Train ML models and iterate systematically with experiment tracking. Full coverage of supervised learning: Naive Bayes, KNN, Discriminant Analysis (LDA/QDA), SVM/SVR, Decision Trees, Ensemble Methods (Random Forest, XGBoost, LightGBM), GLM (Poisson, Gamma, Tweedie), Gaussian Process, Ridge/Lasso/ElasticNet, and Neural Networks (PyTorch). Covers data splitting, cross-validation, metrics, persistence, hyperparameter search, and TSV-based experiment tracking. Use when the user wants to train a model, fit a classifier or regressor, evaluate performance, do cross-validation, run experiments, tune hyperparameters, or compare runs.
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Train ML models and iterate systematically with experiment tracking. Full coverage of supervised learning: Naive Bayes, KNN, Discriminant Analysis (LDA/QDA), SVM/SVR, Decision Trees, Ensemble Methods (Random Forest, XGBoost, LightGBM), GLM (Poisson, Gamma, Tweedie), Gaussian Process, Ridge/Lasso/ElasticNet, and Neural Networks (PyTorch). Covers data splitting, cross-validation, metrics, persistence, hyperparameter search, and TSV-based experiment tracking. Use when the user wants to train a model, fit a classifier or regressor, evaluate performance, do cross-validation, run experiments, tune hyperparameters, or compare runs.
allowed-tools
Bash(uv run * scripts/analyze_results.py *) Read Write Glob Grep
disable-model-invocation
true
argument-hint
path to feature-engineered dataset or results.tsv (e.g. "data/features.csv")
import torch
import torch.nn as nn
classMLP(nn.Module):
def__init__(self, input_dim, hidden=128, output=1):
super().__init__()
self.net = nn.Sequential(
nn.Linear(input_dim, hidden), nn.ReLU(), nn.Dropout(0.2),
nn.Linear(hidden, hidden), nn.ReLU(), nn.Dropout(0.2),
nn.Linear(hidden, output),
)
defforward(self, x): returnself.net(x)
model = MLP(X_train.shape[1])
opt = torch.optim.AdamW(model.parameters(), lr=1e-3, weight_decay=1e-4)
loss_fn = nn.BCEWithLogitsLoss()
for epoch inrange(100):
model.train()
for bx, by in loader:
opt.zero_grad()
loss_fn(model(bx).squeeze(), by).backward()
opt.step()
torch.save(model.state_dict(), 'model.pt')
Naive Bayes
from sklearn.naive_bayes import GaussianNB, MultinomialNB, BernoulliNB
from sklearn.metrics import classification_report
import joblib
# GaussianNB — continuous features (assumes Gaussian distribution per class)
model = GaussianNB()
model.fit(X_train, y_train)
print(classification_report(y_val, model.predict(X_val)))
joblib.dump(model, 'model_nb.joblib')
# MultinomialNB — count/frequency features (e.g. TF-IDF, bag-of-words)# from sklearn.naive_bayes import MultinomialNB# model = MultinomialNB(alpha=1.0) # alpha = Laplace smoothing# BernoulliNB — binary features (word presence/absence)# from sklearn.naive_bayes import BernoulliNB# model = BernoulliNB(alpha=1.0)# Tuning: var_smoothing (GaussianNB), alpha (Multinomial/Bernoulli)# When to use: text classification, spam detection, small data, fast baseline
K-Nearest Neighbors (KNN)
from sklearn.neighbors import KNeighborsClassifier, KNeighborsRegressor
from sklearn.preprocessing import StandardScaler
from sklearn.pipeline import Pipeline
import joblib
# Classification
pipe = Pipeline([
('scaler', StandardScaler()), # KNN is distance-based — scaling is mandatory
('model', KNeighborsClassifier(
n_neighbors=5,
weights='distance', # 'uniform' or 'distance' (closer = more weight)
metric='minkowski', # Euclidean when p=2, Manhattan when p=1
n_jobs=-1,
)),
])
pipe.fit(X_train, y_train)
joblib.dump(pipe, 'model_knn.joblib')
# Regression# pipe = Pipeline([('scaler', StandardScaler()), ('model', KNeighborsRegressor(n_neighbors=5))])# Tuning: n_neighbors (odd to avoid ties), weights, metric# Weakness: O(n) prediction time — slow at inference on large datasets# When to use: small/medium data, non-linear boundaries, anomaly detection
Discriminant Analysis (LDA / QDA)
from sklearn.discriminant_analysis import LinearDiscriminantAnalysis, QuadraticDiscriminantAnalysis
from sklearn.metrics import classification_report
import joblib
# LDA — assumes equal covariance across classes; also works as dimensionality reduction
lda = LinearDiscriminantAnalysis(
solver='svd', # 'svd' (default), 'lsqr', 'eigen'
n_components=None, # reduce to min(n_classes-1, n_features) components
store_covariance=False,
)
lda.fit(X_train, y_train)
print(classification_report(y_val, lda.predict(X_val)))
joblib.dump(lda, 'model_lda.joblib')
# For dimensionality reduction (supervised):# X_reduced = lda.transform(X_train) # reduces to n_classes-1 dimensions# QDA — allows different covariance per class; more flexible but needs more data# qda = QuadraticDiscriminantAnalysis(reg_param=0.0) # reg_param adds regularization# When to use: Gaussian class distributions, interpretable decision boundary,# dimensionality reduction to n_classes-1, well-separated classes
Support Vector Machine (SVM / SVR)
from sklearn.svm import SVC, SVR, LinearSVC
from sklearn.preprocessing import StandardScaler
from sklearn.pipeline import Pipeline
import joblib
# Classification — RBF kernel (best general-purpose choice)
pipe = Pipeline([
('scaler', StandardScaler()), # SVM is distance-based — scaling is mandatory
('model', SVC(
C=1.0, # Regularization: high C = low bias/high variance
kernel='rbf', # 'linear', 'poly', 'rbf', 'sigmoid'
gamma='scale', # 'scale' = 1/(n_features*X.var()), 'auto' = 1/n_features
probability=True, # enables predict_proba (slower fitting)
random_state=42,
class_weight='balanced', # handles class imbalance
)),
])
pipe.fit(X_train, y_train)
print(pipe.predict_proba(X_val)[:5])
joblib.dump(pipe, 'model_svm.joblib')
# For large datasets (>10k): use LinearSVC (much faster, linear kernel only)# pipe = Pipeline([('scaler', StandardScaler()), ('model', LinearSVC(C=1.0, max_iter=2000))])# Regression — SVR# pipe = Pipeline([('scaler', StandardScaler()), ('model', SVR(C=1.0, epsilon=0.1, kernel='rbf'))])# Tuning priority: C first, then gamma (for RBF), then kernel# When to use: small/medium data (<50k), high-dimensional (text, images), clear margin of separation
Decision Tree
from sklearn.tree import DecisionTreeClassifier, DecisionTreeRegressor, export_text
from sklearn.metrics import classification_report
import joblib
# Classification
tree = DecisionTreeClassifier(
max_depth=5, # constrain depth to prevent overfitting
min_samples_split=20, # min samples to split a node
min_samples_leaf=10, # min samples in a leaf
criterion='gini', # 'gini' or 'entropy'
class_weight='balanced',
random_state=42,
)
tree.fit(X_train, y_train)
print(classification_report(y_val, tree.predict(X_val)))
# Print interpretable rules
rules = export_text(tree, feature_names=list(X_train.columns))
print(rules[:2000]) # first 2000 chars of rule set
joblib.dump(tree, 'model_tree.joblib')
# Regression# tree = DecisionTreeRegressor(max_depth=5, min_samples_leaf=10, random_state=42)# Tuning priority: max_depth → min_samples_leaf → criterion# Weakness: high variance (small data changes flip the tree) — prefer ensemble unless interpretability required# When to use: interpretability is mandatory, rule extraction, feature selection proxy
Generalized Linear Model (GLM)
import statsmodels.api as sm
import numpy as np
# Poisson GLM — count data (events per unit time/area)
X_train_sm = sm.add_constant(X_train) # statsmodels needs explicit intercept
glm_poisson = sm.GLM(
y_train,
X_train_sm,
family=sm.families.Poisson(link=sm.families.links.Log()),
)
result = glm_poisson.fit()
print(result.summary())
y_pred = result.predict(sm.add_constant(X_val))
# Gamma GLM — positive continuous, right-skewed (insurance claims, durations)# glm_gamma = sm.GLM(y_train, X_train_sm, family=sm.families.Gamma(link=sm.families.links.Log()))# Tweedie GLM — flexible family (p=0: Normal, p=1: Poisson, p=2: Gamma, 1<p<2: compound)# glm_tweedie = sm.GLM(y_train, X_train_sm, family=sm.families.Tweedie(var_power=1.5))# Negative Binomial — overdispersed count data (variance > mean)# glm_nb = sm.GLM(y_train, X_train_sm, family=sm.families.NegativeBinomial())# Save coefficientsimport json
coefs = dict(zip(['intercept'] + list(X_train.columns), result.params))
withopen('model_glm_coefs.json', 'w') as f:
json.dump(coefs, f, indent=2)
# When to use: count data, rate data, insurance/actuarial, non-Gaussian errors,# heteroscedastic residuals, log/logit link needed for interpretability
Gaussian Process (GP)
from sklearn.gaussian_process import GaussianProcessClassifier, GaussianProcessRegressor
from sklearn.gaussian_process.kernels import RBF, Matern, WhiteKernel, ConstantKernel
from sklearn.preprocessing import StandardScaler
from sklearn.pipeline import Pipeline
import joblib
import numpy as np
# Regression — returns mean prediction AND uncertainty (std dev)
kernel = ConstantKernel(1.0) * Matern(length_scale=1.0, nu=2.5) + WhiteKernel(noise_level=0.1)
gpr = GaussianProcessRegressor(
kernel=kernel,
alpha=1e-6, # numerical stability
normalize_y=True, # subtract mean of y_train
n_restarts_optimizer=5, # restarts to find global kernel hyperparams
random_state=42,
)
gpr.fit(X_train, y_train)
y_pred, y_std = gpr.predict(X_val, return_std=True)
print(f"Val RMSE: {np.sqrt(np.mean((y_pred - y_val)**2)):.4f}")
print(f"Mean uncertainty (std): {y_std.mean():.4f}")
joblib.dump(gpr, 'model_gp.joblib')
# Classification — probabilistic predictions# kernel = ConstantKernel(1.0) * RBF(length_scale=1.0)# gpc = GaussianProcessClassifier(kernel=kernel, n_restarts_optimizer=5, random_state=42)# gpc.fit(X_train, y_train)# probs = gpc.predict_proba(X_val)# Weakness: O(n³) training, O(n²) memory — not viable above ~5k samples# When to use: uncertainty quantification is required, small data (<5k),# spatial/temporal data (use Matern kernel), active learning, Bayesian optimization
Metrics reference
Classification
When to use
Accuracy
Balanced classes
F1
Imbalanced classes
AUC-ROC
Ranking tasks
Precision
FP costly
Recall
FN costly
Regression
When to use
RMSE
Penalize large errors
MAE
Robust to outliers
R-squared
Variance explained
Evaluation report format
=== Training Report ===
Task: Binary Classification
Model: XGBoost (1000 rounds, early stopped at 347)
Split: 35k train / 7.5k val / 7.5k test
Val: Accuracy=0.8634, F1=0.8521, AUC=0.9234
Test: Accuracy=0.8601, F1=0.8489
Top features: feature_a (0.234), feature_b (0.189), feature_c (0.156)
Saved: model.xgb, metrics.json
Rules
Never evaluate on training data
Set random seeds everywhere
Use early stopping for iterative models
Save both model and preprocessing (use Pipeline or save scaler separately)
Status: KEEP (improved), DISCARD (same or worse), CRASH (error/OOM/NaN)
Experiment cycle
1. Hypothesize (what change, why it might help)
2. Modify (one variable at a time)
3. Run (fixed budget: time or epochs)
4. Record (append to results.tsv)
5. Decide: KEEP or DISCARD
6. Repeat
What to try (priority order)
High impact (try first)
Learning rate (3x and 0.3x current)
Model capacity (layers, hidden size)
Batch size (double or halve)
Regularization (dropout, weight decay)
Medium impact
5. Optimizer (Adam → AdamW → SGD+momentum)
6. LR schedule (cosine, warmup, step decay)
7. Data augmentation
8. Feature selection
