progen-torch 0.0.4

Paper - Pytorch

Progen

Implementation of Progen in Pytorch, from the paper "ProGen: Language Modeling for Protein Generation"

GPT for proteins sequences

Paper Link

Appreciation

• Lucidrains
• Agorians

Install

pip install progen-torch

Usage

import torch
from progen.model import ProGen

x = torch.randint(0, 100, (1, 1024))
import torch
from progen.model import ProGen

x = torch.randint(0, 100, (1, 1024))

# Initialize the model with specific parameters
model = ProGen(
    num_tokens=100,  # The size of the vocabulary
    dim=512,  # The dimension of the embeddings
    seq_len=1024,  # The length of the sequences
    depth=6,  # The number of layers in the model
    window_size=256,  # The size of the window for local attention
    global_mlp_depth=2,  # The depth of the MLP in the global attention mechanism
    heads=8,  # The number of attention heads
    dim_head=512,  # The dimension of each attention head
    ff_mult=4,  # The multiplier for the feed-forward network's hidden layer size
    ff_glu=True,  # Whether to use a GLU activation in the feed-forward network
    attn_dim=None,  # The dimension of the attention mechanism (None means it defaults to `dim`)
    clamp_gate=True,  # Whether to clamp the gate values in the GLU activation
    shift_tokens=True,  # Whether to shift the tokens for the causal attention mechanism
    dropout=0.1,  # The dropout rate
)

# Forward pass through the model
logits = model(x)

# The output is the logits for each token in the vocabulary, for each position in the input sequences
# Shape: (batch_size, sequence_length, num_tokens)
print(logits.shape)  # Should print: torch.Size([1, 1024, 100])

Dataset Strategy

Here is a table of the datasets used in the paper with metadata and source links:

Dataset	Description	Source
Uniparc	Contains protein sequences from various sources	https://www.uniprot.org/uniparc/
UniprotKB	Contains protein sequences and annotations	https://www.uniprot.org/uniprot/
SWISS-PROT	Curated protein sequence database	https://www.uniprot.org/swiss-prot/
TrEMBL	Computer-annotated protein sequences	https://www.uniprot.org/trembl/
Pfam	Database of protein families	https://pfam.xfam.org/
NCBI taxonomy	Taxonomic classification of organisms	https://www.ncbi.nlm.nih.gov/taxonomy

Here is a diagram showing the data preprocessing flow:

graph TD
    A[Uniparc] --> B[Filter and merge]
    C[UniprotKB] --> B
    D[SWISS-PROT] --> B 
    E[TrEMBL] --> B
    F[Pfam] --> B
    G[NCBI taxonomy] --> B
    B --> H[Train/test split]
    H --> I[Train set]
    H --> J[ID test set] 
    H --> K[OOD test set]

The Uniparc, UniprotKB, SWISS-PROT, TrEMBL, Pfam, and NCBI taxonomy datasets are filtered and merged in step B. The aggregated dataset is then split into training, in-distribution test, and out-of-distribution test sets in step H.

Architecture

Todo

License

MIT

Citations