labarchive-integration
Electronic lab notebook API integration. Access notebooks, manage entries/attachments, backup notebooks, integrate with Protocols.io/Jupyter/REDCap, for programmatic ELN workflows.
transformers
Work with state-of-the-art machine learning models for NLP, computer vision, audio, and multimodal tasks using HuggingFace Transformers. This skill should be used when fine-tuning pre-trained models, performing inference with pipelines, generating text, training sequence models, or working with B...
Full skill instructions
The Transformers library provides state-of-the-art machine learning models for NLP, computer vision, audio, and multimodal tasks. Apply this skill for quick inference through pipelines, comprehensive training via the Trainer API, and flexible text generation with various decoding strategies.
For rapid inference without complex setup, use the pipeline() API. Pipelines abstract away tokenization, model invocation, and post-processing.
from transformers import pipeline
# Text classification
classifier = pipeline("text-classification")
result = classifier("This product is amazing!")
# Named entity recognition
ner = pipeline("token-classification")
entities = ner("Sarah works at Microsoft in Seattle")
# Question answering
qa = pipeline("question-answering")
answer = qa(question="What is the capital?", context="Paris is the capital of France.")
# Text generation
generator = pipeline("text-generation", model="gpt2")
text = generator("Once upon a time", max_length=50)
# Image classification
image_classifier = pipeline("image-classification")
predictions = image_classifier("image.jpg")
When to use pipelines:
Available pipeline tasks:
For comprehensive pipeline documentation, see references/pipelines.md.
Use the Trainer API for comprehensive model training with support for distributed training, mixed precision, and advanced optimization.
Basic training workflow:
from transformers import (
AutoTokenizer,
AutoModelForSequenceClassification,
TrainingArguments,
Trainer
)
from datasets import load_dataset
# 1. Load and tokenize data
dataset = load_dataset("imdb")
tokenizer = AutoTokenizer.from_pretrained("bert-base-uncased")
def tokenize_function(examples):
return tokenizer(examples["text"], padding="max_length", truncation=True)
tokenized_datasets = dataset.map(tokenize_function, batched=True)
# 2. Load model
model = AutoModelForSequenceClassification.from_pretrained(
"bert-base-uncased",
num_labels=2
)
# 3. Configure training
training_args = TrainingArguments(
output_dir="./results",
num_train_epochs=3,
per_device_train_batch_size=16,
eval_strategy="epoch",
save_strategy="epoch",
load_best_model_at_end=True,
)
# 4. Create trainer and train
trainer = Trainer(
model=model,
args=training_args,
train_dataset=tokenized_datasets["train"],
eval_dataset=tokenized_datasets["test"],
)
trainer.train()
Key training features:
For detailed training documentation, see references/training.md.
Generate text using various decoding strategies including greedy decoding, beam search, sampling, and more.
Generation strategies:
from transformers import AutoModelForCausalLM, AutoTokenizer
model = AutoModelForCausalLM.from_pretrained("gpt2")
tokenizer = AutoTokenizer.from_pretrained("gpt2")
inputs = tokenizer("Once upon a time", return_tensors="pt")
# Greedy decoding (deterministic)
outputs = model.generate(**inputs, max_new_tokens=50)
# Beam search (explores multiple hypotheses)
outputs = model.generate(
**inputs,
max_new_tokens=50,
num_beams=5,
early_stopping=True
)
# Sampling (creative, diverse)
outputs = model.generate(
**inputs,
max_new_tokens=50,
do_sample=True,
temperature=0.7,
top_p=0.9,
top_k=50
)
Generation parameters:
temperature: Controls randomness (0.1-2.0)top_k: Sample from top-k tokenstop_p: Nucleus sampling thresholdnum_beams: Number of beams for beam searchrepetition_penalty: Discourage repetitionno_repeat_ngram_size: Prevent repeating n-gramsFor comprehensive generation documentation, see references/generation_strategies.md.
Common task patterns with appropriate model classes:
Text Classification:
from transformers import AutoModelForSequenceClassification
model = AutoModelForSequenceClassification.from_pretrained(
"bert-base-uncased",
num_labels=3,
id2label={0: "negative", 1: "neutral", 2: "positive"}
)
Named Entity Recognition (Token Classification):
from transformers import AutoModelForTokenClassification
model = AutoModelForTokenClassification.from_pretrained(
"bert-base-uncased",
num_labels=9 # Number of entity types
)
Question Answering:
from transformers import AutoModelForQuestionAnswering
model = AutoModelForQuestionAnswering.from_pretrained("bert-base-uncased")
Summarization and Translation (Seq2Seq):
from transformers import AutoModelForSeq2SeqLM
model = AutoModelForSeq2SeqLM.from_pretrained("t5-base")
Image Classification:
from transformers import AutoModelForImageClassification
model = AutoModelForImageClassification.from_pretrained(
"google/vit-base-patch16-224",
num_labels=num_classes
)
For detailed task-specific workflows including data preprocessing, training, and evaluation, see references/task_patterns.md.
Use Auto classes for automatic architecture selection based on model checkpoints:
from transformers import (
AutoTokenizer, # Tokenization
AutoModel, # Base model (hidden states)
AutoModelForSequenceClassification,
AutoModelForTokenClassification,
AutoModelForQuestionAnswering,
AutoModelForCausalLM, # GPT-style
AutoModelForMaskedLM, # BERT-style
AutoModelForSeq2SeqLM, # T5, BART
AutoProcessor, # For multimodal models
AutoImageProcessor, # For vision models
)
# Load any model by name
tokenizer = AutoTokenizer.from_pretrained("bert-base-uncased")
model = AutoModelForSequenceClassification.from_pretrained("bert-base-uncased")
For comprehensive API documentation, see references/api_reference.md.
Device placement:
model = AutoModel.from_pretrained("bert-base-uncased", device_map="auto")
Mixed precision:
model = AutoModel.from_pretrained(
"model-name",
torch_dtype=torch.float16 # or torch.bfloat16
)
Quantization:
from transformers import BitsAndBytesConfig
quantization_config = BitsAndBytesConfig(
load_in_4bit=True,
bnb_4bit_compute_dtype=torch.float16
)
model = AutoModelForCausalLM.from_pretrained(
"meta-llama/Llama-2-7b-hf",
quantization_config=quantization_config,
device_map="auto"
)
See: scripts/quick_inference.py for comprehensive pipeline examples
trainer.train()trainer.evaluate()See: scripts/fine_tune_classifier.py for complete training example
model.generate()See: scripts/generate_text.py for generation strategy examples
device_map="auto" for automatic placementExecutable Python scripts demonstrating common Transformers workflows:
quick_inference.py - Pipeline examples for NLP, vision, audio, and multimodal tasksfine_tune_classifier.py - Complete fine-tuning workflow with Trainer APIgenerate_text.py - Text generation with various decoding strategiesRun scripts directly to see examples in action:
python scripts/quick_inference.py
python scripts/fine_tune_classifier.py
python scripts/generate_text.py
Comprehensive reference documentation loaded into context as needed:
api_reference.md - Core classes and APIs (Auto classes, Trainer, GenerationConfig, etc.)pipelines.md - All available pipelines organized by modality with examplestraining.md - Training patterns, TrainingArguments, distributed training, callbacksgeneration_strategies.md - Text generation methods, decoding strategies, parameterstask_patterns.md - Complete workflows for common tasks (classification, NER, QA, summarization, etc.)When working on specific tasks or features, load the relevant reference file for detailed guidance.
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