diff --git a/Makefile b/Makefile deleted file mode 100644 index bda886b..0000000 --- a/Makefile +++ /dev/null @@ -1,52 +0,0 @@ -.PHONY: default -default: help - -.PHONY: help -help: ## Show this help message - @awk 'BEGIN {FS = ":.*?## "} /^[a-zA-Z_-]+:.*?## / {printf "\033[36m%-30s\033[0m %s\n", $$1, $$2}' $(MAKEFILE_LIST) - -# ============================================================================= -# ENVIRONMENT SETUP -# ============================================================================= - -.PHONY: setup -setup: ## Setup virtual environment and install dependencies - python -m venv .venv - source .venv/bin/activate - .venv/bin/pip install --upgrade pip - .venv/bin/pip install -r requirements.txt - -.PHONY: install -install: ## Install/update dependencies - pip install --upgrade pip - pip install -r requirements.txt - -# ============================================================================= -# DEVELOPMENT & CODE QUALITY -# ============================================================================= - -.PHONY: format -format: ## Format code with black - black . --line-length 100 - -.PHONY: lint -lint: ## Lint code with flake8 - flake8 . --max-line-length=100 --ignore=E203,W503 --exclude=.venv - -.PHONY: type-check -type-check: ## Type check with mypy - mypy . --ignore-missing-imports - -.PHONY: notebook -notebook: ## Start Jupyter notebook - jupyter notebook notebooks/ - -# ============================================================================= -# DEPLOYMENT & PRODUCTION -# ============================================================================= - -.PHONY: backup -backup: ## Backup datasets and results - @mkdir -p backups/$(shell date +%Y%m%d_%H%M%S) - @cp -r data/ backups/$(shell date +%Y%m%d_%H%M%S)/data/ - @echo "Backup created in backups/$(shell date +%Y%m%d_%H%M%S)/" diff --git a/README.md b/README.md index 91886e7..a040282 100644 --- a/README.md +++ b/README.md @@ -91,11 +91,6 @@ uv run ners research train --name="random_forest" --type="baseline" --env="produ uv run ners research train --name="random_forest_native" --type="baseline" --env="production" uv run ners research train --name="random_forest_surname" --type="baseline" --env="production" -# svm -uv run ners research train --name="svm" --type="baseline" --env="production" -uv run ners research train --name="svm_native" --type="baseline" --env="production" -uv run ners research train --name="svm_surname" --type="baseline" --env="production" - # naive bayes uv run ners research train --name="naive_bayes" --type="baseline" --env="production" uv run ners research train --name="naive_bayes_native" --type="baseline" --env="production" @@ -112,46 +107,6 @@ uv run ners research train --name="xgboost_native" --type="baseline" --env="prod uv run ners research train --name="xgboost_surname" --type="baseline" --env="production" ``` -## TensorFlow on macOS (Intel) with uv - -TensorFlow no longer publishes wheels for macOS Intel. To keep using uv and run TF reliably, use a Linux container with TF preinstalled and install project code with minimal extras inside the container. - -### One-time build - -```bash -docker compose -f docker/compose.tf.yml build - -If you see a message like `tensorflow/tensorflow:: not found`, update `docker/Dockerfile.tf-cpu` to a tag that exists (e.g., `2.17.0`) and rebuild: - -```bash -sed -n '1,20p' docker/Dockerfile.tf-cpu # verify the FROM line -docker pull tensorflow/tensorflow:2.17.0 # quick availability check -docker compose -f docker/compose.tf.yml build -``` -``` - -### Start a shell with uv and TF available - -```bash -docker compose -f docker/compose.tf.yml run --rm tf bash -``` - -Inside the container: - -```bash -# Install project in editable mode without pulling full deps -uv pip install -e . --no-deps - -# Install only what research needs alongside TensorFlow -uv pip install typer pandas scikit-learn seaborn plotly - -# Sanity check -uv run python -c "import tensorflow as tf; print(tf.__version__)" - -# Run an experiment -uv run ners research train --name="lstm" --type="baseline" --env="production" -``` - ## Web Interface This project includes a user-friendly web interface built with Streamlit, allowing non-technical users to run diff --git a/compose.yml b/compose.yml index 640b4cb..abe3bda 100644 --- a/compose.yml +++ b/compose.yml @@ -10,10 +10,12 @@ services: environment: NERS_ENV: production STREAMLIT_SERVER_ADDRESS: 0.0.0.0 + PYTHONPATH: /app/src # expose Streamlit for `ners web run` ports: - "8501:8501" volumes: + - ./src:/app/src - ./assets:/app/assets - ./config:/app/config - ./data:/app/data diff --git a/config/pipeline.development.yaml b/config/pipeline.development.yaml index b9b63fa..6c109db 100644 --- a/config/pipeline.development.yaml +++ b/config/pipeline.development.yaml @@ -30,7 +30,7 @@ llm: # Data handling configuration data: split_evaluation: false - max_dataset_size: 100_000 + max_dataset_size: 10_000 balance_by_sex: true # Enhanced logging for development diff --git a/pyproject.toml b/pyproject.toml index b339851..d51dd97 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -22,6 +22,7 @@ dependencies = [ "streamlit>=1.50.0", "tqdm>=4.67.1", "typer>=0.19.2", + "tensorflow==2.20.0; sys_platform == 'linux' and platform_machine == 'x86_64'", "xgboost>=3.0.5", ] @@ -36,6 +37,3 @@ build-backend = "uv_build" dev = [ "ruff>=0.13.3", ] - -[tool.uv] -required-environments = ["sys_platform == 'linux' and platform_machine == 'x86_64'"] diff --git a/src/ners/cli.py b/src/ners/cli.py index d30cab3..8d717ad 100644 --- a/src/ners/cli.py +++ b/src/ners/cli.py @@ -204,7 +204,6 @@ def web_run( config: Optional[Path] = typer.Option(None, help="Path to configuration file"), env: str = typer.Option("development", help="Environment name"), ) -> None: - """Launch the Streamlit web app via subprocess.""" app_path = Path(__file__).parent / "web" / "app.py" cmd = [ sys.executable, diff --git a/src/ners/core/config/__init__.py b/src/ners/core/config/__init__.py index 4169761..ce852da 100644 --- a/src/ners/core/config/__init__.py +++ b/src/ners/core/config/__init__.py @@ -4,7 +4,6 @@ from typing import Optional, Union from ners.core.utils import ensure_directories from ners.core.config.config_manager import ConfigManager -from ners.core.config.logging_config import LoggingConfig from ners.core.config.pipeline_config import PipelineConfig config_manager = ConfigManager() diff --git a/src/ners/research/models/lightgbm_model.py b/src/ners/research/models/lightgbm_model.py index 1da50b0..4b8c913 100644 --- a/src/ners/research/models/lightgbm_model.py +++ b/src/ners/research/models/lightgbm_model.py @@ -16,6 +16,7 @@ class LightGBMModel(TraditionalModel): # Store vectorizers and encoders to ensure consistent feature space self.vectorizers = {} self.label_encoders = {} + self.feature_columns = [] def build_model(self) -> BaseEstimator: params = self.config.model_params @@ -38,14 +39,16 @@ class LightGBMModel(TraditionalModel): random_state=self.config.random_seed, objective=params.get("objective", "binary"), n_jobs=params.get("n_jobs", -1), - verbose=2, + verbose=params.get("verbose", -1), device=device, gpu_platform_id=gpu_platform_id, gpu_device_id=gpu_device_id, + force_row_wise=params.get("force_row_wise", True), ) - def prepare_features(self, X: pd.DataFrame) -> np.ndarray: + def prepare_features(self, X: pd.DataFrame) -> pd.DataFrame | np.ndarray: features = [] + columns: list[str] = [] for feature_type in self.config.features: if feature_type.value in X.columns: @@ -53,7 +56,9 @@ class LightGBMModel(TraditionalModel): if feature_type.value in ["name_length", "word_count"]: # Numerical features - features.append(column.fillna(0).values.reshape(-1, 1)) + arr = column.fillna(0).values.reshape(-1, 1) + features.append(arr) + columns.append(feature_type.value) elif feature_type.value in ["full_name", "native_name", "surname"]: # Character-level features for names feature_key = f"vectorizer_{feature_type.value}" @@ -63,20 +68,24 @@ class LightGBMModel(TraditionalModel): self.vectorizers[feature_key] = CountVectorizer( analyzer="char", ngram_range=(2, 3), max_features=50 ) - char_features = ( - self.vectorizers[feature_key] - .fit_transform(column.fillna("").astype(str)) - .toarray() - ) + vec = self.vectorizers[feature_key] + char_features = vec.fit_transform( + column.fillna("").astype(str) + ).toarray() + vocab_names = list(vec.get_feature_names_out()) else: # Subsequent times - use existing vectorizer - char_features = ( - self.vectorizers[feature_key] - .transform(column.fillna("").astype(str)) - .toarray() - ) + vec = self.vectorizers[feature_key] + char_features = vec.transform( + column.fillna("").astype(str) + ).toarray() + vocab_names = list(vec.get_feature_names_out()) features.append(char_features) + # Prefix with feature name to avoid collisions + columns.extend( + [f"char_{feature_type.value}_{n}" for n in vocab_names] + ) else: # Categorical features feature_key = f"encoder_{feature_type.value}" @@ -111,5 +120,11 @@ class LightGBMModel(TraditionalModel): ) features.append(encoded.reshape(-1, 1)) + columns.append(f"cat_{feature_type.value}") + if not features: + return pd.DataFrame(index=X.index) - return np.hstack(features) if features else np.array([]).reshape(len(X), 0) + matrix = np.hstack(features) + # Persist column order for consistency + self.feature_columns = columns + return pd.DataFrame(matrix, index=X.index, columns=columns) diff --git a/src/ners/research/models/logistic_regression_model.py b/src/ners/research/models/logistic_regression_model.py index 452397a..983369e 100644 --- a/src/ners/research/models/logistic_regression_model.py +++ b/src/ners/research/models/logistic_regression_model.py @@ -1,3 +1,4 @@ +import logging import numpy as np import pandas as pd from sklearn.base import BaseEstimator @@ -13,22 +14,38 @@ class LogisticRegressionModel(TraditionalModel): def build_model(self) -> BaseEstimator: params = self.config.model_params - # Character n-grams are strong signals for names; (2,5) balances + # Character n-grams are strong signals for names; (2,4) balances # capturing prefixes/suffixes with tractable feature size. + # Ensure tuple for sklearn API (YAML lists -> tuple) + ngram_range = params.get("ngram_range", (2, 4)) + if isinstance(ngram_range, list): + ngram_range = tuple(ngram_range) + vectorizer = CountVectorizer( analyzer="char", - ngram_range=params.get("ngram_range", (2, 5)), + ngram_range=ngram_range, max_features=params.get("max_features", 10000), ) - # liblinear handles sparse, small-to-medium problems well; n_jobs parallelizes - # OvR across classes (no effect for binary). class_weight can mitigate imbalance. + # Choose solver and threads. liblinear ignores n_jobs>1 in recent sklearn + # versions, which raises a warning; clamp to 1 to avoid noise. + solver = params.get("solver", "liblinear") + n_jobs = params.get("n_jobs", -1) + if solver == "liblinear" and (n_jobs is None or n_jobs != 1): + if isinstance(n_jobs, int) and n_jobs != 1: + logging.info( + "LogisticRegression(liblinear): forcing n_jobs=1 to avoid sklearn warning" + ) + n_jobs = 1 + + # liblinear handles sparse, small-to-medium problems well; class_weight can + # mitigate imbalance. For very large, consider solver='saga'. classifier = LogisticRegression( max_iter=params.get("max_iter", 1000), random_state=self.config.random_seed, verbose=2, - solver=params.get("solver", "liblinear"), - n_jobs=params.get("n_jobs", -1), + solver=solver, + n_jobs=n_jobs, class_weight=params.get("class_weight", None), ) diff --git a/src/ners/research/models/naive_bayes_model.py b/src/ners/research/models/naive_bayes_model.py index cf8f027..ca476e8 100644 --- a/src/ners/research/models/naive_bayes_model.py +++ b/src/ners/research/models/naive_bayes_model.py @@ -15,9 +15,14 @@ class NaiveBayesModel(TraditionalModel): params = self.config.model_params # Bag-of-character-ngrams aligns with Multinomial NB assumptions; (1,4) # includes unigrams for coverage and higher n for suffix/prefix cues. + # Ensure tuple for sklearn API (YAML lists -> tuple) + ngram_range = params.get("ngram_range", (2, 4)) + if isinstance(ngram_range, list): + ngram_range = tuple(ngram_range) + vectorizer = CountVectorizer( analyzer="char", - ngram_range=params.get("ngram_range", (2, 5)), + ngram_range=ngram_range, max_features=params.get("max_features", 8000), ) diff --git a/src/ners/research/models/svm_model.py b/src/ners/research/models/svm_model.py deleted file mode 100644 index 2d56a9e..0000000 --- a/src/ners/research/models/svm_model.py +++ /dev/null @@ -1,52 +0,0 @@ -import numpy as np -import pandas as pd -from sklearn.base import BaseEstimator -from sklearn.feature_extraction.text import TfidfVectorizer -from sklearn.pipeline import Pipeline -from sklearn.svm import SVC - -from ners.research.traditional_model import TraditionalModel - - -class SVMModel(TraditionalModel): - """Support Vector Machine with character n-grams and RBF kernel""" - - def build_model(self) -> BaseEstimator: - params = self.config.model_params - # TF-IDF downweights very common patterns; char n-grams (2,4) are effective - # for distinguishing name morphology under RBF kernels. - vectorizer = TfidfVectorizer( - analyzer="char", - ngram_range=params.get("ngram_range", (2, 4)), - max_features=params.get("max_features", 5000), - ) - - # RBF kernel captures non-linear interactions between n-grams; probability=True - # adds calibration at some cost. Larger cache helps speed kernel computations. - classifier = SVC( - kernel=params.get("kernel", "rbf"), - C=params.get("C", 1.0), - gamma=params.get("gamma", "scale"), - probability=True, # Enable probability prediction - class_weight=params.get("class_weight", None), - cache_size=params.get("cache_size", 1000), - random_state=self.config.random_seed, - verbose=2, - ) - - return Pipeline([("vectorizer", vectorizer), ("classifier", classifier)]) - - def prepare_features(self, X: pd.DataFrame) -> np.ndarray: - text_features = [] - - for feature_type in self.config.features: - if feature_type.value in X.columns: - text_features.append(X[feature_type.value].astype(str)) - - if len(text_features) == 1: - return text_features[0].values - else: - combined = text_features[0].astype(str) - for feature in text_features[1:]: - combined = combined + " " + feature.astype(str) - return combined.values diff --git a/src/ners/research/models/transformer_model.py b/src/ners/research/models/transformer_model.py index 2fc460f..1a9876f 100644 --- a/src/ners/research/models/transformer_model.py +++ b/src/ners/research/models/transformer_model.py @@ -24,20 +24,21 @@ class TransformerModel(NeuralNetworkModel): def build_model_with_vocab(self, vocab_size: int, **kwargs) -> Any: params = kwargs + # Use a single resolved max_len everywhere to avoid shape mismatches + max_len = int(params.get("max_len", 6)) # Build Transformer model - inputs = Input(shape=(params.get("max_len", 8),)) + inputs = Input(shape=(max_len,)) x = Embedding( input_dim=vocab_size, output_dim=params.get("embedding_dim", 64), - input_length=params.get("max_len", 8), mask_zero=True, )(inputs) # Add positional encoding - positions = tf.range(start=0, limit=params.get("max_len", 8), delta=1) + positions = tf.range(start=0, limit=max_len, delta=1) pos_embedding = Embedding( - input_dim=params.get("max_len", 8), + input_dim=max_len, output_dim=params.get("embedding_dim", 64), )(positions) x = x + pos_embedding @@ -85,6 +86,6 @@ class TransformerModel(NeuralNetworkModel): # Convert to sequences sequences = self.tokenizer.texts_to_sequences(text_data) - max_len = self.config.model_params.get("max_len", 6) + max_len = int(self.config.model_params.get("max_len", 6)) return pad_sequences(sequences, maxlen=max_len, padding="post") diff --git a/src/ners/research/models/xgboost_model.py b/src/ners/research/models/xgboost_model.py index eaf34e1..a567508 100644 --- a/src/ners/research/models/xgboost_model.py +++ b/src/ners/research/models/xgboost_model.py @@ -20,13 +20,12 @@ class XGBoostModel(TraditionalModel): def build_model(self) -> BaseEstimator: params = self.config.model_params - # Optional GPU acceleration + # Optional GPU acceleration. With modern XGBoost, setting tree_method is + # sufficient and you typically don't need to pass `predictor`; doing so can + # trigger "Parameters ... are not used" warnings with the sklearn API. use_gpu = bool(params.get("use_gpu", False)) default_tree_method = "gpu_hist" if use_gpu else "hist" tree_method = params.get("tree_method", default_tree_method) - predictor = params.get( - "predictor", "gpu_predictor" if tree_method.startswith("gpu") else "auto" - ) # Histogram-based trees and parallelism provide fast training; default # logloss metric suits binary classification of gender. @@ -40,8 +39,7 @@ class XGBoostModel(TraditionalModel): eval_metric="logloss", n_jobs=params.get("n_jobs", -1), tree_method=tree_method, - predictor=predictor, - verbosity=2, + verbosity=params.get("verbosity", 0), ) def prepare_features(self, X: pd.DataFrame) -> np.ndarray: diff --git a/src/ners/research/traditional_model.py b/src/ners/research/traditional_model.py index bce368c..6193947 100644 --- a/src/ners/research/traditional_model.py +++ b/src/ners/research/traditional_model.py @@ -61,18 +61,22 @@ class TraditionalModel(BaseModel): f"Fitting model with {X_prepared.shape[0]} samples and {X_prepared.shape[1]} features" ) - logging.info(X_prepared[0]) + try: + # Log a small sample safely for arrays or DataFrames + if hasattr(X_prepared, "iloc"): + logging.info(X_prepared.iloc[0].to_dict()) + else: + logging.info(X_prepared[0]) + except Exception: + pass logging.info(f"Model parameters: {self.config.model_params}") - history = self.model.fit(X_prepared, y_encoded) + # Fit scikit-learn compatible model. Unlike Keras, sklearn's fit returns + # the estimator itself and does not provide a training history object. + # We therefore do not populate training_history here. + self.model.fit(X_prepared, y_encoded) self.is_fitted = True - - self.training_history = { - "accuracy": history.history["accuracy"], - "loss": history.history["loss"], - "val_accuracy": history.history.get("val_accuracy", []), - "val_loss": history.history.get("val_loss", []), - } + self.training_history = {} return self diff --git a/uv.lock b/uv.lock index cf26eff..7c4d45c 100644 --- a/uv.lock +++ b/uv.lock @@ -2,10 +2,20 @@ version = 1 revision = 3 requires-python = ">=3.11" resolution-markers = [ - "python_full_version >= '3.12'", + "python_full_version >= '3.13'", + "python_full_version == '3.12.*'", "python_full_version < '3.12'", ] +[[package]] +name = "absl-py" +version = "2.3.1" +source = { registry = "https://pypi.org/simple" } +sdist = { url = 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