caca36f940145d0caaeaeff4))

* make mito first chr index 0 in contansts ([`e044e67`](https://github.com/Mjvolk3/torchcell/commit/e044e67e5c002930940674b91811a18c8bd27e14))

* fix inequality value error ([`a46286d`](https://github.com/Mjvolk3/torchcell/commit/a46286d9a0dee8e1fd0c653f6ea75c253b97911c))

* deleted files ([`04cbe8c`](https://github.com/Mjvolk3/torchcell/commit/04cbe8c255bc056d811427421378a106561356a3))

* imports - import trick ([`122becc`](https://github.com/Mjvolk3/torchcell/commit/122becc8af3a9083acc94c5ca79dbb23934437eb))

* dna window resut works ([`d55d02f`](https://github.com/Mjvolk3/torchcell/commit/d55d02fdc096f18e3e58ad39bbeb4c11858812ec))

* DnaWindowResult and dna window helpers ([`2def395`](https://github.com/Mjvolk3/torchcell/commit/2def395fb678de1db0c9da829571ef596f01199a))

* 60kb typo fix ([`3fd00e5`](https://github.com/Mjvolk3/torchcell/commit/3fd00e596e83fb570d6d41d79e847a8a26e5dbe2))

* mito to chromosome const ([`4e5a870`](https://github.com/Mjvolk3/torchcell/commit/4e5a870ee19f9a22a485a1b27f277b520aed6512))

* init import trick ([`e0edc36`](https://github.com/Mjvolk3/torchcell/commit/e0edc36471435b2134bb446e9943a3b1296fb039))

* sequence.py sgd yeast ([`965ab96`](https://github.com/Mjvolk3/torchcell/commit/965ab9640216f9c7ee9e67a5f17cace77e932b2a))

* sequence torch library ([`158dd2f`](https://github.com/Mjvolk3/torchcell/commit/158dd2f7e79649f9538959c8834ec5429596d77d))

* workspace config ([`604bfb0`](https://github.com/Mjvolk3/torchcell/commit/604bfb0e527d6b9f7bc606329dec7c5e6496400e))

* dendron msc ([`d339a34`](https://github.com/Mjvolk3/torchcell/commit/d339a344980954a01e74737e7b5d9f9d5ecacb08))

* readme update ([`6597c04`](https://github.com/Mjvolk3/torchcell/commit/6597c04c40d7a1006947d98f863dba7ab5091ebe))

* src dump ([`b8d79ec`](https://github.com/Mjvolk3/torchcell/commit/b8d79ec587de45064684019ea19339714a58193a))

* docs ([`0fd8716`](https://github.com/Mjvolk3/torchcell/commit/0fd87168645a79b253a1c008a68dce1a09d56105))

* notes ([`4a1de25`](https://github.com/Mjvolk3/torchcell/commit/4a1de25ae1c4548eea71a3e15f2cc055c30ef093))

* pipeline image update ([`2437cdb`](https://github.com/Mjvolk3/torchcell/commit/2437cdb302496c9988827ae69b3df7d7168fb49b))

* locus pydantic check ([`9764d2e`](https://github.com/Mjvolk3/torchcell/commit/9764d2e10520d1eaded9e3759dcce966ed327b72))

* sgd no async ([`09c8cee`](https://github.com/Mjvolk3/torchcell/commit/09c8ceecc027a52a6132d9592f828f8545131ce4))

* first commit ([`6fad713`](https://github.com/Mjvolk3/torchcell/commit/6fad7130cab6a5d0d432d9f645f4ee45087ab12d))

* Initial commit ([`ff9f291`](https://github.com/Mjvolk3/torchcell/commit/ff9f2912ea32a958aa905774d543112fda42bf88))