Upload 3 files
Browse files- app.py +753 -0
- packages.txt +1 -0
- requirements.txt +8 -0
app.py
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|
| 1 |
+
import os
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| 2 |
+
import re
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| 3 |
+
import shutil
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| 4 |
+
import subprocess
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| 5 |
+
import sys
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| 6 |
+
import threading
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| 7 |
+
from itertools import groupby
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| 8 |
+
from pathlib import Path
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| 9 |
+
from tempfile import NamedTemporaryFile
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| 10 |
+
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| 11 |
+
import gradio as gr
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| 12 |
+
import matplotlib.pyplot as plt
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| 13 |
+
import numpy as np
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| 14 |
+
import pandas as pd
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| 15 |
+
import spaces
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| 16 |
+
import torch
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| 17 |
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from transformers import T5EncoderModel, T5Tokenizer
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| 18 |
+
|
| 19 |
+
# -----------------------------------------------------------------------------
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| 20 |
+
# Reproducible upstream sources: these match the working TREAD Colab demo.
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| 21 |
+
# -----------------------------------------------------------------------------
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| 22 |
+
TREAD_REPO = "https://github.com/KYQiu21/TREAD.git"
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| 23 |
+
TREAD_COMMIT = "7a7b3f571778cb89035c798c88df7eacb63ed2c1"
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| 24 |
+
PROTT5_MODEL = "Rostlab/prot_t5_xl_half_uniref50-enc"
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| 25 |
+
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| 26 |
+
APP_DIR = Path(__file__).resolve().parent
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| 27 |
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TREAD_DIR = APP_DIR / ".tread_source"
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| 28 |
+
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| 29 |
+
# Web-demo guardrails only; these are not biological/model validity limits.
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| 30 |
+
MAX_GPU_SEQUENCE_LENGTH = int(os.getenv("TREAD_MAX_GPU_SEQUENCE_LENGTH", "1200"))
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| 31 |
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MAX_CPU_SEQUENCE_LENGTH = int(os.getenv("TREAD_MAX_CPU_SEQUENCE_LENGTH", "600"))
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| 32 |
+
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| 33 |
+
REPEAT_HEADS = [
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| 34 |
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"Any repeat (segmentation head)",
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| 35 |
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"Alpha solenoid",
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| 36 |
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"TIM-barrel",
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| 37 |
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"Beta-propeller",
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| 38 |
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"Beta-barrel",
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| 39 |
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"Beta-solenoid",
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| 40 |
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"Alpha/beta solenoid",
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| 41 |
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]
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| 42 |
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TYPE_HEAD_INDEX = {
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| 43 |
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"Alpha solenoid": 0,
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| 44 |
+
"TIM-barrel": 1,
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| 45 |
+
"Beta-propeller": 2,
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| 46 |
+
"Beta-barrel": 3,
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| 47 |
+
"Beta-solenoid": 4,
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| 48 |
+
"Alpha/beta solenoid": 5,
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| 49 |
+
}
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| 50 |
+
|
| 51 |
+
EXAMPLE_REPEAT = (
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| 52 |
+
"MMKRNILAVIVPALLVAGTANAAEIYNKDGNKVDLYGKAVGLHYFSKGNGENSYGGNGDMTYARLGFKGETQINSDLTGYGQWEYNFQGNNSEGADAQTGNKTRLAFAGLKYADVGSFDYGRNYGVVYDALGYTDMLPEFGGDTAYSDDFFVGRVGGVATYRNSNFFGLVDGLNFAVQYLGKNERDTARRSNGDGVGGSISYEYEGFGIVGAYGAADRTNLQEAQPLGNGKKAEQWATGLKYDANNIYLAANYGETRNATPITNKFTNTSGFANKTQDVLLVAQYQFDFGLRPSIAYTKSKAKDVEGIGDVDLVNYFEVGATYYFNKNMSTYVDYIINQIDSDNKLGVGSDDTVAVGIVYQF"
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| 53 |
+
)
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| 54 |
+
EXAMPLE_PROPELLER = (
|
| 55 |
+
"MEQVLYLGSYTKRESKGVHQIILDTDKKELRDYRLIAEVDSPTYLDLSADKGTLYSISKTDEGGGITSFKKNENGTYDKVAEISAEGSAPCYIHYDEDKKLIFTANYHGGYLTVYKENADGSFTMSDRAQHEGSSIHENQTIPHVHYSALSPDKKFLLACDLGTDEVYTYTVSDEGKLTEAARYKATPGTGPRHLVFHPNGKVAYLFGELSSDVEVLAYEAATGTFSLLQVITTIPAEHTGFNGGAAIRISADGKFVYASNRGHDSLVVYAVSEDGETLSLVEYVPTEGNTPRDFNLDPSGQFVIVAHQDSDNLTLFERDATTGKLTLVQKDVYAPECVCVFY"
|
| 56 |
+
)
|
| 57 |
+
|
| 58 |
+
# -----------------------------------------------------------------------------
|
| 59 |
+
# Model state
|
| 60 |
+
#
|
| 61 |
+
# ZeroGPU path:
|
| 62 |
+
# The GPU models are placed on "cuda" during app startup. In a ZeroGPU Space,
|
| 63 |
+
# Hugging Face's CUDA emulation handles this even though a real GPU is only
|
| 64 |
+
# assigned while a @spaces.GPU function is executing.
|
| 65 |
+
#
|
| 66 |
+
# CPU path:
|
| 67 |
+
# A separate float32 copy is loaded lazily only if somebody presses the CPU
|
| 68 |
+
# button. This avoids paying the RAM cost unless CPU fallback is actually used.
|
| 69 |
+
# -----------------------------------------------------------------------------
|
| 70 |
+
_gpu_tokenizer = None
|
| 71 |
+
_gpu_encoder = None
|
| 72 |
+
_gpu_repeat_model = None
|
| 73 |
+
_gpu_propeller_model = None
|
| 74 |
+
_gpu_init_error = None
|
| 75 |
+
|
| 76 |
+
_cpu_lock = threading.Lock()
|
| 77 |
+
_cpu_tokenizer = None
|
| 78 |
+
_cpu_encoder = None
|
| 79 |
+
_cpu_repeat_model = None
|
| 80 |
+
_cpu_propeller_model = None
|
| 81 |
+
_cpu_init_error = None
|
| 82 |
+
|
| 83 |
+
|
| 84 |
+
def _ensure_tread_source():
|
| 85 |
+
"""Fetch exactly the same TREAD commit used by the public Colab demo."""
|
| 86 |
+
package_init = TREAD_DIR / "tread" / "__init__.py"
|
| 87 |
+
if package_init.is_file():
|
| 88 |
+
if str(TREAD_DIR) not in sys.path:
|
| 89 |
+
sys.path.insert(0, str(TREAD_DIR))
|
| 90 |
+
return
|
| 91 |
+
|
| 92 |
+
shutil.rmtree(TREAD_DIR, ignore_errors=True)
|
| 93 |
+
subprocess.run(["git", "init", str(TREAD_DIR)], check=True)
|
| 94 |
+
subprocess.run(
|
| 95 |
+
["git", "-C", str(TREAD_DIR), "remote", "add", "origin", TREAD_REPO],
|
| 96 |
+
check=True,
|
| 97 |
+
)
|
| 98 |
+
subprocess.run(
|
| 99 |
+
[
|
| 100 |
+
"git",
|
| 101 |
+
"-C",
|
| 102 |
+
str(TREAD_DIR),
|
| 103 |
+
"fetch",
|
| 104 |
+
"--depth",
|
| 105 |
+
"1",
|
| 106 |
+
"origin",
|
| 107 |
+
TREAD_COMMIT,
|
| 108 |
+
],
|
| 109 |
+
check=True,
|
| 110 |
+
)
|
| 111 |
+
subprocess.run(
|
| 112 |
+
["git", "-C", str(TREAD_DIR), "checkout", "--detach", "FETCH_HEAD"],
|
| 113 |
+
check=True,
|
| 114 |
+
)
|
| 115 |
+
|
| 116 |
+
if not package_init.is_file():
|
| 117 |
+
raise FileNotFoundError(
|
| 118 |
+
f"TREAD installation incomplete: {package_init} not found"
|
| 119 |
+
)
|
| 120 |
+
|
| 121 |
+
if str(TREAD_DIR) not in sys.path:
|
| 122 |
+
sys.path.insert(0, str(TREAD_DIR))
|
| 123 |
+
|
| 124 |
+
|
| 125 |
+
def _build_repeat_model(DMDModel, device):
|
| 126 |
+
model = DMDModel(
|
| 127 |
+
per_resi_emb_dim=1024,
|
| 128 |
+
out_channel=64,
|
| 129 |
+
hidden_dim=64,
|
| 130 |
+
num_block=2,
|
| 131 |
+
dropout=0.2,
|
| 132 |
+
bilstm=True,
|
| 133 |
+
kernel_size_conv1=3,
|
| 134 |
+
kernel_size_block=7,
|
| 135 |
+
multi=True,
|
| 136 |
+
num_types=6,
|
| 137 |
+
device=device,
|
| 138 |
+
)
|
| 139 |
+
state = torch.load(
|
| 140 |
+
TREAD_DIR / "trained_model" / "linear-edge_model_repeatsdb.pt",
|
| 141 |
+
map_location="cpu",
|
| 142 |
+
weights_only=True,
|
| 143 |
+
)
|
| 144 |
+
model.load_state_dict(state)
|
| 145 |
+
model = model.to(device).eval()
|
| 146 |
+
return model
|
| 147 |
+
|
| 148 |
+
|
| 149 |
+
def _build_propeller_model(DMDModel, device):
|
| 150 |
+
model = DMDModel(
|
| 151 |
+
per_resi_emb_dim=1024,
|
| 152 |
+
out_channel=128,
|
| 153 |
+
hidden_dim=64,
|
| 154 |
+
num_block=1,
|
| 155 |
+
dropout=0.2,
|
| 156 |
+
bilstm=True,
|
| 157 |
+
kernel_size_conv1=11,
|
| 158 |
+
kernel_size_block=7,
|
| 159 |
+
device=device,
|
| 160 |
+
)
|
| 161 |
+
state = torch.load(
|
| 162 |
+
TREAD_DIR / "trained_model" / "linear-edge_model_propeller_blade.pt",
|
| 163 |
+
map_location="cpu",
|
| 164 |
+
weights_only=True,
|
| 165 |
+
)
|
| 166 |
+
model.load_state_dict(state)
|
| 167 |
+
model = model.to(device).eval()
|
| 168 |
+
return model
|
| 169 |
+
|
| 170 |
+
|
| 171 |
+
def initialize_gpu_models_at_startup():
|
| 172 |
+
"""Prepare the ZeroGPU model copy on emulated CUDA during app startup."""
|
| 173 |
+
global _gpu_tokenizer, _gpu_encoder, _gpu_repeat_model
|
| 174 |
+
global _gpu_propeller_model, _gpu_init_error
|
| 175 |
+
|
| 176 |
+
try:
|
| 177 |
+
_ensure_tread_source()
|
| 178 |
+
from tread.model import DMDModel
|
| 179 |
+
|
| 180 |
+
_gpu_tokenizer = T5Tokenizer.from_pretrained(
|
| 181 |
+
PROTT5_MODEL,
|
| 182 |
+
do_lower_case=False,
|
| 183 |
+
legacy=True,
|
| 184 |
+
)
|
| 185 |
+
_gpu_encoder = T5EncoderModel.from_pretrained(PROTT5_MODEL)
|
| 186 |
+
_gpu_encoder = _gpu_encoder.to("cuda").eval()
|
| 187 |
+
|
| 188 |
+
_gpu_repeat_model = _build_repeat_model(DMDModel, torch.device("cuda"))
|
| 189 |
+
_gpu_propeller_model = _build_propeller_model(
|
| 190 |
+
DMDModel, torch.device("cuda")
|
| 191 |
+
)
|
| 192 |
+
|
| 193 |
+
print("ZeroGPU model copy initialized successfully.")
|
| 194 |
+
|
| 195 |
+
except Exception as exc:
|
| 196 |
+
# Do not kill the whole web app: CPU fallback may still work and the
|
| 197 |
+
# error will be shown clearly if the ZeroGPU button is pressed.
|
| 198 |
+
_gpu_init_error = (
|
| 199 |
+
f"{type(exc).__name__}: {exc}"
|
| 200 |
+
)
|
| 201 |
+
print("ZeroGPU initialization failed:", _gpu_init_error)
|
| 202 |
+
|
| 203 |
+
|
| 204 |
+
def initialize_cpu_models():
|
| 205 |
+
"""Load a separate CPU copy only when the CPU fallback is requested."""
|
| 206 |
+
global _cpu_tokenizer, _cpu_encoder, _cpu_repeat_model
|
| 207 |
+
global _cpu_propeller_model, _cpu_init_error
|
| 208 |
+
|
| 209 |
+
if all(
|
| 210 |
+
x is not None
|
| 211 |
+
for x in (
|
| 212 |
+
_cpu_tokenizer,
|
| 213 |
+
_cpu_encoder,
|
| 214 |
+
_cpu_repeat_model,
|
| 215 |
+
_cpu_propeller_model,
|
| 216 |
+
)
|
| 217 |
+
):
|
| 218 |
+
return
|
| 219 |
+
|
| 220 |
+
if _cpu_init_error is not None:
|
| 221 |
+
raise RuntimeError(_cpu_init_error)
|
| 222 |
+
|
| 223 |
+
with _cpu_lock:
|
| 224 |
+
if all(
|
| 225 |
+
x is not None
|
| 226 |
+
for x in (
|
| 227 |
+
_cpu_tokenizer,
|
| 228 |
+
_cpu_encoder,
|
| 229 |
+
_cpu_repeat_model,
|
| 230 |
+
_cpu_propeller_model,
|
| 231 |
+
)
|
| 232 |
+
):
|
| 233 |
+
return
|
| 234 |
+
|
| 235 |
+
try:
|
| 236 |
+
_ensure_tread_source()
|
| 237 |
+
from tread.model import DMDModel
|
| 238 |
+
|
| 239 |
+
# Tokenizers are device independent. Reuse the one already loaded
|
| 240 |
+
# for ZeroGPU if available.
|
| 241 |
+
_cpu_tokenizer = _gpu_tokenizer
|
| 242 |
+
if _cpu_tokenizer is None:
|
| 243 |
+
_cpu_tokenizer = T5Tokenizer.from_pretrained(
|
| 244 |
+
PROTT5_MODEL,
|
| 245 |
+
do_lower_case=False,
|
| 246 |
+
legacy=True,
|
| 247 |
+
)
|
| 248 |
+
|
| 249 |
+
# CPU inference uses float32 for broad PyTorch CPU compatibility.
|
| 250 |
+
# low_cpu_mem_usage reduces peak RAM while loading this large model.
|
| 251 |
+
_cpu_encoder = T5EncoderModel.from_pretrained(
|
| 252 |
+
PROTT5_MODEL,
|
| 253 |
+
torch_dtype=torch.float32,
|
| 254 |
+
low_cpu_mem_usage=True,
|
| 255 |
+
)
|
| 256 |
+
_cpu_encoder = _cpu_encoder.to("cpu").eval()
|
| 257 |
+
|
| 258 |
+
_cpu_repeat_model = _build_repeat_model(
|
| 259 |
+
DMDModel, torch.device("cpu")
|
| 260 |
+
)
|
| 261 |
+
_cpu_propeller_model = _build_propeller_model(
|
| 262 |
+
DMDModel, torch.device("cpu")
|
| 263 |
+
)
|
| 264 |
+
|
| 265 |
+
print("CPU fallback model copy initialized successfully.")
|
| 266 |
+
|
| 267 |
+
except Exception as exc:
|
| 268 |
+
_cpu_init_error = f"{type(exc).__name__}: {exc}"
|
| 269 |
+
raise RuntimeError(_cpu_init_error) from exc
|
| 270 |
+
|
| 271 |
+
|
| 272 |
+
def clean_sequence(raw_sequence: str, max_length: int) -> str:
|
| 273 |
+
if raw_sequence is None:
|
| 274 |
+
raise gr.Error("Please paste a protein sequence.")
|
| 275 |
+
|
| 276 |
+
text = raw_sequence.strip()
|
| 277 |
+
if not text:
|
| 278 |
+
raise gr.Error("Please paste a protein sequence.")
|
| 279 |
+
|
| 280 |
+
# Accept either a raw sequence or a single FASTA record.
|
| 281 |
+
lines = [line.strip() for line in text.splitlines() if line.strip()]
|
| 282 |
+
if lines and lines[0].startswith(">"):
|
| 283 |
+
lines = [line for line in lines[1:] if not line.startswith(">")]
|
| 284 |
+
|
| 285 |
+
sequence = "".join(lines)
|
| 286 |
+
sequence = re.sub(r"\s+", "", sequence).upper()
|
| 287 |
+
|
| 288 |
+
if not sequence:
|
| 289 |
+
raise gr.Error("No amino-acid sequence was found.")
|
| 290 |
+
|
| 291 |
+
# Standard 20 amino acids plus the symbols handled by the notebook's
|
| 292 |
+
# ProtT5 preprocessing (U, Z, O, B -> X) and X itself.
|
| 293 |
+
allowed = set("ACDEFGHIKLMNPQRSTVWYUZOBX")
|
| 294 |
+
invalid = sorted(set(sequence) - allowed)
|
| 295 |
+
if invalid:
|
| 296 |
+
raise gr.Error(
|
| 297 |
+
"Invalid sequence characters: "
|
| 298 |
+
+ ", ".join(invalid)
|
| 299 |
+
+ ". Paste amino-acid letters only (a FASTA header is allowed)."
|
| 300 |
+
)
|
| 301 |
+
|
| 302 |
+
if len(sequence) > max_length:
|
| 303 |
+
raise gr.Error(
|
| 304 |
+
f"This backend currently accepts up to {max_length} residues; "
|
| 305 |
+
f"your sequence has {len(sequence)} residues."
|
| 306 |
+
)
|
| 307 |
+
|
| 308 |
+
return sequence
|
| 309 |
+
|
| 310 |
+
|
| 311 |
+
def get_prott5_embedding(sequence, tokenizer, encoder, device):
|
| 312 |
+
processed = " ".join(list(re.sub(r"[UZOB]", "X", sequence)))
|
| 313 |
+
ids = tokenizer(
|
| 314 |
+
[processed],
|
| 315 |
+
add_special_tokens=True,
|
| 316 |
+
padding="longest",
|
| 317 |
+
truncation=False,
|
| 318 |
+
return_attention_mask=True,
|
| 319 |
+
)
|
| 320 |
+
|
| 321 |
+
input_ids = torch.tensor(ids["input_ids"], device=device)
|
| 322 |
+
attention_mask = torch.tensor(ids["attention_mask"], device=device)
|
| 323 |
+
|
| 324 |
+
with torch.inference_mode():
|
| 325 |
+
embedding_repr = encoder(
|
| 326 |
+
input_ids=input_ids,
|
| 327 |
+
attention_mask=attention_mask,
|
| 328 |
+
)
|
| 329 |
+
|
| 330 |
+
# Drop the terminal special token, exactly as in the working Colab demo.
|
| 331 |
+
emb = embedding_repr.last_hidden_state[0, :-1]
|
| 332 |
+
|
| 333 |
+
if emb.shape[0] != len(sequence):
|
| 334 |
+
raise RuntimeError(
|
| 335 |
+
f"ProtT5 returned {emb.shape[0]} residue embeddings for a "
|
| 336 |
+
f"{len(sequence)}-residue sequence."
|
| 337 |
+
)
|
| 338 |
+
|
| 339 |
+
return emb
|
| 340 |
+
|
| 341 |
+
|
| 342 |
+
def get_ranges(preds, cutoff1=0.5, min_len=15, cutoff2=0.5, frac2=0.5):
|
| 343 |
+
"""Same motif-range logic as tread.utils.get_ranges."""
|
| 344 |
+
preds = np.asarray(preds).flatten()
|
| 345 |
+
above_threshold = preds > cutoff1
|
| 346 |
+
peaks = []
|
| 347 |
+
|
| 348 |
+
for key, group in groupby(enumerate(above_threshold), key=lambda x: x[1]):
|
| 349 |
+
if key:
|
| 350 |
+
group = list(group)
|
| 351 |
+
if len(group) >= min_len:
|
| 352 |
+
beg = group[0][0]
|
| 353 |
+
end = beg + len(group)
|
| 354 |
+
if (
|
| 355 |
+
len(np.where(preds[beg:end] > cutoff2)[0]) / len(group)
|
| 356 |
+
>= frac2
|
| 357 |
+
):
|
| 358 |
+
peaks.append((beg, end))
|
| 359 |
+
|
| 360 |
+
return peaks
|
| 361 |
+
|
| 362 |
+
|
| 363 |
+
def make_plot(scores, ranges, title, cutoff):
|
| 364 |
+
scores = np.asarray(scores).flatten()
|
| 365 |
+
x = np.arange(1, len(scores) + 1)
|
| 366 |
+
|
| 367 |
+
fig, ax = plt.subplots(figsize=(10, 4.5), dpi=150)
|
| 368 |
+
ax.plot(x, scores, linewidth=1.5)
|
| 369 |
+
ax.axhline(
|
| 370 |
+
cutoff,
|
| 371 |
+
linestyle="--",
|
| 372 |
+
linewidth=1.0,
|
| 373 |
+
alpha=0.7,
|
| 374 |
+
label=f"cutoff = {cutoff:g}",
|
| 375 |
+
)
|
| 376 |
+
for start0, end0 in ranges:
|
| 377 |
+
ax.axvspan(start0 + 1, end0, alpha=0.18)
|
| 378 |
+
|
| 379 |
+
ax.set_xlim(1, max(1, len(scores)))
|
| 380 |
+
ax.set_ylim(0, 1)
|
| 381 |
+
ax.set_xlabel("Residue")
|
| 382 |
+
ax.set_ylabel("Residue score")
|
| 383 |
+
ax.set_title(title)
|
| 384 |
+
ax.legend(loc="upper right")
|
| 385 |
+
fig.tight_layout()
|
| 386 |
+
|
| 387 |
+
return fig
|
| 388 |
+
|
| 389 |
+
|
| 390 |
+
def make_download_table(sequence, scores, ranges):
|
| 391 |
+
scores = np.asarray(scores).flatten()
|
| 392 |
+
predicted = np.zeros(len(sequence), dtype=bool)
|
| 393 |
+
|
| 394 |
+
for start0, end0 in ranges:
|
| 395 |
+
predicted[start0:end0] = True
|
| 396 |
+
|
| 397 |
+
return pd.DataFrame(
|
| 398 |
+
{
|
| 399 |
+
"residue": np.arange(1, len(sequence) + 1),
|
| 400 |
+
"amino_acid": list(sequence),
|
| 401 |
+
"score": scores,
|
| 402 |
+
"predicted_motif": predicted,
|
| 403 |
+
}
|
| 404 |
+
)
|
| 405 |
+
|
| 406 |
+
|
| 407 |
+
def save_csv(df: pd.DataFrame):
|
| 408 |
+
temp = NamedTemporaryFile(
|
| 409 |
+
prefix="tread_prediction_",
|
| 410 |
+
suffix=".csv",
|
| 411 |
+
delete=False,
|
| 412 |
+
)
|
| 413 |
+
temp.close()
|
| 414 |
+
df.to_csv(temp.name, index=False)
|
| 415 |
+
return temp.name
|
| 416 |
+
|
| 417 |
+
|
| 418 |
+
def _predict_core(
|
| 419 |
+
sequence_text,
|
| 420 |
+
model_choice,
|
| 421 |
+
repeat_head,
|
| 422 |
+
cutoff,
|
| 423 |
+
min_len,
|
| 424 |
+
*,
|
| 425 |
+
tokenizer,
|
| 426 |
+
encoder,
|
| 427 |
+
repeat_model,
|
| 428 |
+
propeller_model,
|
| 429 |
+
device,
|
| 430 |
+
backend_label,
|
| 431 |
+
max_length,
|
| 432 |
+
):
|
| 433 |
+
sequence = clean_sequence(sequence_text, max_length=max_length)
|
| 434 |
+
|
| 435 |
+
embedding = get_prott5_embedding(
|
| 436 |
+
sequence,
|
| 437 |
+
tokenizer=tokenizer,
|
| 438 |
+
encoder=encoder,
|
| 439 |
+
device=device,
|
| 440 |
+
)
|
| 441 |
+
|
| 442 |
+
with torch.inference_mode():
|
| 443 |
+
if model_choice == "RepeatsDB repeat annotation":
|
| 444 |
+
seg_prediction, type_prediction = repeat_model.predict_single(
|
| 445 |
+
embedding
|
| 446 |
+
)
|
| 447 |
+
|
| 448 |
+
if repeat_head == "Any repeat (segmentation head)":
|
| 449 |
+
scores = seg_prediction
|
| 450 |
+
else:
|
| 451 |
+
scores = type_prediction[TYPE_HEAD_INDEX[repeat_head]]
|
| 452 |
+
|
| 453 |
+
profile_name = repeat_head
|
| 454 |
+
title = f"TREAD RepeatsDB — {profile_name}"
|
| 455 |
+
|
| 456 |
+
else:
|
| 457 |
+
scores = propeller_model.predict_single(embedding)
|
| 458 |
+
profile_name = "Beta-propeller blade"
|
| 459 |
+
title = "TREAD — beta-propeller blade annotation"
|
| 460 |
+
|
| 461 |
+
ranges = get_ranges(
|
| 462 |
+
scores,
|
| 463 |
+
cutoff1=float(cutoff),
|
| 464 |
+
min_len=int(min_len),
|
| 465 |
+
)
|
| 466 |
+
fig = make_plot(scores, ranges, title, float(cutoff))
|
| 467 |
+
|
| 468 |
+
# Convert notebook's 0-based, end-exclusive ranges to user-facing
|
| 469 |
+
# 1-based inclusive residue coordinates.
|
| 470 |
+
if ranges:
|
| 471 |
+
ranges_df = pd.DataFrame(
|
| 472 |
+
[
|
| 473 |
+
{
|
| 474 |
+
"Start (1-based)": start0 + 1,
|
| 475 |
+
"End (1-based)": end0,
|
| 476 |
+
"Length": end0 - start0,
|
| 477 |
+
}
|
| 478 |
+
for start0, end0 in ranges
|
| 479 |
+
]
|
| 480 |
+
)
|
| 481 |
+
range_text = ", ".join(f"{s + 1}–{e}" for s, e in ranges)
|
| 482 |
+
else:
|
| 483 |
+
ranges_df = pd.DataFrame(
|
| 484 |
+
columns=["Start (1-based)", "End (1-based)", "Length"]
|
| 485 |
+
)
|
| 486 |
+
range_text = "None at the current thresholds"
|
| 487 |
+
|
| 488 |
+
profile_df = make_download_table(sequence, scores, ranges)
|
| 489 |
+
csv_path = save_csv(profile_df)
|
| 490 |
+
|
| 491 |
+
status = (
|
| 492 |
+
f"**Sequence length:** {len(sequence)} aa \n"
|
| 493 |
+
f"**Model:** {model_choice} \n"
|
| 494 |
+
f"**Profile:** {profile_name} \n"
|
| 495 |
+
f"**Predicted motif ranges:** {range_text} \n"
|
| 496 |
+
f"**Compute backend:** {backend_label}"
|
| 497 |
+
)
|
| 498 |
+
|
| 499 |
+
return status, fig, ranges_df, csv_path
|
| 500 |
+
|
| 501 |
+
|
| 502 |
+
@spaces.GPU(duration=120)
|
| 503 |
+
def predict_gpu(sequence_text, model_choice, repeat_head, cutoff, min_len):
|
| 504 |
+
"""ZeroGPU path. A real GPU is allocated only for this function call."""
|
| 505 |
+
if _gpu_init_error is not None:
|
| 506 |
+
raise gr.Error(
|
| 507 |
+
"The ZeroGPU model copy could not be initialized. "
|
| 508 |
+
f"Startup error: {_gpu_init_error}"
|
| 509 |
+
)
|
| 510 |
+
|
| 511 |
+
if any(
|
| 512 |
+
x is None
|
| 513 |
+
for x in (
|
| 514 |
+
_gpu_tokenizer,
|
| 515 |
+
_gpu_encoder,
|
| 516 |
+
_gpu_repeat_model,
|
| 517 |
+
_gpu_propeller_model,
|
| 518 |
+
)
|
| 519 |
+
):
|
| 520 |
+
raise gr.Error(
|
| 521 |
+
"ZeroGPU models are not initialized. Check the Space runtime log."
|
| 522 |
+
)
|
| 523 |
+
|
| 524 |
+
device_name = "ZeroGPU"
|
| 525 |
+
try:
|
| 526 |
+
device_name = f"ZeroGPU — {torch.cuda.get_device_name(0)}"
|
| 527 |
+
except Exception:
|
| 528 |
+
pass
|
| 529 |
+
|
| 530 |
+
return _predict_core(
|
| 531 |
+
sequence_text,
|
| 532 |
+
model_choice,
|
| 533 |
+
repeat_head,
|
| 534 |
+
cutoff,
|
| 535 |
+
min_len,
|
| 536 |
+
tokenizer=_gpu_tokenizer,
|
| 537 |
+
encoder=_gpu_encoder,
|
| 538 |
+
repeat_model=_gpu_repeat_model,
|
| 539 |
+
propeller_model=_gpu_propeller_model,
|
| 540 |
+
device=torch.device("cuda"),
|
| 541 |
+
backend_label=device_name,
|
| 542 |
+
max_length=MAX_GPU_SEQUENCE_LENGTH,
|
| 543 |
+
)
|
| 544 |
+
|
| 545 |
+
|
| 546 |
+
def predict_cpu(sequence_text, model_choice, repeat_head, cutoff, min_len):
|
| 547 |
+
"""CPU fallback. Does not consume ZeroGPU quota, but is much slower."""
|
| 548 |
+
try:
|
| 549 |
+
initialize_cpu_models()
|
| 550 |
+
except Exception as exc:
|
| 551 |
+
raise gr.Error(f"CPU model initialization failed: {exc}") from exc
|
| 552 |
+
|
| 553 |
+
return _predict_core(
|
| 554 |
+
sequence_text,
|
| 555 |
+
model_choice,
|
| 556 |
+
repeat_head,
|
| 557 |
+
cutoff,
|
| 558 |
+
min_len,
|
| 559 |
+
tokenizer=_cpu_tokenizer,
|
| 560 |
+
encoder=_cpu_encoder,
|
| 561 |
+
repeat_model=_cpu_repeat_model,
|
| 562 |
+
propeller_model=_cpu_propeller_model,
|
| 563 |
+
device=torch.device("cpu"),
|
| 564 |
+
backend_label="CPU fallback",
|
| 565 |
+
max_length=MAX_CPU_SEQUENCE_LENGTH,
|
| 566 |
+
)
|
| 567 |
+
|
| 568 |
+
|
| 569 |
+
def load_repeat_example():
|
| 570 |
+
return (
|
| 571 |
+
EXAMPLE_REPEAT,
|
| 572 |
+
"RepeatsDB repeat annotation",
|
| 573 |
+
"Beta-barrel",
|
| 574 |
+
0.8,
|
| 575 |
+
20,
|
| 576 |
+
)
|
| 577 |
+
|
| 578 |
+
|
| 579 |
+
def load_propeller_example():
|
| 580 |
+
return (
|
| 581 |
+
EXAMPLE_PROPELLER,
|
| 582 |
+
"Beta-propeller blade annotation",
|
| 583 |
+
"Beta-propeller",
|
| 584 |
+
0.8,
|
| 585 |
+
20,
|
| 586 |
+
)
|
| 587 |
+
|
| 588 |
+
|
| 589 |
+
# IMPORTANT for ZeroGPU:
|
| 590 |
+
# Prepare the CUDA/emulated-CUDA model copy at module level, before requests.
|
| 591 |
+
initialize_gpu_models_at_startup()
|
| 592 |
+
|
| 593 |
+
|
| 594 |
+
with gr.Blocks(title="TREAD — Protein Repeat Annotation") as demo:
|
| 595 |
+
gr.Markdown(
|
| 596 |
+
"""
|
| 597 |
+
# TREAD — Protein Repeat Annotation
|
| 598 |
+
|
| 599 |
+
Paste a protein sequence and run one of the two pretrained TREAD models.
|
| 600 |
+
|
| 601 |
+
- **RepeatsDB repeat annotation:** residue-wise repeat segmentation plus six repeat-fold heads.
|
| 602 |
+
- **Beta-propeller blade annotation:** residue-wise blade prediction.
|
| 603 |
+
|
| 604 |
+
**Recommended:** use **Run with ZeroGPU**.
|
| 605 |
+
**Fallback:** use **Run on CPU** if GPU quota/availability is a problem; CPU inference is substantially slower.
|
| 606 |
+
|
| 607 |
+
ProtT5 embeddings are generated on the fly with `Rostlab/prot_t5_xl_half_uniref50-enc`.
|
| 608 |
+
"""
|
| 609 |
+
)
|
| 610 |
+
|
| 611 |
+
with gr.Row():
|
| 612 |
+
with gr.Column(scale=3):
|
| 613 |
+
sequence_input = gr.Textbox(
|
| 614 |
+
label="Protein sequence",
|
| 615 |
+
lines=10,
|
| 616 |
+
placeholder=(
|
| 617 |
+
"Paste a raw amino-acid sequence or a single FASTA record..."
|
| 618 |
+
),
|
| 619 |
+
)
|
| 620 |
+
model_choice = gr.Radio(
|
| 621 |
+
choices=[
|
| 622 |
+
"RepeatsDB repeat annotation",
|
| 623 |
+
"Beta-propeller blade annotation",
|
| 624 |
+
],
|
| 625 |
+
value="RepeatsDB repeat annotation",
|
| 626 |
+
label="Model",
|
| 627 |
+
)
|
| 628 |
+
repeat_head = gr.Dropdown(
|
| 629 |
+
choices=REPEAT_HEADS,
|
| 630 |
+
value="Beta-barrel",
|
| 631 |
+
label="RepeatsDB profile to display",
|
| 632 |
+
info=(
|
| 633 |
+
"Used only for the RepeatsDB model. "
|
| 634 |
+
"The default matches the public Colab example."
|
| 635 |
+
),
|
| 636 |
+
)
|
| 637 |
+
|
| 638 |
+
with gr.Column(scale=2):
|
| 639 |
+
cutoff = gr.Slider(
|
| 640 |
+
minimum=0.0,
|
| 641 |
+
maximum=1.0,
|
| 642 |
+
value=0.8,
|
| 643 |
+
step=0.01,
|
| 644 |
+
label="Residue score threshold",
|
| 645 |
+
)
|
| 646 |
+
min_len = gr.Slider(
|
| 647 |
+
minimum=1,
|
| 648 |
+
maximum=100,
|
| 649 |
+
value=20,
|
| 650 |
+
step=1,
|
| 651 |
+
label="Minimum motif length",
|
| 652 |
+
)
|
| 653 |
+
|
| 654 |
+
gpu_button = gr.Button(
|
| 655 |
+
"Run with ZeroGPU (recommended)",
|
| 656 |
+
variant="primary",
|
| 657 |
+
)
|
| 658 |
+
cpu_button = gr.Button(
|
| 659 |
+
"Run on CPU (slow fallback)",
|
| 660 |
+
variant="secondary",
|
| 661 |
+
)
|
| 662 |
+
|
| 663 |
+
with gr.Row():
|
| 664 |
+
repeat_example_button = gr.Button("Load RepeatsDB example")
|
| 665 |
+
propeller_example_button = gr.Button("Load propeller example")
|
| 666 |
+
|
| 667 |
+
gr.Markdown("## Results")
|
| 668 |
+
status_output = gr.Markdown()
|
| 669 |
+
plot_output = gr.Plot(label="Residue-wise score profile")
|
| 670 |
+
ranges_output = gr.Dataframe(
|
| 671 |
+
headers=["Start (1-based)", "End (1-based)", "Length"],
|
| 672 |
+
label="Predicted motif ranges",
|
| 673 |
+
interactive=False,
|
| 674 |
+
)
|
| 675 |
+
download_output = gr.File(label="Download per-residue CSV")
|
| 676 |
+
|
| 677 |
+
gr.Markdown(
|
| 678 |
+
f"""
|
| 679 |
+
### Notes
|
| 680 |
+
|
| 681 |
+
- ZeroGPU accepts sequences up to **{MAX_GPU_SEQUENCE_LENGTH} aa** in this web demo.
|
| 682 |
+
- CPU fallback accepts sequences up to **{MAX_CPU_SEQUENCE_LENGTH} aa** by default because ProtT5-XL is very slow on the free CPU backend.
|
| 683 |
+
- The range-calling logic uses the same thresholding rule as the public Colab/TREAD utility.
|
| 684 |
+
- The web table reports **1-based inclusive** residue coordinates for readability.
|
| 685 |
+
- Rare/ambiguous residues `U`, `Z`, `O`, and `B` are mapped to `X` for ProtT5 embedding, matching the Colab demo.
|
| 686 |
+
|
| 687 |
+
Source code and pretrained TREAD checkpoints: [KYQiu21/TREAD](https://github.com/KYQiu21/TREAD)
|
| 688 |
+
"""
|
| 689 |
+
)
|
| 690 |
+
|
| 691 |
+
gpu_button.click(
|
| 692 |
+
fn=predict_gpu,
|
| 693 |
+
inputs=[
|
| 694 |
+
sequence_input,
|
| 695 |
+
model_choice,
|
| 696 |
+
repeat_head,
|
| 697 |
+
cutoff,
|
| 698 |
+
min_len,
|
| 699 |
+
],
|
| 700 |
+
outputs=[
|
| 701 |
+
status_output,
|
| 702 |
+
plot_output,
|
| 703 |
+
ranges_output,
|
| 704 |
+
download_output,
|
| 705 |
+
],
|
| 706 |
+
)
|
| 707 |
+
|
| 708 |
+
cpu_button.click(
|
| 709 |
+
fn=predict_cpu,
|
| 710 |
+
inputs=[
|
| 711 |
+
sequence_input,
|
| 712 |
+
model_choice,
|
| 713 |
+
repeat_head,
|
| 714 |
+
cutoff,
|
| 715 |
+
min_len,
|
| 716 |
+
],
|
| 717 |
+
outputs=[
|
| 718 |
+
status_output,
|
| 719 |
+
plot_output,
|
| 720 |
+
ranges_output,
|
| 721 |
+
download_output,
|
| 722 |
+
],
|
| 723 |
+
)
|
| 724 |
+
|
| 725 |
+
repeat_example_button.click(
|
| 726 |
+
fn=load_repeat_example,
|
| 727 |
+
inputs=[],
|
| 728 |
+
outputs=[
|
| 729 |
+
sequence_input,
|
| 730 |
+
model_choice,
|
| 731 |
+
repeat_head,
|
| 732 |
+
cutoff,
|
| 733 |
+
min_len,
|
| 734 |
+
],
|
| 735 |
+
)
|
| 736 |
+
|
| 737 |
+
propeller_example_button.click(
|
| 738 |
+
fn=load_propeller_example,
|
| 739 |
+
inputs=[],
|
| 740 |
+
outputs=[
|
| 741 |
+
sequence_input,
|
| 742 |
+
model_choice,
|
| 743 |
+
repeat_head,
|
| 744 |
+
cutoff,
|
| 745 |
+
min_len,
|
| 746 |
+
],
|
| 747 |
+
)
|
| 748 |
+
|
| 749 |
+
|
| 750 |
+
demo.queue()
|
| 751 |
+
|
| 752 |
+
if __name__ == "__main__":
|
| 753 |
+
demo.launch()
|
packages.txt
ADDED
|
@@ -0,0 +1 @@
|
|
|
|
|
|
|
| 1 |
+
git
|
requirements.txt
ADDED
|
@@ -0,0 +1,8 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
torch==2.9.1
|
| 2 |
+
transformers==4.57.6
|
| 3 |
+
huggingface-hub==0.36.2
|
| 4 |
+
accelerate>=1,<2
|
| 5 |
+
sentencepiece>=0.2
|
| 6 |
+
numpy>=1.26,<3
|
| 7 |
+
pandas>=2.0,<3
|
| 8 |
+
matplotlib>=3.8
|