python_code stringlengths 0 4.04M | repo_name stringlengths 7 58 | file_path stringlengths 5 147 |
|---|---|---|
# Copyright (c) Meta Platforms, Inc. and affiliates.
# All rights reserved.
#
# This source code is licensed under the license found in the
# LICENSE file in the root directory of this source tree.
import torch
import torch.nn.functional as F
import numpy as np
from tqdm import tqdm
from scipy.spatial import KDTree
... | CT2Hair-main | CT2Hair/modules/strands_opt.py |
# Copyright (c) Meta Platforms, Inc. and affiliates.
# All rights reserved.
#
# This source code is licensed under the license found in the
# LICENSE file in the root directory of this source tree.
import os
import csv
import torch
import torch.nn as nn
from modules.networks import *
from utils.utils import batched... | CT2Hair-main | CT2Hair/modules/strands_codec.py |
# Copyright (c) Meta Platforms, Inc. and affiliates.
# All rights reserved.
#
# This source code is licensed under the license found in the
# LICENSE file in the root directory of this source tree.
import copy
import torch
import inspect
import numpy as np
from typing import Dict, List, Optional, Tuple
from torch.nn... | CT2Hair-main | CT2Hair/modules/networks.py |
# Copyright (c) Meta Platforms, Inc. and affiliates.
# All rights reserved.
#
# This source code is licensed under the license found in the
# LICENSE file in the root directory of this source tree.
import os
import sys
import argparse
from pyhocon import ConfigFactory
from termcolor import colored
sys.path.append('C... | CT2Hair-main | scripts/interpolation.py |
# Copyright (c) Meta Platforms, Inc. and affiliates.
# All rights reserved.
#
# This source code is licensed under the license found in the
# LICENSE file in the root directory of this source tree.
import os
import sys
import argparse
from pyhocon import ConfigFactory
from termcolor import colored
sys.path.append('C... | CT2Hair-main | scripts/optimization.py |
# Copyright (c) Meta Platforms, Inc. and affiliates.
# All rights reserved.
#
# This source code is licensed under the license found in the
# LICENSE file in the root directory of this source tree.
import os
import platform
import argparse
from pyhocon import ConfigFactory
from termcolor import colored
parser = argp... | CT2Hair-main | scripts/est_orientations.py |
# Copyright (c) Meta Platforms, Inc. and affiliates.
# All rights reserved.
#
# This source code is licensed under the license found in the
# LICENSE file in the root directory of this source tree.
import os
import platform
import argparse
from shutil import copyfile
from pyhocon import ConfigFactory
from termcolor i... | CT2Hair-main | scripts/gen_guide_strands.py |
"""Copyright (c) Facebook, Inc. and its affiliates.
All rights reserved.
This source code is licensed under the license found in the
LICENSE file in the root directory of this source tree.
Portions of the source code are from the n2nmn project which
notice below and in LICENSE.n2nmn in the root directory of
this sour... | corefnmn-main | models_vd/decoder.py |
"""Copyright (c) Facebook, Inc. and its affiliates.
All rights reserved.
This source code is licensed under the license found in the
LICENSE file in the root directory of this source tree.
Portions of the source code are from the n2nmn project which
notice below and in LICENSE.n2nmn in the root directory of
this sour... | corefnmn-main | models_vd/generator_attnet.py |
corefnmn-main | models_vd/__init__.py | |
"""Copyright (c) Facebook, Inc. and its affiliates.
All rights reserved.
This source code is licensed under the license found in the
LICENSE file in the root directory of this source tree.
Portions of the source code are from the n2nmn project which
notice below and in LICENSE.n2nmn in the root directory of
this sour... | corefnmn-main | models_vd/assembler.py |
"""Copyright (c) Facebook, Inc. and its affiliates.
All rights reserved.
This source code is licensed under the license found in the
LICENSE file in the root directory of this source tree.
Portions of the source code are from the n2nmn project which
notice below and in LICENSE.n2nmn in the root directory of
this sour... | corefnmn-main | models_vd/model.py |
"""Copyright (c) Facebook, Inc. and its affiliates.
All rights reserved.
This source code is licensed under the license found in the
LICENSE file in the root directory of this source tree.
Portions of the source code are from the n2nmn project which
notice below and in LICENSE.n2nmn in the root directory of
this sour... | corefnmn-main | models_vd/generator.py |
"""Copyright (c) Facebook, Inc. and its affiliates.
All rights reserved.
This source code is licensed under the license found in the
LICENSE file in the root directory of this source tree.
Portions of the source code are from the n2nmn project which
notice below and in LICENSE.n2nmn in the root directory of
this sour... | corefnmn-main | models_vd/modules.py |
"""Copyright (c) Facebook, Inc. and its affiliates.
All rights reserved.
This source code is licensed under the license found in the
LICENSE file in the root directory of this source tree.
Portions of the source code are from the n2nmn project which
notice below and in LICENSE.n2nmn in the root directory of
this sour... | corefnmn-main | models_vd/executor.py |
"""Copyright (c) Facebook, Inc. and its affiliates.
All rights reserved.
This source code is licensed under the license found in the
LICENSE file in the root directory of this source tree.
Portions of the source code are from the n2nmn project which
notice below and in LICENSE.n2nmn in the root directory of
this sour... | corefnmn-main | util/metrics.py |
"""Copyright (c) Facebook, Inc. and its affiliates.
All rights reserved.
This source code is licensed under the license found in the
LICENSE file in the root directory of this source tree.
Portions of the source code are from the n2nmn project which
notice below and in LICENSE.n2nmn in the root directory of
this sour... | corefnmn-main | util/support.py |
"""Copyright (c) Facebook, Inc. and its affiliates.
All rights reserved.
This source code is licensed under the license found in the
LICENSE file in the root directory of this source tree.
Portions of the source code are from the n2nmn project which
notice below and in LICENSE.n2nmn in the root directory of
this sour... | corefnmn-main | util/clean.py |
"""Copyright (c) Facebook, Inc. and its affiliates.
All rights reserved.
This source code is licensed under the license found in the
LICENSE file in the root directory of this source tree.
Portions of the source code are from the n2nmn project which
notice below and in LICENSE.n2nmn in the root directory of
this sour... | corefnmn-main | util/convert_nmn_layouts.py |
"""Copyright (c) Facebook, Inc. and its affiliates.
All rights reserved.
This source code is licensed under the license found in the
LICENSE file in the root directory of this source tree.
Portions of the source code are from the n2nmn project which
notice below and in LICENSE.n2nmn in the root directory of
this sour... | corefnmn-main | util/extract_coreference_supervision.py |
"""Copyright (c) Facebook, Inc. and its affiliates.
All rights reserved.
This source code is licensed under the license found in the
LICENSE file in the root directory of this source tree.
Portions of the source code are from the n2nmn project which
notice below and in LICENSE.n2nmn in the root directory of
this sour... | corefnmn-main | util/text_processing.py |
"""Copyright (c) Facebook, Inc. and its affiliates.
All rights reserved.
This source code is licensed under the license found in the
LICENSE file in the root directory of this source tree.
Portions of the source code are from the n2nmn project which
notice below and in LICENSE.n2nmn in the root directory of
this sour... | corefnmn-main | util/collect_glove_features.py |
"""Copyright (c) Facebook, Inc. and its affiliates.
All rights reserved.
This source code is licensed under the license found in the
LICENSE file in the root directory of this source tree.
Portions of the source code are from the n2nmn project which
notice below and in LICENSE.n2nmn in the root directory of
this sour... | corefnmn-main | util/build_imdb_mnist.py |
corefnmn-main | util/__init__.py | |
"""Copyright (c) Facebook, Inc. and its affiliates.
All rights reserved.
This source code is licensed under the license found in the
LICENSE file in the root directory of this source tree.
Portions of the source code are from the n2nmn project which
notice below and in LICENSE.n2nmn in the root directory of
this sour... | corefnmn-main | util/cnn.py |
"""Copyright (c) Facebook, Inc. and its affiliates.
All rights reserved.
This source code is licensed under the license found in the
LICENSE file in the root directory of this source tree.
Portions of the source code are from the n2nmn project which
notice below and in LICENSE.n2nmn in the root directory of
this sour... | corefnmn-main | util/dataset_to_text.py |
"""Copyright (c) Facebook, Inc. and its affiliates.
All rights reserved.
This source code is licensed under the license found in the
LICENSE file in the root directory of this source tree.
Portions of the source code are from the n2nmn project which
notice below and in LICENSE.n2nmn in the root directory of
this sour... | corefnmn-main | util/compress_parser_trees.py |
"""Copyright (c) Facebook, Inc. and its affiliates.
All rights reserved.
This source code is licensed under the license found in the
LICENSE file in the root directory of this source tree.
Portions of the source code are from the n2nmn project which
notice below and in LICENSE.n2nmn in the root directory of
this sour... | corefnmn-main | util/build_imdb.py |
#!/usr/bin/env python2
"""Copyright (c) Facebook, Inc. and its affiliates.
All rights reserved.
This source code is licensed under the license found in the
LICENSE file in the root directory of this source tree.
Portions of the source code are from the n2nmn project which
notice below and in LICENSE.n2nmn in the root... | corefnmn-main | util/parse.py |
"""Copyright (c) Facebook, Inc. and its affiliates.
All rights reserved.
This source code is licensed under the license found in the
LICENSE file in the root directory of this source tree.
Portions of the source code are from the n2nmn project which
notice below and in LICENSE.n2nmn in the root directory of
this sour... | corefnmn-main | util/empty_safe_conv.py |
"""Copyright (c) Facebook, Inc. and its affiliates.
All rights reserved.
This source code is licensed under the license found in the
LICENSE file in the root directory of this source tree.
Portions of the source code are from the n2nmn project which
notice below and in LICENSE.n2nmn in the root directory of
this sour... | corefnmn-main | exp_mnist/options.py |
"""Copyright (c) Facebook, Inc. and its affiliates.
All rights reserved.
This source code is licensed under the license found in the
LICENSE file in the root directory of this source tree.
Portions of the source code are from the n2nmn project which
notice below and in LICENSE.n2nmn in the root directory of
this sour... | corefnmn-main | exp_mnist/visualize_sl.py |
"""Copyright (c) Facebook, Inc. and its affiliates.
All rights reserved.
This source code is licensed under the license found in the
LICENSE file in the root directory of this source tree.
Portions of the source code are from the n2nmn project which
notice below and in LICENSE.n2nmn in the root directory of
this sour... | corefnmn-main | exp_mnist/eval_sl.py |
"""Copyright (c) Facebook, Inc. and its affiliates.
All rights reserved.
This source code is licensed under the license found in the
LICENSE file in the root directory of this source tree.
Portions of the source code are from the n2nmn project which
notice below and in LICENSE.n2nmn in the root directory of
this sour... | corefnmn-main | exp_mnist/train_sl.py |
"""Copyright (c) Facebook, Inc. and its affiliates.
All rights reserved.
This source code is licensed under the license found in the
LICENSE file in the root directory of this source tree.
Portions of the source code are from the n2nmn project which
notice below and in LICENSE.n2nmn in the root directory of
this sour... | corefnmn-main | loader_mnist/data_reader.py |
"""Copyright (c) Facebook, Inc. and its affiliates.
All rights reserved.
This source code is licensed under the license found in the
LICENSE file in the root directory of this source tree.
Portions of the source code are from the n2nmn project which
notice below and in LICENSE.n2nmn in the root directory of
this sour... | corefnmn-main | vis/html.py |
"""Copyright (c) Facebook, Inc. and its affiliates.
All rights reserved.
This source code is licensed under the license found in the
LICENSE file in the root directory of this source tree.
Portions of the source code are from the n2nmn project which
notice below and in LICENSE.n2nmn in the root directory of
this sour... | corefnmn-main | vis/visualize_dialogs.py |
"""Copyright (c) Facebook, Inc. and its affiliates.
All rights reserved.
This source code is licensed under the license found in the
LICENSE file in the root directory of this source tree.
Portions of the source code are from the n2nmn project which
notice below and in LICENSE.n2nmn in the root directory of
this sour... | corefnmn-main | models_mnist/decoder.py |
"""Copyright (c) Facebook, Inc. and its affiliates.
All rights reserved.
This source code is licensed under the license found in the
LICENSE file in the root directory of this source tree.
Portions of the source code are from the n2nmn project which
notice below and in LICENSE.n2nmn in the root directory of
this sour... | corefnmn-main | models_mnist/generator_attnet.py |
corefnmn-main | models_mnist/__init__.py | |
"""Copyright (c) Facebook, Inc. and its affiliates.
All rights reserved.
This source code is licensed under the license found in the
LICENSE file in the root directory of this source tree.
Portions of the source code are from the n2nmn project which
notice below and in LICENSE.n2nmn in the root directory of
this sour... | corefnmn-main | models_mnist/assembler.py |
"""Copyright (c) Facebook, Inc. and its affiliates.
All rights reserved.
This source code is licensed under the license found in the
LICENSE file in the root directory of this source tree.
Portions of the source code are from the n2nmn project which
notice below and in LICENSE.n2nmn in the root directory of
this sour... | corefnmn-main | models_mnist/model.py |
"""Copyright (c) Facebook, Inc. and its affiliates.
All rights reserved.
This source code is licensed under the license found in the
LICENSE file in the root directory of this source tree.
Portions of the source code are from the n2nmn project which
notice below and in LICENSE.n2nmn in the root directory of
this sour... | corefnmn-main | models_mnist/generator.py |
"""Copyright (c) Facebook, Inc. and its affiliates.
All rights reserved.
This source code is licensed under the license found in the
LICENSE file in the root directory of this source tree.
Portions of the source code are from the n2nmn project which
notice below and in LICENSE.n2nmn in the root directory of
this sour... | corefnmn-main | models_mnist/modules.py |
"""Copyright (c) Facebook, Inc. and its affiliates.
All rights reserved.
This source code is licensed under the license found in the
LICENSE file in the root directory of this source tree.
Portions of the source code are from the n2nmn project which
notice below and in LICENSE.n2nmn in the root directory of
this sour... | corefnmn-main | models_mnist/executor.py |
"""Copyright (c) Facebook, Inc. and its affiliates.
All rights reserved.
This source code is licensed under the license found in the
LICENSE file in the root directory of this source tree.
Portions of the source code are from the n2nmn project which
notice below and in LICENSE.n2nmn in the root directory of
this sour... | corefnmn-main | loader_vd/data_reader.py |
"""Copyright (c) Facebook, Inc. and its affiliates.
All rights reserved.
This source code is licensed under the license found in the
LICENSE file in the root directory of this source tree.
Portions of the source code are from the n2nmn project which
notice below and in LICENSE.n2nmn in the root directory of
this sour... | corefnmn-main | exp_vd/options.py |
r"""Copyright (c) Facebook, Inc. and its affiliates.
All rights reserved.
This source code is licensed under the license found in the
LICENSE file in the root directory of this source tree.
Portions of the source code are from the n2nmn project which
notice below and in LICENSE.n2nmn in the root directory of
this sou... | corefnmn-main | exp_vd/visualize_sl.py |
r"""Copyright (c) Facebook, Inc. and its affiliates.
All rights reserved.
This source code is licensed under the license found in the
LICENSE file in the root directory of this source tree.
Portions of the source code are from the n2nmn project which
notice below and in LICENSE.n2nmn in the root directory of
this sou... | corefnmn-main | exp_vd/eval_sl.py |
r"""Copyright (c) Facebook, Inc. and its affiliates.
All rights reserved.
This source code is licensed under the license found in the
LICENSE file in the root directory of this source tree.
Portions of the source code are from the n2nmn project which
notice below and in LICENSE.n2nmn in the root directory of
this sou... | corefnmn-main | exp_vd/train_sl.py |
# -*- coding: utf-8 -*-
"""HyenaDNA training & inference example (Public)
This code is adapted from the original colab tutorial on HyenaDNA. Check that out for an easier entry point into the code.
We provide the code here as an example for those who want something outside collab, with Huggingface integration.
Origin... | hyena-dna-main | standalone_hyenadna.py |
#@title Huggingface Pretrained Wrapper
"""
This is script is a simple HuggingFace wrapper around a HyenaDNA model, to enable a one click example
of how to load the pretrained weights and get embeddings.
It will instantiate a HyenaDNA model (model class is in the `standalone_hyenadna.py`), and handle the downloading... | hyena-dna-main | huggingface.py |
import copy
import os
import random
import time
from functools import partial, wraps
from typing import Callable, List, Sequence
import hydra
import numpy as np
import pytorch_lightning as pl
import torch
import torch.nn as nn
import wandb
from hydra.utils import get_original_cwd
from omegaconf import DictConfig, Omeg... | hyena-dna-main | train.py |
import torch
import torch.nn.functional as F
from einops import rearrange
from fftconv import fftconv_fwd, fftconv_bwd
def fftconv_ref(u, k, D, dropout_mask):
seqlen = u.shape[-1]
fft_size = 2 * seqlen
k_f = torch.fft.rfft(k, n=fft_size) / fft_size
u_f = torch.fft.rfft(u.to(dtype=k.dtype), n=fft_siz... | hyena-dna-main | csrc/fftconv/launch_fftconv.py |
# Adapted from https://github.com/NVIDIA/apex/blob/master/setup.py
import torch
from torch.utils.cpp_extension import BuildExtension, CppExtension, CUDAExtension, CUDA_HOME
from setuptools import setup, find_packages
import subprocess
import sys
import warnings
import os
# ninja build does not work unless include_dir... | hyena-dna-main | csrc/fftconv/setup.py |
import math
import re
import numpy as np
# N = 8192
N = 16384
# The case of 0 / N is special, we want to simplify it to 0 / 2 instead of 0 / 1
numerator = np.arange(1, N // 8 + 1)
gcd = np.gcd(numerator, N)
num = numerator // gcd
denom = N // gcd
lut_vals = ['T_2_0'] + [f'T_{d}_{n}' for n, d in zip(num, denom)]
lut_... | hyena-dna-main | csrc/fftconv/lut_code_gen.py |
#!/usr/bin/env python3
import argparse
import yaml
from tqdm import tqdm
import typing as tp
import numpy as np
import pandas as pd
from copy import deepcopy
from collections import OrderedDict
import torch
torch.backends.cuda.matmul.allow_tf32 = True
torch.backends.cudnn.allow_tf32 = True
import torch.nn.functional ... | hyena-dna-main | evals/soft_prompting_genomics.py |
#!/usr/bin/env python3
import argparse
import yaml
from tqdm import tqdm
import typing as tp
import numpy as np
import pandas as pd
from copy import deepcopy
from collections import OrderedDict
import torch
torch.backends.cuda.matmul.allow_tf32 = True
torch.backends.cudnn.allow_tf32 = True
import torch.nn.functional ... | hyena-dna-main | evals/instruction_tuned_genomics.py |
import torch
import argparse
import os
import sys
import yaml
from tqdm import tqdm
import json
from src.models.sequence.long_conv_lm import DNAEmbeddingModel
from src.tasks.decoders import SequenceDecoder
from src.dataloaders import SequenceDataset
import numpy as np
from src.dataloaders.datasets.hg38_char_token... | hyena-dna-main | evals/hg38_inference_decoder.py |
import torch
import argparse
import os
import sys
import yaml
from tqdm import tqdm
import json
sys.path.append(os.environ.get("SAFARI_PATH", "."))
from src.models.sequence.long_conv_lm import ConvLMHeadModel
# from transformers import AutoTokenizer, GPT2LMHeadModel
# from spacy.lang.en.stop_words import STOP_WO... | hyena-dna-main | evals/hg38_inference.py |
import math
import torch
import torch.nn.functional as F
from sklearn.metrics import f1_score, roc_auc_score
from functools import partial
import torchmetrics.functional as tm_f
import torch.distributions as dist
from sklearn.metrics import f1_score, roc_auc_score, matthews_corrcoef
from torchmetrics import Metric
from... | hyena-dna-main | src/tasks/metrics.py |
# Inspired by https://github.com/NVIDIA/NeMo/blob/main/nemo/collections/common/metrics/perplexity.py
# But we compute the perplexity correctly: exp(average(nll)), not average(exp(nll))
# Also adapted from https://github.com/Lightning-AI/metrics/blob/master/src/torchmetrics/text/perplexity.py
# But we pass in the loss t... | hyena-dna-main | src/tasks/torchmetrics.py |
from typing import Optional, List, Tuple
import math
import functools
import collections
import torch
import torch.nn as nn
import torch.nn.functional as F
from einops import rearrange
from omegaconf import ListConfig
from src.models.nn.components import ReversibleInstanceNorm1dInput, ReversibleInstanceNorm1dOutput, \
... | hyena-dna-main | src/tasks/tasks.py |
import torch
import torch.nn as nn
import torch.nn.functional as F
from einops import rearrange, reduce
import src.models.nn.utils as U
import src.utils as utils
import src.utils.config
import src.utils.train
log = src.utils.train.get_logger(__name__)
class Decoder(nn.Module):
"""This class doesn't do much but ... | hyena-dna-main | src/tasks/decoders.py |
import datetime
import math
from typing import ForwardRef
import torch
from torch import nn
import torch.nn.functional as F
from einops import rearrange, repeat
import src.models.nn.utils as U
import src.utils as utils
import src.utils.config
from src.models.sequence.block import SequenceResidualBlock
from src.models... | hyena-dna-main | src/tasks/encoders.py |
from typing import Any
import pytorch_lightning as pl
from pytorch_lightning.utilities import rank_zero_only
from pytorch_lightning.utilities.parsing import AttributeDict
class ParamsLog(pl.Callback):
""" Log the number of parameters of the model """
def __init__(
self,
total: bool = True,
... | hyena-dna-main | src/callbacks/params.py |
import torch
from pytorch_lightning import Callback, Trainer, LightningModule
import logging
log = logging.getLogger(__name__) # We want a logger for each process, not just the rank 0
def l2_promote():
import ctypes
_libcudart = ctypes.CDLL('libcudart.so')
# Set device limit on the current device
... | hyena-dna-main | src/callbacks/gpu_affinity.py |
### https://github.com/HazyResearch/transformers/blob/master/src/callbacks/wandb_callbacks.py
import glob
import os
from typing import List
import matplotlib.pyplot as plt
import pandas as pd
import seaborn as sn
import torch
import wandb
from pytorch_lightning import Callback, Trainer
from pytorch_lightning.loggers ... | hyena-dna-main | src/callbacks/wandb.py |
### https://github.com/HazyResearch/transformers/blob/master/src/callbacks/speed_monitor.py
# Adapted from https://pytorch-lightning.readthedocs.io/en/latest/_modules/pytorch_lightning/callbacks/gpu_stats_monitor.html#GPUStatsMonitor
# We only need the speed monitoring, not the GPU monitoring
import time
from typing i... | hyena-dna-main | src/callbacks/timer.py |
r"""
Sequence Length Warmup by Reloading
====================
Change sequence lengths according to a stage schedule. The stage parameters sets the sequence length
and batch size.
TODO (not yet supported):
If batch size is not provided for that stage, calculate the batch size based on the
sequence length reshaping in... | hyena-dna-main | src/callbacks/seqlen_warmup_reload.py |
import pytorch_lightning as pl
from pytorch_lightning.utilities import rank_zero_only
from pytorch_lightning.utilities.parsing import AttributeDict
from omegaconf import OmegaConf
class TrackNorms(pl.Callback):
# TODO do callbacks happen before or after the method in the main LightningModule?
# @rank_zero_onl... | hyena-dna-main | src/callbacks/norms.py |
import numpy as np
from pytorch_lightning.callbacks import Callback
import src.utils as utils
from src.utils import registry
class ProgressiveResizing(Callback):
def __init__(self, stage_params: list):
"""
stage_params is a list of dicts
e.g. stage_params = [
{'resolution': 4... | hyena-dna-main | src/callbacks/progressive_resizing.py |
"""
ET Dataset from Informer Paper.
Dataset: https://github.com/zhouhaoyi/ETDataset
Dataloader: https://github.com/zhouhaoyi/Informer2020
"""
from typing import List
import os
import numpy as np
import pandas as pd
from pandas.tseries import offsets
from pandas.tseries.frequencies import to_offset
import torch
from to... | hyena-dna-main | src/dataloaders/et.py |
from . import et, genomics
from .base import SequenceDataset
| hyena-dna-main | src/dataloaders/__init__.py |
# Adapted from https://github.com/huggingface/transformers/blob/master/examples/pytorch/language-modeling/run_clm.py
# Adapted from https://github.com/HazyResearch/flash-attention/blob/main/training/src/datamodules/language_modeling_hf.py
from pathlib import Path
from typing import Any, List, Union
from torch.utils.dat... | hyena-dna-main | src/dataloaders/genomics.py |
# Adapted from https://github.com/Lightning-AI/lightning/blob/2845e7565dbe6b765ae32870e7d2bc456529c30a/tests/tests_pytorch/utilities/test_auto_restart.py#L1397
from typing import Iterator
import math
import torch
from torch.utils.data import RandomSampler, DistributedSampler
class RandomFaultTolerantSampler(RandomSa... | hyena-dna-main | src/dataloaders/fault_tolerant_sampler.py |
""" Datasets for core experimental results """
import os
import pickle
from functools import partial
from pathlib import Path
import numpy as np
import torch
import torchvision
from einops import rearrange
from einops.layers.torch import Rearrange
from src.utils import is_list, permutations
from torch.nn import funct... | hyena-dna-main | src/dataloaders/base.py |
import torch
import csv
import pandas as pd
import numpy as np
from tqdm import tqdm
import liftover
from pathlib import Path
from pyfaidx import Fasta
from random import randrange, random
def exists(val):
return val is not None
def coin_flip():
return random() > 0.5
string_complement_map = {'A': 'T', 'C': ... | hyena-dna-main | src/dataloaders/datasets/chromatin_profile_dataset.py |
from pyfaidx import Fasta
import torch
from random import random
from pathlib import Path
from src.dataloaders.datasets.hg38_char_tokenizer import CharacterTokenizer
def coin_flip():
return random() > 0.5
# augmentations
string_complement_map = {'A': 'T', 'C': 'G', 'G': 'C', 'T': 'A', 'a': 't', 'c': 'g', 'g': ... | hyena-dna-main | src/dataloaders/datasets/nucleotide_transformer_dataset.py |
from itertools import islice
from functools import partial
import os
import functools
# import json
# from pathlib import Path
# from pyfaidx import Fasta
# import polars as pl
# import pandas as pd
import torch
from random import randrange, random
import numpy as np
from pathlib import Path
from src.dataloaders.data... | hyena-dna-main | src/dataloaders/datasets/genomic_bench_dataset.py |
"""
From: https://github.com/dariush-bahrami/character-tokenizer/blob/master/charactertokenizer/core.py
CharacterTokenzier for Hugging Face Transformers.
This is heavily inspired from CanineTokenizer in transformers package.
"""
import json
import os
from pathlib import Path
from typing import Dict, List, Optional, S... | hyena-dna-main | src/dataloaders/datasets/hg38_char_tokenizer.py |
from pathlib import Path
from pyfaidx import Fasta
import polars as pl
import pandas as pd
import torch
from random import randrange, random
import numpy as np
"""
Dataset for sampling arbitrary intervals from the human genome.
"""
# helper functions
def exists(val):
return val is not None
def coin_flip():... | hyena-dna-main | src/dataloaders/datasets/hg38_dataset.py |
# Inspired by https://github.com/NVIDIA/Megatron-LM/blob/main/tasks/zeroshot_gpt/datasets.py
# Except we don't pad the last block and don't use overlapping eval
# And we return both the input and the target
import math
import numpy as np
import torch
class LMDataset(torch.utils.data.Dataset):
def __init__(self,... | hyena-dna-main | src/dataloaders/datasets/lm_dataset.py |
import torch
from random import random, randint
import numpy as np
from pathlib import Path
from src.dataloaders.datasets.hg38_char_tokenizer import CharacterTokenizer
from genomic_benchmarks.loc2seq import download_dataset
from genomic_benchmarks.data_check import is_downloaded
"""
In-Context learning version of G... | hyena-dna-main | src/dataloaders/datasets/icl_genomics_dataset.py |
from itertools import islice
from functools import partial
# import tensorflow as tf
import os
import functools
import json
from pathlib import Path
from pyfaidx import Fasta
import polars as pl
import pandas as pd
import torch
from random import randrange, random, randint
import numpy as np
from src.dataloaders.datase... | hyena-dna-main | src/dataloaders/datasets/hg38_icl_dataset.py |
import os
from pathlib import Path
from pyfaidx import Fasta
import torch
import shutil
import gzip
import random
from typing import Optional, Union, Dict, List
from src.dataloaders.datasets.hg38_char_tokenizer import CharacterTokenizer
import collections
"""
Dataset that randomly samples sequences of length (X) from ... | hyena-dna-main | src/dataloaders/datasets/species_dataset.py |
from pathlib import Path
from pyfaidx import Fasta
import torch
"""
Just a fixed length dataset for 2 test chromosomes, to ensure the test set is the same.
"""
# helper functions
def exists(val):
return val is not None
class HG38FixedDataset(torch.utils.data.Dataset):
'''
Loop thru bed file, retrieve... | hyena-dna-main | src/dataloaders/datasets/hg38_fixed_dataset.py |
# Copyright (c) 2019-2020, NVIDIA CORPORATION. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by... | hyena-dna-main | src/dataloaders/utils/vocabulary.py |
"""Utilities for special optimizer hyperparameters.
group_parameters_for_optimizer is a modification of timm's optimizer logic, which is currently unused
add_optimizer_hooks is an improved version that uses this codebase's _optim dictionary
"""
import inspect
import torch.nn as nn
import hydra
def add_optimizer_h... | hyena-dna-main | src/utils/optim_groups.py |
""" Utilities for dealing with collection objects (lists, dicts) and configs """
from typing import Sequence, Mapping, Optional, Callable
import functools
import hydra
from omegaconf import ListConfig, DictConfig
# TODO this is usually used in a pattern where it's turned into a list, so can just do that here
def is_li... | hyena-dna-main | src/utils/config.py |
optimizer = {
"adam": "torch.optim.Adam",
"adamw": "torch.optim.AdamW",
"rmsprop": "torch.optim.RMSprop",
"sgd": "torch.optim.SGD",
"lamb": "src.utils.optim.lamb.JITLamb",
}
scheduler = {
"constant": "transformers.get_constant_schedule",
"plateau": "torch.optim.lr_scheduler.ReduceLROnPlatea... | hyena-dna-main | src/utils/registry.py |
from .config import is_list, is_dict, to_list, to_dict, get_class, instantiate
| hyena-dna-main | src/utils/__init__.py |
import math
import numpy as np
import torch
### Bit reversal permutation
def bitreversal_po2(n):
m = int(math.log(n)/math.log(2))
perm = np.arange(n).reshape(n,1)
for i in range(m):
n1 = perm.shape[0]//2
perm = np.hstack((perm[:n1],perm[n1:]))
return perm.squeeze(0)
def bitreversal_p... | hyena-dna-main | src/utils/permutations.py |
# Copyright (c) 2019-2020, NVIDIA CORPORATION. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by... | hyena-dna-main | src/utils/distributed.py |
""" Utils for the training loop. Copied from https://github.com/HazyResearch/transformers/blob/master/src/utils/utils.py """
import logging
import os
import warnings
from typing import List, Sequence
import torch.nn as nn
import pytorch_lightning as pl
import rich.syntax
import rich.tree
from omegaconf import DictConf... | hyena-dna-main | src/utils/train.py |
import torch
import torch.utils.benchmark as benchmark
def _get_gpu_mem(synchronize=True, empty_cache=True):
return torch.cuda.memory_allocated() / (
(2**20) * 1000
), torch.cuda.memory_cached() / ((2**20) * 1000)
def _generate_mem_hook(handle_ref, mem, idx, hook_type, exp):
def hook(self, *args... | hyena-dna-main | src/utils/profiling.py |
# Copyright (c) 2019-2020, NVIDIA CORPORATION. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by... | hyena-dna-main | src/utils/optim/lamb.py |
"""Custom learning rate schedulers"""
import math
import warnings
import torch
from timm.scheduler import CosineLRScheduler
# https://pytorch.org/docs/stable/_modules/torch/optim/lr_scheduler.html
class CosineWarmup(torch.optim.lr_scheduler.CosineAnnealingLR):
def __init__(self, optimizer, T_max, eta_min=0, wa... | hyena-dna-main | src/utils/optim/schedulers.py |
""" Implementations of different types of residual functions. """
import torch
from torch import nn
class Residual(nn.Module):
""" Residual connection with constant affine weights. Can simulate standard residual, no residual, and "constant gates". """
def __init__(self, i_layer, d_input, d_model, alpha=1.0, ... | hyena-dna-main | src/models/nn/residual.py |
# Copyright (c) 2019-2020, NVIDIA CORPORATION. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by... | hyena-dna-main | src/models/nn/adaptive_softmax.py |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.