Code

Flash v2 #137

Code

Draft

hypnopump wants to merge 92 commits intodptech-corp:maindptech-corp/Uni-Fold:mainfrom hypnopump:hypnopump/flashattn2hypnopump/Uni-Fold:hypnopump/flashattn2Copy head branch name to clipboard

+8,107-298

Commits

Commits on Aug 1, 2022

• Refine documentation (dptech-corp#1)

  Show description for 87a05d2
  ZiyaoLi

  authored
  87a05d2

• add the convert script and alphafold original configs (dptech-corp#2)

  BaozCWJ

  authored
  c900ca8

• change scripts, example data and introduction (dptech-corp#3)

  Show description for e2d555c
  ZiyaoLi

  authored
  e2d555c

• fix typos (dptech-corp#4)

  ZiyaoLi

  authored
  aad1250

• add docker auto-build workflow (dptech-corp#5)

  guolinke

  authored
  6d24472

• add a simple install command (dptech-corp#6)

  guolinke

  authored
  087f49c

• code clean for imports

  guolinke

  committed
  7553b29

• fix violation loss weight in monomer fine-tune

  guolinke

  authored
  bb2d556

Commits on Aug 2, 2022

• add the convert script for AlphaFold and modify the README (dptech-corp#7)

  Show description for 2e30eb9
  BaozCWJ

  authored
  2e30eb9

• improve details (dptech-corp#8)

  ZiyaoLi

  authored
  0153644

• add evaluation set (dptech-corp#9)

  ZiyaoLi

  authored
  a2b00e8

Commits on Aug 3, 2022

• add the description about downloading Uni-Fold pretrained model parameters (dptech-corp#11)

  BaozCWJ

  authored
  f5a4157

• add script for benchmarking & benchmark results (dptech-corp#10)

  Show description for 7c7ea7b
  guolinke

  authored
  7c7ea7b

Commits on Aug 5, 2022

• dynamic length for extra_msa

  guolinke

  committed
  d167d60

• add config for model_1_ft

  guolinke

  authored
  f50639e

• fix feature stack of recycling

  guolinke

  committed
  a97d7e9

Commits on Aug 6, 2022

• Update README.md

  guolinke

  authored
  d0c4c13

• refine model parameters descriptions

  guolinke

  committed
  32fbcf9

• citation (dptech-corp#12)

  ZiyaoLi

  authored
  c2c12c3

• add evaluation results (dptech-corp#13)

  Show description for b88286f
  ZiyaoLi

  authored
  b88286f

Commits on Aug 9, 2022

• link to nvidia-docker-2 (dptech-corp#16)

  ZiyaoLi

  authored
  2f633b6

• use bf16 in demo by default

  guolinke

  committed
  e05de86

Commits on Aug 10, 2022

• Hermite (dptech-corp#17)

  Show description for 782592c
  ZiyaoLi

  authored
  782592c

Commits on Aug 12, 2022

• save extra msa mem (dptech-corp#18)

  Show description for 7fe51ed
  

  ZiyaoLi

  and

  guolinke

  authored
  7fe51ed

• add the colab version of Uni-Fold (dptech-corp#19)

  Show description for 21754b8
  BaozCWJ

  authored
  21754b8

• fix the error of unexpected keyword argument in unifold.ipynb (dptech-corp#21)

  BaozCWJ

  authored
  adb011d

• hide the code blocks for default setting (dptech-corp#22)

  BaozCWJ

  authored
  cf6cb27

• add citation

  guolinke

  committed
  89f8efb

• update the license in colab notebook

  guolinke

  committed
  ffe132c

• fix the error about pair.a3m (dptech-corp#24)

  BaozCWJ

  authored
  94fffd8

• add the section of download for colab notebook (dptech-corp#25)

  Show description for 58fedb1
  BaozCWJ

  authored
  58fedb1

• Update unifold.ipynb

  guolinke

  authored
  931703d

• Update unifold.ipynb

  guolinke

  authored
  dd4ad8f

• refine notebook descriptions

  guolinke

  committed
  5daf108

• fix typo in notebook

  guolinke

  authored
  b418f72

• [colab] less verbosity & faster hhsuite installation

  guolinke

  committed
  0daa5e0

Commits on Aug 13, 2022

• Update unifold.ipynb

  guolinke

  authored
  8f239d8

• Update README.md

  guolinke

  authored
  42295f3

Commits on Aug 14, 2022

• Update setup.py

  guolinke

  authored
  dbe9ed6

• [colab] fix wheel for p100

  guolinke

  committed
  572d450

• refine unicore installation

  guolinke

  committed
  9126d38

• fix typo in dockerfile

  guolinke

  committed
  ba152ad

• add links in the header.

  guolinke

  committed
  68787e2

• Update README.md

  guolinke

  authored
  78352bd

• optimize the consumption of memory in inference with chunked setting (dptech-corp#27)

  Show description for 768908b
  

  BaozCWJ

  and

  guolinke

  authored
  768908b

Commits on Aug 16, 2022

• correct the denominator of average memory in benchmark; fix the tri_mul_in/out in template when chunked inference (dptech-corp#29)

  BaozCWJ

  authored
  c676727

Commits on Aug 18, 2022

• add TODO tag into template pair stack

  guolinke

  authored
  52dc273

• Add BladeDISC Introduction to Readme. (dptech-corp#31)

  yuchaoli

  authored
  8ad306f

Commits on Aug 21, 2022

• update bioRxiv url

  guolinke

  authored
  d57a199

Commits on Aug 22, 2022

• optimize the memory efficiency for Inference (dptech-corp#32)

  Show description for 8acf998
  

  BaozCWJ

  and

  guolinke

  authored
  8acf998

Commits on Aug 24, 2022

• reduce memory cost in multimer inference (dptech-corp#33)

  Show description for 78f860f
  

  guolinke

  and

  BaozCWJ

  authored
  78f860f

Commits on Aug 25, 2022

• feat(docker): Add opencontainers image-spec to Dockerfile (dptech-corp#34)

  Show description for ef5b88f
  SauravMaheshkar

  authored
  ef5b88f

• fix potential bug of is_monomer arg passing (dptech-corp#35)

  ZiyaoLi

  authored
  8b8fc0a

Commits on Aug 26, 2022

• Update Dockerfile

  guolinke

  authored
  b0d7ec5

• update mode option for inference (dptech-corp#36)

  BaozCWJ

  authored
  1d130ef

Commits on Aug 31, 2022

• swap case study (dptech-corp#39)

  ZiyaoLi

  authored
  74a63ef

Commits on Sep 1, 2022

• add the automatic settings of block size for various lengths of prediction (dptech-corp#38)

  Show description for 52adabe
  BaozCWJ

  authored
  52adabe

Commits on Sep 7, 2022

• change the definition of target name, which will directly depends on fasta file (dptech-corp#42)

  BaozCWJ

  authored
  dfdebfb

• UF-Symmetry inference code (dptech-corp#44)

  Show description for f1f7baa
  ZiyaoLi

  authored
  f1f7baa

• minor fix of uf-symmetry (dptech-corp#45)

  Show description for 79b5811
  ZiyaoLi

  authored
  79b5811

• fix typo

  ZiyaoLi

  authored
  e6d076f

Commits on Sep 9, 2022

• fix download link in README.md (dptech-corp#47)

  avilella

  authored
  02adce3

• update paper link in readme

  guolinke

  authored
  fb7e757

• Update download_pdb70.sh (dptech-corp#48)

  avilella

  authored
  f06b1b0

• prevent the redundant processes when touching run all (dptech-corp#49)

  BaozCWJ

  authored
  1c8238e

Commits on Sep 16, 2022

• change the download source of uf symmetry parameters to google drive (dptech-corp#51)

  BaozCWJ

  authored
  8dae0b7

Commits on Sep 22, 2022

• Refine colab notebook (dptech-corp#52)

  Show description for 86ea44b
  

  ZiyaoLi

  and

  guolinke

  authored
  86ea44b

Commits on Sep 27, 2022

• add the default chains.txt for single-chain fasta (dptech-corp#54)

  BaozCWJ

  authored
  abe7f88

Commits on Oct 10, 2022

• change default model name (dptech-corp#61)

  Show description for 4e65a4e
  ZiyaoLi

  authored
  4e65a4e

Commits on Oct 19, 2022

• move model parameters to github release (dptech-corp#64)

  guolinke

  authored
  029b078

Commits on Oct 29, 2022

• fix uf-symmetry wget url (dptech-corp#68)

  Show description for 2ae159d
  ZiyaoLi

  authored
  2ae159d

Commits on Nov 1, 2022

• skip download af params (dptech-corp#70)

  Show description for 5a93161
  ZiyaoLi

  authored
  5a93161

Commits on Nov 8, 2022

• refine colab notebook (dptech-corp#72)

  Show description for de21c73
  ZiyaoLi

  authored
  de21c73

Commits on Nov 15, 2022

• Add documentation about the full dataset download (dptech-corp#75)

  guolinke

  authored
  6730e3b

Commits on Nov 21, 2022

• refine cmd line for model names (dptech-corp#76)

  guolinke

  authored
  1fd074b

Commits on Dec 1, 2022

• move colab url from google drive to github release (dptech-corp#78)

  Show description for 5c223a1
  ZiyaoLi

  authored
  5c223a1

• mv to py38 to satisfy colab (dptech-corp#79)

  Show description for 856e8ea
  ZiyaoLi

  authored
  856e8ea

Commits on Dec 12, 2022

• add script for the evaluation (dptech-corp#82)

  guolinke

  authored
  5b87b7e

Commits on Jan 6, 2023

• add script for label extraction (dptech-corp#89)

  teslacool

  authored
  ab4b89a

Commits on Jan 12, 2023

• fix type after model.float() (dptech-corp#92)

  teslacool

  authored
  413c78b

Commits on Feb 15, 2023

• update get assembly from mmcif (dptech-corp#96)

  Show description for b57e54a
  teslacool

  authored
  b57e54a

Commits on Mar 3, 2023

• add dataset download via Volcengine (dptech-corp#103)

  Show description for 61edb37
  

  guolinke

  and

  ZiyaoLi

  authored
  61edb37

Commits on Mar 24, 2023

• Update unifold.ipynb (dptech-corp#109)

  ZiyaoLi

  authored
  cc2ede9

Commits on Apr 11, 2023

• add symmetry utils to process input structures (dptech-corp#110)

  Show description for cc7a511
  ZiyaoLi

  authored
  cc7a511

Commits on May 9, 2023

• fix import libmsym (dptech-corp#117)

  ZiyaoLi

  authored
  5596948

Commits on May 11, 2023

• Update unifold.ipynb to cu118torch2.0.0-cp310 (dptech-corp#118)

  ZiyaoLi

  authored
  a94b03c

• tolerate inconsistencies between pdb_assembly and multi_label (dptech-corp#119)

  Show description for a272252
  ZiyaoLi

  authored
  a272252

Commits on Jun 12, 2023

• add alphafold v3 param parse & config (dptech-corp#122)

  ZiyaoLi

  authored
  af278f0

Commits on Jun 19, 2023

• correct load v3 (dptech-corp#125)

  teslacool

  authored
  7e03aa2

Commits on Oct 21, 2023

• adding flash v2 torch for mask, custom for bias

  hypnopump

  committed
  263d6dd

Commits on Dec 21, 2023

• 40% faster but grads are nan

  hypnopump

  committed
  9fa677d

• 40% faster but grads are nan

  hypnopump

  committed
  189443e