Implementation and replication of ProGen, Language Modeling for Protein Generation, in Jax

Related tags

Deep Learning deep-learning proteins artificial-intelligence
Overview

ProGen - (wip)

Implementation and replication of ProGen, Language Modeling for Protein Generation, in Pytorch and Jax (the weights will be made easily transferrable between the two)

Install

$ pip install progen-transformer

Usage

from jax import random
from haiku import PRNGSequence
from progen_transformer import ProGen

model = ProGen(
    num_tokens = 256,
    dim = 512,
    seq_len = 1024,
    window_size = 256,       # local attention window size
    depth = 12,              # depth
    heads = 8,               # attention heads
    dim_head = 64,           # dimension per head
    ff_glu = True,           # use GLU in feedforward, from Noam's paper
    global_mlp_depth = 2     # last N global gmlp layers
)

rng = PRNGSequence(42)
seq = random.randint(next(rng), (1024,), 0, 256)

params = model.init(next(rng), seq)
logits = model.apply(params, next(rng), seq) # (1024, 256)

Training from Uniref

Download Uniref50 from UniProt and place uniref50.fasta in the root directory

$ python gen_train_data.py

You should see a lot of green if everything succeeds. Then

$ python train.py

By default, the script will checkpoint and resume automatically, but if you wish to clear your progress and restart, just add a --new flag

$ python train.py --new

Model checkpoints will be saved periodically to ./ckpts

Todo

  • train tfrecords from google cloud storage path
  • generate validation tfrecords
  • add panda integration with GO annotations
  • resume from correct place in tfrecord even if batch size is changed inbetween runs, display number of sequences processed (aiming for 1 billion)
  • model parallelism with pjit
  • bfloat16 on xla
  • checkpoint and resume from a google cloud storage path
  • config to annotation to template string with jinja2 - use jinja2 for wandb html logging as well
  • manage experimental tracker state, and also allow ability to turn it off by piping to noop
  • add a confirmation before clearing a folder for --new run
  • engineer mask in cross entropy loss so that padding can be reused as end-of-string token
  • flip seq # annotation order with prob set in config
  • keep N last checkpoints

Citations

@misc{madani2020progen,
    title   = {ProGen: Language Modeling for Protein Generation}, 
    author  = {Ali Madani and Bryan McCann and Nikhil Naik and Nitish Shirish Keskar and Namrata Anand and Raphael R. Eguchi and Po-Ssu Huang and Richard Socher},
    year    = {2020},
    eprint  = {2004.03497},
    archivePrefix = {arXiv},
    primaryClass = {q-bio.BM}
}
@misc{su2021roformer,
    title   = {RoFormer: Enhanced Transformer with Rotary Position Embedding},
    author  = {Jianlin Su and Yu Lu and Shengfeng Pan and Bo Wen and Yunfeng Liu},
    year    = {2021},
    eprint  = {2104.09864},
    archivePrefix = {arXiv},
    primaryClass = {cs.CL}
}
@misc{shazeer2020glu,
    title   = {GLU Variants Improve Transformer},
    author  = {Noam Shazeer},
    year    = {2020},
    url     = {https://arxiv.org/abs/2002.05202}
}
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Comments
  • protein bert uniref90 dataset

    protein bert uniref90 dataset

    (discussed in discord)

    after running the first step (create_uniref_db) of https://github.com/nadavbra/protein_bert I got a 24GB file "uniref_proteins_and_annotations.db" . It seems it could be useful for generate sequences for this project, sharing the links there

    • https://gitlab.com/rom1504/uniref data
    • colab to get the db and do a few queries https://colab.research.google.com/drive/1BGYEBDmD0yToLNou2T-t-QbJV5wCtIBz#scrollTo=21U3PpCp-pxr There are 135301051 records in the db, in a table looking like:
    CREATE TABLE "protein_annotations" (
    "index"    INTEGER,
    "tax_id"    REAL,
    "uniprot_name"    TEXT,
    "go_annotations"    TEXT,
    "flat_go_annotations"    TEXT,
    "n_go_annotations"    INTEGER,
    "complete_go_annotation_indices"    TEXT,
    "n_complete_go_annotations"    INTEGER
);

    Sample look like this:

    | | index | tax_id | uniprot_name | go_annotations | flat_go_annotations | n_go_annotations | complete_go_annotation_indices | n_complete_go_annotations | |---:|--------:|-----------------:|:-----------------|:----------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------|-------------------:|:---------------------------------|----------------------------:| | 0 | 0 | 1.57204e+06 | A0A5A9P0L4_9TELE | {"GO Molecular Function": ["GO:0003755", "GO:0005524", "GO:0004672", "GO:0005509"], "GO Biological Process": [], "GO Cellular Component": []} | ["GO:0003755", "GO:0004672", "GO:0005509", "GO:0005524"] | 4 | [2761, 3561, 4193, 4205] | 4 | | 1 | 1 | 648755 | UPI0016133188 | {"GO Molecular Function": [], "GO Biological Process": [], "GO Cellular Component": []} | [] | 0 | [] | 0 | | 2 | 2 | 1.93059e+06 | A0A410P257_9BACT | {"GO Molecular Function": [], "GO Biological Process": [], "GO Cellular Component": []} | [] | 0 | [] | 0 | | 3 | 3 | 519421 | UPI0019403D63 | {"GO Molecular Function": [], "GO Biological Process": [], "GO Cellular Component": []} | [] | 0 | [] | 0 | | 4 | 4 | 72004 | A0A6B0RPA5_9CETA | {"GO Molecular Function": ["GO:0005524", "GO:0004672"], "GO Biological Process": [], "GO Cellular Component": []} | ["GO:0004672", "GO:0005524"] | 2 | [3561, 4205] | 2 | | 5 | 5 | 375764 | A0A672ZWI7_9TELE | {"GO Molecular Function": [], "GO Biological Process": [], "GO Cellular Component": []} | [] | 0 | [] | 0 | | 6 | 6 | 1.41558e+06 | A0A6P7YNV3_9AMPH | {"GO Molecular Function": ["GO:0005524", "GO:0004672"], "GO Biological Process": [], "GO Cellular Component": ["GO:0005886"]} | ["GO:0004672", "GO:0005524", "GO:0005886"] | 3 | [3561, 4205, 4526] | 3 | | 7 | 7 | 240159 | A0A4U5TZD8_COLLU | {"GO Molecular Function": ["GO:0005524", "GO:0004672"], "GO Biological Process": [], "GO Cellular Component": ["GO:0016021", "GO:0005886"]} | ["GO:0004672", "GO:0005524", "GO:0005886", "GO:0016021"] | 4 | [3561, 4205, 4526, 10019] | 4 | | 8 | 8 | 146911 | UPI00074FFD9C | {"GO Molecular Function": [], "GO Biological Process": [], "GO Cellular Component": []} | [] | 0 | [] | 0 | | 9 | 9 | 260995 | A0A6P8RG40_GEOSA | {"GO Molecular Function": ["GO:0005524", "GO:0004672"], "GO Biological Process": [], "GO Cellular Component": ["GO:0005886"]} | ["GO:0004672", "GO:0005524", "GO:0005886"] | 3 | [3561, 4205, 4526] | 3 |

    opened by rom1504 4
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Owner
Phil Wang
Working with Attention
Phil Wang
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