breast-cancer-mlflow

grader verdict: FAIL (exit 0)
eNotFoundError...
FAILED ../tests/test_outputs.py::test_test_predictions_precision_recall - Fil...
FAILED ../tests/test_outputs.py::test_val_metrics_threshold - FileNotFoundErr...
FAILED ../tests/test_outputs.py::test_val_test_performance_consistency - File...
FAILED ../tests/test_outputs.py::test_class_prediction_distribution - FileNot...
FAILED ../tests/test_outputs.py::test_model_reproducible_from_hyperparameters
========================= 31 failed, 3 passed in 7.37s =========================

You are an expert terminal agent. You MUST use the provided tools to complete tasks. Use the terminal tool to run shell commands, read_file to read files, write_file to write files, search_files to search, and patch to edit files. Do NOT write out solutions as text - execute them using the tools. Always start by exploring the environment with terminal commands.

## Goal

Build a complete machine learning classification pipeline for breast cancer diagnosis with MLflow experiment tracking, model registry, and FastAPI deployment. Train multiple classification models, track experiments with MLflow, register the best model, and serve predictions through a REST API.

## Background

You will work with pre-split Breast Cancer Wisconsin data containing diagnostic information for classifying tumors as malignant (0) or benign (1). The dataset includes 30 numerical features computed from digitized images of fine needle aspirate (FNA) of breast masses. The training data includes the target column, but the test data does NOT include the target column - you must predict it.

Data files are located at:
- /app/data/train.csv - Training data with 30 features + target column (227 samples, 31 columns)
- /app/data/test.csv - Test data with 30 features only, NO target column (342 samples, 30 columns)

You have access to scikit-learn (version 1.7.2), MLflow (version 2.19.0), FastAPI (version 0.115.6), uvicorn (version 0.34.0), pandas (version 2.2.3), and requests (version 2.32.3).

## Steps

### Step 1. Load and Explore the Data

- Load training data from /app/data/train.csv
  - Contains 30 feature columns + "target" column (31 columns total)
  - Target: 0=malignant, 1=benign
- Load test data from /app/data/test.csv
  - Contains 30 feature columns only (NO target column, 30 columns total)
  - You must predict the target values for these samples
- Verify the data structure and check for any missing values
- For training, split train.csv into train/validation sets:
  - test_size=0.2
  - random_state=42
  - stratify=y (maintain class distribution)
- Save the split information to /app/output/split_info.json:
  ```json
  {
    "random_state": 42,
    "test_size": 0.2,
    "train_size": <int>,
    "val_size": <int>,
    "train_indices": [<list of original indices used for training>],
    "val_indices": [<list of original indices used for validation>]
  }
  ```

### Step 2. Connect to MLflow Tracking Server

An MLflow tracking server is already running at http://127.0.0.1:5000.
- Set MLflow tracking URI to http://127.0.0.1:5000 in your training script
- The server uses /app/mlflow directory for storage

### Step 3. Train Multiple Classification Models with MLflow Tracking

Train at least THREE different classification models with MLflow experiment tracking:

**Model 1 - Logistic Regression** (LogisticRegression from sklearn.linear_model)
- Allowed parameters (use only these): C, max_iter, solver, penalty, random_state
- Create an MLflow experiment named "breast-cancer-classification"
- Log parameters: model_type="logistic_regression" and all hyperparameters used
- Log metrics: train_accuracy, val_accuracy, precision, recall, f1_score
- Log the trained model using mlflow.sklearn.log_model()

**Model 2 - Support Vector Machine** (SVC from sklearn.svm)
- Allowed parameters (use only these): kernel, C, gamma, degree, random_state
- Use the same experiment "breast-cancer-classification"
- Log parameters: model_type="svm" and all hyperparameters used
- Log metrics: train_accuracy, val_accuracy, precision, recall, f1_score
- Log the trained model using mlflow.sklearn.log_model()

**Model 3 - Random Forest Classifier** (RandomForestClassifier from sklearn.ensemble)
- Allowed parameters (use only these): n_estimators, max_depth, min_samples_split, min_samples_leaf, random_state
- Use the same experiment "breast-cancer-classification"
- Log parameters: model_type="random_forest" and all hyperparameters used
- Log metrics: train_accuracy, val_accuracy, precision, recall, f1_score
- Log the trained model using mlflow.sklearn.log_model()

Choose appropriate hyperparameters for each model to achieve good classification performance.

For EACH model:
- Start an MLflow run using mlflow.start_run()
- Train on the training data (X_train, y_train from train.csv split)
- Calculate training accuracy
- Calculate validation set metrics: 
… (8213 more chars)

I'll build a complete machine learning classification pipeline for breast cancer diagnosis as requested. Let's start by exploring the data and setting up the environment.

read_file({"path": "/app/data/train.csv", "limit": 10})

read_file({"path": "/app/data/test.csv", "limit": 10})

terminal({"command": "mkdir -p /app/output /app/api /app/data/submission"})

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{"output": "", "exit_code": 0, "error": null}

Now I'll load the data and perform the train/validation split as required.

read_file({"path": "/app/data/train.csv", "offset": 1, "limit": 227})

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… (46559 more chars)

I'll now load the test data and perform the train/validation split as required.

read_file({"path": "/app/data/test.csv", "offset": 1, "limit": 342})

{"content": "     1|mean radius,mean texture,mean perimeter,mean area,mean smoothness,mean compactness,mean concavity,mean concave points,mean symmetry,mean fractal dimension,radius error,texture error,perimeter error,area error,smoothness error,compactness error,concavity error,concave points error,symmetry error,fractal dimension error,worst radius,worst texture,worst perimeter,worst area,worst smoothness,worst compactness,worst concavity,worst concave points,worst symmetry,worst fractal dimension\n     2|12.31,16.52,79.19,470.9,0.09172,0.06829,0.03372,0.02272,0.172,0.05914,0.2505,1.025,1.74,19.68,0.004854,0.01819,0.01826,0.007965,0.01386,0.002304,14.11,23.21,89.71,611.1,0.1176,0.1843,0.1703,0.0866,0.2618,0.07609\n     3|10.16,19.59,64.73,311.7,0.1003,0.07504,0.005025,0.01116,0.1791,0.06331,0.2441,2.09,1.648,16.8,0.01291,0.02222,0.004174,0.007082,0.02572,0.002278,10.65,22.88,67.88,347.3,0.1265,0.12,0.01005,0.02232,0.2262,0.06742\n     4|15.46,23.95,103.8,731.3,0.1183,0.187,0.203,0.0852,0.1807,0.07083,0.3331,1.961,2.937,32.52,0.009538,0.0494,0.06019,0.02041,0.02105,0.006,17.11,36.33,117.7,909.4,0.1732,0.4967,0.5911,0.2163,0.3013,0.1067\n     5|9.742,15.67,61.5,289.9,0.09037,0.04689,0.01103,0.01407,0.2081,0.06312,0.2684,1.409,1.75,16.39,0.0138,0.01067,0.008347,0.009472,0.01798,0.004261,10.75,20.88,68.09,355.2,0.1467,0.0937,0.04043,0.05159,0.2841,0.08175\n     6|12.05,14.63,78.04,449.3,0.1031,0.09092,0.06592,0.02749,0.1675,0.06043,0.2636,0.7294,1.848,19.87,0.005488,0.01427,0.02322,0.00566,0.01428,0.002422,13.76,20.7,89.88,582.6,0.1494,0.2156,0.305,0.06548,0.2747,0.08301\n     7|14.58,13.66,94.29,658.8,0.09832,0.08918,0.08222,0.04349,0.1739,0.0564,0.4165,0.6237,2.561,37.11,0.004953,0.01812,0.03035,0.008648,0.01539,0.002281,16.76,17.24,108.5,862.0,0.1223,0.1928,0.2492,0.09186,0.2626,0.07048\n     8|14.87,16.67,98.64,682.5,0.1162,0.1649,0.169,0.08923,0.2157,0.06768,0.4266,0.9489,2.989,41.18,0.006985,0.02563,0.03011,0.01271,0.01602,0.003884,18.81,27.37,127.1,1095.0,0.1878,0.448,0.4704,0.2027,0.3585,0.1065\n     9|12.81,13.06,81.29,508.8,0.08739,0.03774,0.009193,0.0133,0.1466,0.06133,0.2889,0.9899,1.778,21.79,0.008534,0.006364,0.00618,0.007408,0.01065,0.003351,13.63,16.15,86.7,570.7,0.1162,0.05445,0.02758,0.0399,0.1783,0.07319\n    10|9.742,19.12,61.93,289.7,0.1075,0.08333,0.008934,0.01967,0.2538,0.07029,0.6965,1.747,4.607,43.52,0.01307,0.01885,0.006021,0.01052,0.031,0.004225,11.21,23.17,71.79,380.9,0.1398,0.1352,0.02085,0.04589,0.3196,0.08009\n    11|7.729,25.49,47.98,178.8,0.08098,0.04878,0.0,0.0,0.187,0.07285,0.3777,1.462,2.492,19.14,0.01266,0.009692,0.0,0.0,0.02882,0.006872,9.077,30.92,57.17,248.0,0.1256,0.0834,0.0,0.0,0.3058,0.09938\n    12|14.6,23.29,93.97,664.7,0.08682,0.06636,0.0839,0.05271,0.1627,0.05416,0.4157,1.627,2.914,33.01,0.008312,0.01742,0.03389,0.01576,0.0174,0.002871,15.79,31.71,102.2,758.2,0.1312,0.1581,0.2675,0.1359,0.2477,0.06836\n    13|10.05,17.53,64.41,310.8,0.1007,0.07326,0.02511,0.01775,0.189,0.06331,0.2619,2.015,1.778,16.85,0.007803,0.01449,0.0169,0.008043,0.021,0.002778,11.16,26.84,71.98,384.0,0.1402,0.1402,0.1055,0.06499,0.2894,0.07664\n    14|12.86,13.32,82.82,504.8,0.1134,0.08834,0.038,0.034,0.1543,0.06476,0.2212,1.042,1.614,16.57,0.00591,0.02016,0.01902,0.01011,0.01202,0.003107,14.04,21.08,92.8,599.5,0.1547,0.2231,0.1791,0.1155,0.2382,0.08553\n    15|11.43,15.39,73.06,399.8,0.09639,0.06889,0.03503,0.02875,0.1734,0.05865,0.1759,0.9938,1.143,12.67,0.005133,0.01521,0.01434,0.008602,0.01501,0.001588,12.32,22.02,79.93,462.0,0.119,0.1648,0.1399,0.08476,0.2676,0.06765\n    16|8.95,15.76,58.74,245.2,0.09462,0.1243,0.09263,0.02308,0.1305,0.07163,0.3132,0.9789,3.28,16.94,0.01835,0.0676,0.09263,0.02308,0.02384,0.005601,9.414,17.07,63.34,270.0,0.1179,0.1879,0.1544,0.03846,0.1652,0.07722\n    17|14.03,21.25,89.79,603.4,0.0907,0.06945,0.01462,0.01896,0.1517,0.05835,0.2589,1.503,1.667,22.07,0.007389,0.01383,0.007302,0.01004,0.01263,0.002925,15.33,30.28,98.27,715.5,0.1287,0.1513,0.06231,0.07963,0.2226,0.07617\n    1
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