ADMET property prediction for drug candidates. Full pharmacokinetic panel (Caco-2, PPB, clearance, CYP), toxicity (hERG, AMES, DILI), drug-likeness (Lipinski, QED), using RDKit descriptors and TDC models.
中文简介正在准备中。当前显示原文说明。
Simplest distributed training API. 4 lines to add distributed support to any PyTorch script. Unified API for DeepSpeed/FSDP/Megatron/DDP. Automatic device placement, mixed precision (FP16/BF16/FP8). Interactive config, single launch command. HuggingFace ecosystem standard.
中文简介正在准备中。当前显示原文说明。
安装前可以查看交给 AI 代理的指令内容。
Accelerate simplifies distributed training to 4 lines of code.
Installation:
pip install accelerate
Convert PyTorch script (4 lines):
import torch
+ from accelerate import Accelerator
+ accelerator = Accelerator()
model = torch.nn.Transformer()
optimizer = torch.optim.Adam(model.parameters())
dataloader = torch.utils.data.DataLoader(dataset)
+ model, optimizer, dataloader = accelerator.prepare(model, optimizer, dataloader)
for batch in dataloader:
optimizer.zero_grad()
loss = model(batch)
- loss.backward()
+ accelerator.backward(loss)
optimizer.step()
Run (single command):
accelerate launch train.py
Original script:
# train.py
import torch
model = torch.nn.Linear(10, 2).to('cuda')
optimizer = torch.optim.Adam(model.parameters())
dataloader = torch.utils.data.DataLoader(dataset, batch_size=32)
for epoch in range(10):
for batch in dataloader:
batch = batch.to('cuda')
optimizer.zero_grad()
loss = model(batch).mean()
loss.backward()
optimizer.step()
With Accelerate (4 lines added):
# train.py
import torch
from accelerate import Accelerator # +1
accelerator = Accelerator() # +2
model = torch.nn.Linear(10, 2)
optimizer = torch.optim.Adam(model.parameters())
dataloader = torch.utils.data.DataLoader(dataset, batch_size=32)
model, optimizer, dataloader = accelerator.prepare(model, optimizer, dataloader) # +3
for epoch in range(10):
for batch in dataloader:
# No .to('cuda') needed - automatic!
optimizer.zero_grad()
loss = model(batch).mean()
accelerator.backward(loss) # +4
optimizer.step()
Configure (interactive):
accelerate config
Questions:
Launch (works on any setup):
# Single GPU
accelerate launch train.py
# Multi-GPU (8 GPUs)
accelerate launch --multi_gpu --num_processes 8 train.py
# Multi-node
accelerate launch --multi_gpu --num_processes 16 \
--num_machines 2 --machine_rank 0 \
--main_process_ip $MASTER_ADDR \
train.py
Enable FP16/BF16:
from accelerate import Accelerator
# FP16 (with gradient scaling)
accelerator = Accelerator(mixed_precision='fp16')
# BF16 (no scaling, more stable)
accelerator = Accelerator(mixed_precision='bf16')
# FP8 (H100+)
accelerator = Accelerator(mixed_precision='fp8')
model, optimizer, dataloader = accelerator.prepare(model, optimizer, dataloader)
# Everything else is automatic!
for batch in dataloader:
with accelerator.autocast(): # Optional, done automatically
loss = model(batch)
accelerator.backward(loss)
Enable DeepSpeed ZeRO-2:
from accelerate import Accelerator
accelerator = Accelerator(
mixed_precision='bf16',
deepspeed_plugin={
"zero_stage": 2, # ZeRO-2
"offload_optimizer": False,
"gradient_accumulation_steps": 4
}
)
# Same code as before!
model, optimizer, dataloader = accelerator.prepare(model, optimizer, dataloader)
Or via config:
accelerate config
# Select: DeepSpeed → ZeRO-2
deepspeed_config.json:
{
"fp16": {"enabled": false},
"bf16": {"enabled": true},
"zero_optimization": {
"stage": 2,
"offload_optimizer": {"device": "cpu"},
"allgather_bucket_size": 5e8,
"reduce_bucket_size": 5e8
}
}
Launch:
accelerate launch --config_file deepspeed_config.json train.py
Enable FSDP:
from accelerate import Accelerator, FullyShardedDataParallelPlugin
fsdp_plugin = FullyShardedDataParallelPlugin(
sharding_strategy="FULL_SHARD", # ZeRO-3 equivalent
auto_wrap_policy="TRANSFORMER_AUTO_WRAP",
cpu_offload=False
)
accelerator = Accelerator(
mixed_precision='bf16',
fsdp_plugin=fsdp_plugin
)
model, optimizer, dataloader = accelerator.prepare(model, optimizer, dataloader)
Or via config:
accelerate config
# Select: FSDP → Full Shard → No CPU Offload
Accumulate gradients:
from accelerate import Accelerator
accelerator = Accelerator(gradient_accumulation_steps=4)
model, optimizer, dataloader = accelerator.prepare(model, optimizer, dataloader)
for batch in dataloader:
with accelerator.accumulate(model): # Handles accumulation
optimizer.zero_grad()
loss = model(batch)
accelerator.backward(loss)
optimizer.step()
Effective batch size: batch_size * num_gpus * gradient_accumulation_steps
Use Accelerate when:
Key advantages:
Use alternatives instead:
Issue: Wrong device placement
Don't manually move to device:
# WRONG
batch = batch.to('cuda')
# CORRECT
# Accelerate handles it automatically after prepare()
Issue: Gradient accumulation not working
Use context manager:
# CORRECT
with accelerator.accumulate(model):
optimizer.zero_grad()
accelerator.backward(loss)
optimizer.step()
Issue: Checkpointing in distributed
Use accelerator methods:
# Save only on main process
if accelerator.is_main_process:
accelerator.save_state('checkpoint/')
# Load on all processes
accelerator.load_state('checkpoint/')
Issue: Different results with FSDP
Ensure same random seed:
from accelerate.utils import set_seed
set_seed(42)
Megatron integration: See references/megatron-integration.md for tensor parallelism, pipeline parallelism, and sequence parallelism setup.
Custom plugins: See references/custom-plugins.md for creating custom distributed plugins and advanced configuration.
Performance tuning: See references/performance.md for profiling, memory optimization, and best practices.
Launcher requirements:
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ADMET property prediction for drug candidates. Full pharmacokinetic panel (Caco-2, PPB, clearance, CYP), toxicity (hERG, AMES, DILI), drug-likeness (Lipinski, QED), using RDKit descriptors and TDC models.
中文简介正在准备中。当前显示原文说明。
Interpretable ADMET analysis with mechanistic reasoning. Maps liabilities to structural causes and biological pathways. Based on CoTox (Park 2025) and DrugR (Liu 2026).
中文简介正在准备中。当前显示原文说明。
This skill should be used for time series machine learning tasks including classification, regression, clustering, forecasting, anomaly detection, segmentation, and similarity search. Use when working with temporal data, sequential patterns, or time-indexed observations requiring specialized algorithms beyond standard ML approaches. Particularly suited for univariate and multivariate time series analysis with scikit-learn compatible APIs.
中文简介正在准备中。当前显示原文说明。
Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use when analyzing transcriptomics data (bulk RNA-seq, single-cell RNA-seq) to identify transcription factor-target gene relationships and regulatory interactions. Supports distributed computation for large-scale datasets.
中文简介正在准备中。当前显示原文说明。
Comprehensive Python library for astronomy and astrophysics. This skill should be used when working with astronomical data including celestial coordinates, physical units, FITS files, cosmological calculations, time systems, tables, world coordinate systems (WCS), and astronomical data analysis. Use when tasks involve coordinate transformations, unit conversions, FITS file manipulation, cosmological distance calculations, time scale conversions, or astronomical data processing.
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PyTorch library for audio generation including text-to-music (MusicGen) and text-to-sound (AudioGen). Use when you need to generate music from text descriptions, create sound effects, or perform melody-conditioned music generation.
中文简介正在准备中。当前显示原文说明。