Add SapientML to automl benchmark (#630)

* Add SapientML to automl benchmark Signed-off-by: Kosaku Kimura <kimura.kosaku@fujitsu.com> * fix setup.sh (#2) * WIP Signed-off-by: Kosaku Kimura <kimura.kosaku@fujitsu.com> * Issue fix in setup.sh for SapientML * Updation of config file as Sapientml supports Python version 3.9 Signed-off-by: HimanshuRRai <himanshu.rai@fujitsu.com> --------- Signed-off-by: Kosaku Kimura <kimura.kosaku@fujitsu.com> Signed-off-by: HimanshuRRai <himanshu.rai@fujitsu.com> Co-authored-by: muhammed-nafi-k-a <muhammednafi.a@fujitsu.com> Co-authored-by: HimanshuRRai <himanshu.rai@fujitsu.com> * Remove requirement.txt file from master branch Signed-off-by: HimanshuRRai <himanshu.rai@fujitsu.com> --------- Signed-off-by: Kosaku Kimura <kimura.kosaku@fujitsu.com> Signed-off-by: HimanshuRRai <himanshu.rai@fujitsu.com> Co-authored-by: muhammed-nafi-k-a <muhammednafi.a@fujitsu.com> Co-authored-by: HimanshuRRai <himanshu.rai@fujitsu.com>
openml · Nov 15, 2024 · ac09497 · ac09497
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diff --git a/docs/website/frameworks.html b/docs/website/frameworks.html
@@ -944,6 +944,85 @@ <h3 class="paper-title">
             </svg>
           </label>
         </div>
+        <div class="accordion acard">
+          <div class="framework-header">
+            <img src="img/logos/Sapientml_favicon.ico" height="28px" />
+            <h3>SapientML</h3>
+            <div class="framework-links">
+              <a href="https://github.com/sapientml/sapientml" target="_blank"
+                ><img src="img/logos/GitHub-Mark-64px.png" height="24px"
+              /></a>
+              <a href="https://sapientml.readthedocs.io/en/latest/#" target="_blank"
+                >📖</a
+              >
+            </div>
+          </div>
+          <div>
+            SapientML is an AutoML technology that can learn from a corpus of existing datasets and their human-written pipelines, and efficiently generate a high-quality pipeline for a predictive task on a new dataset.
+          </div>
+          <input type="checkbox" id="more-SapientML" class="accordion-input" />
+          <div class="accordion-content">
+            <div class="paper">
+              <h3 class="paper-title">
+                SapientML: Synthesizing Machine Learning Pipelines by Learning from Human-Written Solutions
+              </h3>
+              <div class="paper-authors">
+                Ripon K. Saha, Akira Ura, Sonal Mahajan, Chenguang Zhu, Linyi Li, Yang Hu, Hiroaki Yoshida, Sarfraz Khurshid, Mukul R. Prasad
+              </div>
+              <div class="paper-abstract">
+                Automatic machine learning, or AutoML, holds the promise of truly democratizing the use of machine learning (ML), by substantially automating the work of data scientists. However, the huge combinatorial search space of candidate pipelines means that current AutoML techniques, generate sub-optimal pipelines, or none at all, especially on large,
+                complex datasets. In this work we propose an AutoML technique SapientML, that can learn from a corpus of existing datasets and their human-written pipelines, and efficiently generate a high-quality pipeline for a predictive task on a new dataset. To combat the search space explosion of AutoML,
+                SapientML employs a novel divide-and-conquer strategy realized as a three-stage program synthesis approach, that reasons on successively smaller search spaces. The first stage uses a machine-learned model to predict a set of plausible ML components to constitute a pipeline. In the second stage, this is then refined into a small pool of viable concrete pipelines using syntactic constraints derived from the corpus and the machine-learned model. Dynamically evaluating these few pipelines, in the third stage, provides the best solution. We instantiate SapientML as part of a fully automated tool-chain that creates a cleaned, labeled learning corpus by mining Kaggle, learns from it, and uses the learned models to then synthesize pipelines for new predictive tasks. We have created a training corpus of 1094 pipelines spanning 170 datasets, and evaluated SapientML on a set of 41 benchmark datasets, including 10 new, large, real-world datasets from Kaggle, and against 3 state-of-the-art AutoML tools and 2 baselines. Our evaluation shows that SapientML produces the best or comparable accuracy on 27 of the benchmarks while the second best tool fails to even produce a pipeline on 9 of the instances.
+              </div>
+              <div class="paper-links">
+                <div class="hover-expand">
+                  <strong>2022</strong>
+                  <div>
+                    ICSE '22: Proceedings of the 44th International Conference on Software Engineering,May 2022,Pages 1932–1944
+                  </div>
+                </div>
+                <a href="https://arxiv.org/pdf/2202.10451.pdf" target="_blank"
+                  >PDF</a
+                >
+                <a
+                  href="https://arxiv.org/abs/2202.10451"
+                  target="_blank"
+                  >arxiv</a
+                >
+              </div>
+            </div>
+          </div>
+          <label for="more-SapientML">
+            <svg
+              xmlns="http://www.w3.org/2000/svg"
+              class="accordion-chevron-down accordion-icon"
+              fill="none"
+              viewBox="0 0 24 24"
+              stroke="currentColor"
+              stroke-width="2"
+            >
+              <path
+                stroke-linecap="round"
+                stroke-linejoin="round"
+                d="M19 9l-7 7-7-7"
+              />
+            </svg>
+            <svg
+              xmlns="http://www.w3.org/2000/svg"
+              class="accordion-chevron-up accordion-icon"
+              fill="none"
+              viewBox="0 0 24 24"
+              stroke="currentColor"
+              stroke-width="2"
+            >
+              <path
+                stroke-linecap="round"
+                stroke-linejoin="round"
+                d="M5 15l7-7 7 7"
+              />
+            </svg>
+          </label>
+        </div>
       </section>
     </div>
   </body>

diff --git a/frameworks/SapientML/__init__.py b/frameworks/SapientML/__init__.py
@@ -0,0 +1,25 @@
+from amlb.benchmark import TaskConfig
+from amlb.data import Dataset
+from amlb.utils import call_script_in_same_dir
+
+
+def setup(*args, **kwargs):
+    call_script_in_same_dir(__file__, "setup.sh", *args, **kwargs)
+
+
+def run(dataset: Dataset, config: TaskConfig):
+    from frameworks.shared.caller import run_in_venv
+
+    data = dict(
+        train=dict(path=dataset.train.data_path("csv")),
+        test=dict(path=dataset.test.data_path("csv")),
+        target=dict(name=dataset.target.name, classes=dataset.target.values),
+        problem_type=dataset.type.name,
+    )
+    return run_in_venv(
+        __file__,
+        "exec.py",
+        input_data=data,
+        dataset=dataset,
+        config=config,
+    )
diff --git a/frameworks/SapientML/exec.py b/frameworks/SapientML/exec.py
@@ -0,0 +1,97 @@
+import logging
+import os
+import tempfile as tmp
+
+from frameworks.shared.callee import call_run, result
+from frameworks.shared.utils import Timer
+from sapientml import SapientML
+from sapientml.util.logging import setup_logger
+from sklearn.preprocessing import OneHotEncoder
+
+os.environ["JOBLIB_TEMP_FOLDER"] = tmp.gettempdir()
+os.environ["OMP_NUM_THREADS"] = "1"
+os.environ["OPENBLAS_NUM_THREADS"] = "1"
+os.environ["MKL_NUM_THREADS"] = "1"
+
+
+log = logging.getLogger(__name__)
+
+
+def run(dataset, config):
+    import re
+
+    import pandas as pd
+
+    log.info(f"\n**** Sapientml ****\n")
+
+    is_classification = config.type == "classification"
+    is_multiclass = dataset.problem_type = "multiclass"
+    training_params = {k: v for k, v in config.framework_params.items() if not k.startswith("_")}
+
+    train_path, test_path = dataset.train.path, dataset.test.path
+    target_col = dataset.target.name
+
+    # Read parquet using pandas
+    X_train = pd.read_csv(train_path)
+    X_test = pd.read_csv(test_path)
+
+    # Removing unwanted sybols from column names (exception case)
+    X_train.columns = [re.sub("[^A-Za-z0-9_.]+", "", col) for col in X_train.columns]
+    X_test.columns = [re.sub("[^A-Za-z0-9_.]+", "", col) for col in X_test.columns]
+    target_col = re.sub("[^A-Za-z0-9_.]+", "", target_col)
+
+    # y_train and y_test
+    y_train = X_train[target_col].reset_index(drop=True)
+    y_test = X_test[target_col].reset_index(drop=True)
+
+    # Drop target col from X_test
+    X_test.drop([target_col], axis=1, inplace=True)
+
+    # Sapientml
+    output_dir = config.output_dir + "/" + "outputs" + "/" + config.name + "/" + str(config.fold)
+    predictor = SapientML([target_col], task_type="classification" if is_classification else "regression")
+
+    # Fit the model
+    with Timer() as training:
+        predictor.fit(X_train, output_dir=output_dir)
+    log.info(f"Finished fit in {training.duration}s.")
+
+    # predict
+    with Timer() as predict:
+        predictions = predictor.predict(X_test)
+    log.info(f"Finished predict in {predict.duration}s.")
+
+    if is_classification:
+
+        predictions[target_col] = predictions[target_col].astype(str)
+        predictions[target_col] = predictions[target_col].str.lower()
+        predictions[target_col] = predictions[target_col].str.strip()
+        y_test = y_test.to_frame()
+        y_test[target_col] = y_test[target_col].astype(str)
+        y_test[target_col] = y_test[target_col].str.lower()
+        y_test[target_col] = y_test[target_col].str.strip()
+
+    if is_classification:
+        probabilities = OneHotEncoder(handle_unknown="ignore").fit_transform(predictions.to_numpy())
+        probabilities = pd.DataFrame(probabilities.toarray(), columns=dataset.target.classes)
+
+        return result(
+            output_file=config.output_predictions_file,
+            predictions=predictions,
+            truth=y_test,
+            probabilities=probabilities,
+            training_duration=training.duration,
+            predict_duration=predict.duration,
+        )
+    else:
+        return result(
+            output_file=config.output_predictions_file,
+            predictions=predictions,
+            truth=y_test,
+            training_duration=training.duration,
+            predict_duration=predict.duration,
+        )
+
+
+if __name__ == "__main__":
+    call_run(run)
diff --git a/frameworks/SapientML/setup.sh b/frameworks/SapientML/setup.sh
@@ -0,0 +1,26 @@
+#!/usr/bin/env bash
+HERE=$(dirname "$0")
+VERSION=${1:-"stable"}
+REPO=${2:-"https://github.com/sapientml/sapientml"}
+PKG=${3:-"sapientml"}
+if [[ "$VERSION" == "latest" ]]; then
+    VERSION="main"
+fi
+
+#create local venv
+. ${HERE}/../shared/setup.sh ${HERE} true
+
+# PIP install -r ${HERE}/requirements.txt
+if [[ "$VERSION" == "stable" ]]; then
+    PIP install --no-cache-dir -U ${PKG}
+elif [[ "$VERSION" =~ ^[0-9] ]]; then
+    PIP install --no-cache-dir -U ${PKG}==${VERSION}
+else
+#    PIP install --no-cache-dir -e git+${REPO}@${VERSION}#egg=${PKG}
+    TARGET_DIR="${HERE}/lib/${PKG}"
+    rm -Rf ${TARGET_DIR}
+    git clone --depth 1 --single-branch --branch ${VERSION} --recurse-submodules ${REPO} ${TARGET_DIR}
+    PIP install -U -e ${TARGET_DIR}
+fi
+
+PY -c "import pkg_resources; print(pkg_resources.get_distribution('sapientml').version)" >> "${HERE}/.setup/installed"
diff --git a/resources/frameworks.yaml b/resources/frameworks.yaml
@@ -215,6 +215,11 @@ FEDOT:
 #  params:
 #    _save_artifacts: ['leaderboard', 'models', 'info']
 
+SapientML:
+  description: |
+    SapientML is an AutoML tool that can learn from a corpus of existing datasets and their human-written pipelines, and efficiently generate a high-quality pipeline for a predictive task on a new dataset.
+  project: https://github.com/sapientml/sapientml
+
 #######################################
 ### Non AutoML reference frameworks ###
 #######################################