workbench 0.8.228__tar.gz → 0.8.231__tar.gz

{workbench-0.8.228 → workbench-0.8.231}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: workbench
-Version: 0.8.228
+Version: 0.8.231
 Summary: Workbench: A Dashboard and Python API for creating and deploying AWS SageMaker Model Pipelines
 Author-email: SuperCowPowers LLC <support@supercowpowers.com>
 License: MIT License
@@ -60,7 +60,7 @@ Requires-Dist: plotly>=6.0.0; extra == "ui"
 Requires-Dist: dash>=3.0.0; extra == "ui"
 Requires-Dist: dash-bootstrap-components>=1.6.0; extra == "ui"
 Requires-Dist: dash-bootstrap-templates>=1.3.0; extra == "ui"
-Requires-Dist: dash_ag_grid; extra == "ui"
+Requires-Dist: dash_ag_grid>=33.3.3; extra == "ui"
 Requires-Dist: tabulate>=0.9.0; extra == "ui"
 Requires-Dist: matplotlib>=3.9.2; extra == "ui"
 Provides-Extra: dev

{workbench-0.8.228 → workbench-0.8.231}/applications/aws_dashboard/Dockerfile

@@ -1,4 +1,16 @@
-# Base image: python:3.12.5-bookworm
+# Define workbench version once at the top
+ARG WORKBENCH_VERSION=0.8.230
+
+# Stage 1: Extract dependencies from workbench[ui]
+FROM python:3.12.5-bookworm AS deps-extractor
+ARG WORKBENCH_VERSION
+RUN pip install --no-cache-dir pip-tools && \
+    pip download --no-deps "workbench[ui]==${WORKBENCH_VERSION}" -d /tmp/pkg && \
+    cd /tmp/pkg && unzip -q *.whl -d /tmp/extracted && \
+    cat /tmp/extracted/*.dist-info/METADATA | grep "^Requires-Dist:" | \
+    sed 's/Requires-Dist: //' | sed 's/;.*//' | sed 's/ (.*//' > /tmp/deps.txt
+
+# Stage 2: Build the final image
 FROM python:3.12.5-bookworm AS base
 WORKDIR /app
 EXPOSE 8000
@@ -6,9 +18,6 @@ EXPOSE 8000
 # Set PYTHONHASHSEED to ensure consistent hashing across processes
 ENV PYTHONHASHSEED=0
 
-# Define workbench version
-ARG WORKBENCH_VERSION=0.8.227
-
 # Install system packages and gunicorn in one layer
 RUN apt-get update && apt-get install -y --no-install-recommends \
     nginx supervisor libnghttp2-dev && \
@@ -16,13 +25,13 @@ RUN apt-get update && apt-get install -y --no-install-recommends \
     rm -rf /var/lib/apt/lists/* && \
     pip install --no-cache-dir gunicorn
 
-# Dependency Layer: Install all dependencies of workbench[ui]
-RUN pip install --no-cache-dir "workbench[ui]==${WORKBENCH_VERSION}" && \
-    pip uninstall -y workbench && \
-    pip cache purge
+# Copy and install dependencies (this layer only changes when deps change)
+COPY --from=deps-extractor /tmp/deps.txt /tmp/deps.txt
+RUN pip install --no-cache-dir -r /tmp/deps.txt && rm /tmp/deps.txt
 
 # Install workbench[ui] in separate layer (dependencies already satisfied)
-RUN pip install --no-cache-dir "workbench[ui]==${WORKBENCH_VERSION}"
+ARG WORKBENCH_VERSION
+RUN pip install --no-cache-dir --no-deps "workbench[ui]==${WORKBENCH_VERSION}"
 
 # Copy app code and configuration (after pip installs to avoid cache invalidation)
 COPY . /app

{workbench-0.8.228 → workbench-0.8.231}/applications/aws_dashboard/pages/models/callbacks.py

@@ -140,11 +140,14 @@ def setup_plugin_callbacks(plugins, scatter_plot_plugin: ScatterPlot, confusion_
             if isinstance(target, list):
                 target = next((t for t in target if t in inference_run), target[0])
 
+            # Check if "confidence" column exists for coloring
+            color_col = "confidence" if "confidence" in df.columns else "prediction"
+
             scatter_props = scatter_plot_plugin.update_properties(
                 df,
                 x=target,
                 y="prediction",
-                color="confidence",
+                color=color_col,
                 regression_line=True,
             )
             cm_props = [no_update] * len(confusion_matrix_plugin.properties)

{workbench-0.8.228 → workbench-0.8.231}/aws_setup/workbench_core/workbench_core/workbench_core_stack.py

@@ -180,6 +180,7 @@ class WorkbenchCoreStack(Stack):
                 "glue:GetDatabases",
                 "glue:GetTable",
                 "glue:GetTables",
+                "glue:GetPartitions",
                 "glue:SearchTables",
             ],
             resources=[f"arn:aws:glue:{self.region}:{self.account}:catalog"],

{workbench-0.8.228 → workbench-0.8.231}/aws_setup/workbench_dashboard_full/app.py

@@ -12,7 +12,7 @@ print(f"Account: {aws_account}")
 print(f"Region: {aws_region}")
 
 # When you want a different docker image change this line
-dashboard_image = "public.ecr.aws/m6i5k1r2/workbench_dashboard:v0_8_227_amd64"
+dashboard_image = "public.ecr.aws/m6i5k1r2/workbench_dashboard:v0_8_230_amd64"
 
 # Workbench Configuration
 try:

{workbench-0.8.228 → workbench-0.8.231}/aws_setup/workbench_dashboard_lite/app.py

@@ -12,7 +12,7 @@ print(f"Account: {aws_account}")
 print(f"Region: {aws_region}")
 
 # When you want a different docker image change this line
-dashboard_image = "public.ecr.aws/m6i5k1r2/workbench_dashboard:v0_8_227_amd64"
+dashboard_image = "public.ecr.aws/m6i5k1r2/workbench_dashboard:v0_8_230_amd64"
 
 # Workbench Configuration
 try:

{workbench-0.8.228 → workbench-0.8.231}/aws_setup/workbench_dashboard_lite/workbench_dashboard_lite/workbench_dashboard_stack.py

@@ -105,13 +105,13 @@ class WorkbenchDashboardStack(Stack):
             self,
             "WorkbenchTaskDef",
             task_role=workbench_execution_role,
-            memory_limit_mib=2048,
-            cpu=1024,
+            memory_limit_mib=4096,
+            cpu=2048,
         )
         container = task_definition.add_container(
             "WorkbenchContainer",
             image=ecs.ContainerImage.from_registry(props.dashboard_image),
-            memory_limit_mib=2048,
+            memory_limit_mib=4096,
             environment={
                 "REDIS_HOST": redis_endpoint,
                 "WORKBENCH_BUCKET": props.workbench_bucket,
@@ -167,10 +167,10 @@ class WorkbenchDashboardStack(Stack):
             self,
             "WorkbenchService",
             cluster=cluster,
-            cpu=1024,
+            cpu=2048,
             desired_count=1,
             task_definition=task_definition,
-            memory_limit_mib=2048,
+            memory_limit_mib=4096,
             public_load_balancer=props.public,
             security_groups=[lb_security_group],
             open_listener=props.public,

{workbench-0.8.228 → workbench-0.8.231}/docs/admin/dashboard_docker_push.md

@@ -6,9 +6,10 @@ Notes and information on how to do the Dashboard Docker Builds and Push to AWS E
 ```
 cd applications/aws_dashboard
 vi Dockerfile
+...
 
-# Install workbench[ui] in separate layer
-RUN pip install --no-cache-dir "workbench[ui]==0.8.116"  <-- change this
+# Install workbench[ui] in separate layer (dependencies already satisfied)
+ARG WORKBENCH_VERSION=0.8.227  <-- change this
 ```
 
 ### Run the Deploy Script

{workbench-0.8.228 → workbench-0.8.231}/model_docker_images/ml_pipelines/Dockerfile

@@ -29,7 +29,7 @@ COPY --from=builder /usr/local/lib/python3.12/site-packages /usr/local/lib/pytho
 COPY --from=builder /usr/local/bin /usr/local/bin
 
 # Install workbench only
-RUN pip install --no-cache-dir workbench==0.8.223
+RUN pip install --no-cache-dir workbench==0.8.229
 
 # Add the script runner
 COPY ml_pipeline_runner.py /app/ml_pipeline_runner.py

{workbench-0.8.228 → workbench-0.8.231}/pyproject.toml

@@ -52,7 +52,7 @@ ui = [
     "dash>=3.0.0",
     "dash-bootstrap-components>=1.6.0",
     "dash-bootstrap-templates>=1.3.0",
-    "dash_ag_grid",
+    "dash_ag_grid>=33.3.3",
     "tabulate>=0.9.0",
     "matplotlib>=3.9.2",
 ]

workbench-0.8.231/scripts/admin/redis_reaper.py

@@ -0,0 +1,97 @@
+import argparse
+import redis
+import heapq
+
+
+def redis_reaper(host, port, size_limit=512000, expire=7, batch_size=1000):
+    """Reap keys from Redis based on size and age.
+
+    Args:
+        host (str): Redis host.
+        port (int): Redis port.
+        size_limit (int): Size limit in bytes (default: 500KB).
+        expire (int): Number of days before a key is considered expired (default: 7 days).
+        batch_size (int): Number of keys to process per pipeline batch (default: 1000).
+    """
+    client = redis.Redis(host=host, port=port)
+    total_keys = client.dbsize()
+    keys_deleted = 0
+    expire_seconds = expire * 86400
+    largest_keys = []  # min-heap for top 5
+    keys_to_delete = []
+
+    # Process keys in batches using pipelines
+    batch = []
+    for key in client.scan_iter(count=batch_size):
+        batch.append(key)
+        if len(batch) >= batch_size:
+            keys_deleted += process_batch(client, batch, size_limit, expire_seconds, largest_keys, keys_to_delete)
+            batch = []
+
+    # Process remaining keys
+    if batch:
+        keys_deleted += process_batch(client, batch, size_limit, expire_seconds, largest_keys, keys_to_delete)
+
+    # Batch delete all marked keys
+    if keys_to_delete:
+        client.delete(*keys_to_delete)
+
+    # Report
+    print(f"\nTotal keys: {total_keys}")
+    print("\nTop 5 largest keys (by size):")
+    for size, key in sorted(largest_keys, reverse=True):
+        print(f"Key: {key}, Size: {size} bytes")
+    print(f"\nTotal keys deleted: {keys_deleted}")
+
+
+def process_batch(client, keys, size_limit, expire_seconds, largest_keys, keys_to_delete):
+    """Process a batch of keys using pipeline for efficiency."""
+    # Pipeline to get memory usage and idle time for all keys
+    pipe = client.pipeline(transaction=False)
+    for key in keys:
+        pipe.memory_usage(key)
+        pipe.object("idletime", key)
+    results = pipe.execute()
+
+    deleted = 0
+    for i, key in enumerate(keys):
+        size = results[i * 2] or 0
+        idle_time = results[i * 2 + 1]
+
+        # Track largest keys
+        heapq.heappush(largest_keys, (size, key))
+        if len(largest_keys) > 5:
+            heapq.heappop(largest_keys)
+
+        # Check deletion criteria
+        if size > size_limit:
+            print(f"Deleting key {key} (size: {size} bytes)")
+            keys_to_delete.append(key)
+            deleted += 1
+        elif idle_time is not None and idle_time > expire_seconds:
+            print(f"Deleting key {key} (age: {idle_time / 86400:.2f} days)")
+            keys_to_delete.append(key)
+            deleted += 1
+        elif b"Crashed" in key:
+            print(f"Deleting key {key} (contains 'Crashed')")
+            keys_to_delete.append(key)
+            deleted += 1
+
+    return deleted
+
+
+if __name__ == "__main__":
+    # Argument parsing
+    parser = argparse.ArgumentParser(description="Redis Reaper: Delete keys based on size and age.")
+    parser.add_argument("--host", type=str, default="localhost", help="Redis host (or host:port)")
+    parser.add_argument("-p", "--port", type=int, default=6379, help="Redis port (default: 6379)")
+    parser.add_argument("--size-limit", type=int, default=1048576, help="Size limit in bytes (default: 1MB)")
+    parser.add_argument("--expire", type=int, default=7, help="Expiration days (default: 7 days)")
+    args = parser.parse_args()
+
+    # Parse host:port if provided
+    host, port = (args.host.split(":") + [args.port])[:2]
+    port = int(port)
+
+    # Run the Redis Reaper
+    redis_reaper(host, port, args.size_limit, args.expire)

{workbench-0.8.228 → workbench-0.8.231}/src/workbench/algorithms/dataframe/__init__.py

@@ -9,10 +9,12 @@ from .proximity import Proximity
 from .feature_space_proximity import FeatureSpaceProximity
 from .fingerprint_proximity import FingerprintProximity
 from .projection_2d import Projection2D
+from .smart_aggregator import smart_aggregator
 
 __all__ = [
     "Proximity",
     "FeatureSpaceProximity",
     "FingerprintProximity",
     "Projection2D",
+    "smart_aggregator",
 ]

workbench-0.8.231/src/workbench/algorithms/dataframe/smart_aggregator.py

@@ -0,0 +1,161 @@
+"""SmartSample: Intelligently reduce DataFrame rows by aggregating similar rows together."""
+
+import pandas as pd
+import numpy as np
+from sklearn.preprocessing import StandardScaler
+from sklearn.cluster import MiniBatchKMeans
+import logging
+
+# Set up logging
+log = logging.getLogger("workbench")
+
+
+def smart_aggregator(df: pd.DataFrame, target_rows: int = 1000, outlier_column: str = "residual") -> pd.DataFrame:
+    """
+    Reduce DataFrame rows by aggregating similar rows based on numeric column similarity.
+
+    This is a performant (2-pass) algorithm:
+    1. Pass 1: Normalize numeric columns and cluster similar rows using MiniBatchKMeans
+    2. Pass 2: Aggregate each cluster (mean for numeric, first for non-numeric)
+
+    Args:
+        df: Input DataFrame.
+        target_rows: Target number of rows in output (default: 1000).
+        outlier_column: Column where high values should resist aggregation (default: "residual").
+                       Rows with high values in this column will be kept separate while rows
+                       with low values cluster together. Set to None to disable.
+
+    Returns:
+        Reduced DataFrame with 'aggregation_count' column showing how many rows were combined.
+    """
+    if df is None or df.empty:
+        return df
+
+    n_rows = len(df)
+
+    # Preserve original column order
+    original_columns = df.columns.tolist()
+
+    # If already at or below target, just add the count column and return
+    if n_rows <= target_rows:
+        result = df.copy()
+        result["aggregation_count"] = 1
+        return result
+
+    log.info(f"smart_aggregator: Reducing {n_rows} rows to ~{target_rows} rows")
+
+    # Identify columns by type
+    df = df.copy()
+    numeric_cols = df.select_dtypes(include=["number"]).columns.tolist()
+    non_numeric_cols = [c for c in df.columns if c not in numeric_cols]
+
+    if not numeric_cols:
+        log.warning("smart_aggregator: No numeric columns for clustering, falling back to random sample")
+        result = df.sample(n=target_rows)
+        result["aggregation_count"] = 1
+        return result.reset_index(drop=True)
+
+    # Handle NaN values - fill with column median
+    df_for_clustering = df[numeric_cols].fillna(df[numeric_cols].median())
+
+    # Normalize and cluster
+    X = StandardScaler().fit_transform(df_for_clustering)
+    df["_cluster"] = MiniBatchKMeans(
+        n_clusters=min(target_rows, n_rows), random_state=42, batch_size=min(1024, n_rows), n_init=3
+    ).fit_predict(X)
+
+    # Post-process: give high-outlier rows their own unique clusters so they don't get aggregated
+    if outlier_column and outlier_column in df.columns:
+        # Top 10% of outlier values get their own clusters, capped at 200
+        n_to_isolate = min(int(n_rows * 0.1), 200)
+        threshold = df[outlier_column].nlargest(n_to_isolate).min()
+        high_outlier_mask = df[outlier_column] >= threshold
+        n_high_outliers = high_outlier_mask.sum()
+        # Assign unique cluster IDs starting after the max existing cluster
+        max_cluster = df["_cluster"].max()
+        df.loc[high_outlier_mask, "_cluster"] = range(max_cluster + 1, max_cluster + 1 + n_high_outliers)
+        log.info(f"smart_aggregator: Isolated {n_high_outliers} high-outlier rows (>= {threshold:.3f})")
+    elif outlier_column:
+        log.warning(f"smart_aggregator: outlier_column '{outlier_column}' not found in columns")
+
+    # Aggregate each cluster (mean for numeric, first for non-numeric)
+    agg_dict = {col: "mean" for col in numeric_cols} | {col: "first" for col in non_numeric_cols}
+    grouped = df.groupby("_cluster")
+    result = grouped.agg(agg_dict).reset_index(drop=True)
+    result["aggregation_count"] = grouped.size().values
+
+    # Restore original column order, with aggregation_count at the end
+    result = result[original_columns + ["aggregation_count"]]
+
+    log.info(f"smart_aggregator: Reduced to {len(result)} rows")
+    return result
+
+
+# Testing
+if __name__ == "__main__":
+    pd.set_option("display.max_columns", None)
+    pd.set_option("display.width", 1000)
+
+    # Create test data with clusters
+    np.random.seed(42)
+    n_samples = 10000
+
+    # Create 3 distinct clusters
+    cluster_1 = np.random.randn(n_samples // 3, 3) + np.array([0, 0, 0])
+    cluster_2 = np.random.randn(n_samples // 3, 3) + np.array([5, 5, 5])
+    cluster_3 = np.random.randn(n_samples // 3, 3) + np.array([10, 0, 5])
+
+    features = np.vstack([cluster_1, cluster_2, cluster_3])
+
+    # Create target and prediction columns, then compute residuals
+    target = features[:, 0] + features[:, 1] * 0.5 + np.random.randn(len(features)) * 0.1
+    prediction = target + np.random.randn(len(features)) * 0.5  # Add noise for residuals
+    residuals = np.abs(target - prediction)
+
+    data = {
+        "id": [f"id_{i}" for i in range(len(features))],
+        "A": features[:, 0],
+        "B": features[:, 1],
+        "C": features[:, 2],
+        "category": np.random.choice(["cat1", "cat2", "cat3"], len(features)),
+        "target": target,
+        "prediction": prediction,
+        "residual": residuals,
+    }
+    df = pd.DataFrame(data)
+
+    print(f"Original DataFrame: {len(df)} rows")
+    print(df.head())
+    print()
+
+    # Test smart_aggregator with residuals preservation
+    result = smart_aggregator(df, target_rows=500)
+    print(f"smart_aggregator result: {len(result)} rows")
+    print(result.head(20))
+    print()
+    print("Aggregation count stats:")
+    print(result["aggregation_count"].describe())
+    print()
+    # Show that high-residual points have lower aggregation counts
+    print("Aggregation count by residual quartile:")
+    result["residual_quartile"] = pd.qcut(result["residual"], 4, labels=["Q1 (low)", "Q2", "Q3", "Q4 (high)"])
+    print(result.groupby("residual_quartile")["aggregation_count"].mean())
+
+    # Test with real Workbench data
+    print("\n" + "=" * 80)
+    print("Testing with Workbench data...")
+    print("=" * 80)
+
+    from workbench.api import Model
+
+    model = Model("abalone-regression")
+    df = model.get_inference_predictions()
+    if df is not None:
+        print(f"\nOriginal DataFrame: {len(df)} rows")
+        print(df.head())
+
+        result = smart_aggregator(df, target_rows=500)
+        print(f"\nsmart_aggregator result: {len(result)} rows")
+        print(result.head())
+        print("\nAggregation count stats:")
+        print(result["aggregation_count"].describe())

{workbench-0.8.228 → workbench-0.8.231}/src/workbench/cached/cached_model.py

@@ -6,6 +6,7 @@ import pandas as pd
 # Workbench Imports
 from workbench.core.artifacts.model_core import ModelCore, ModelType
 from workbench.core.artifacts.cached_artifact_mixin import CachedArtifactMixin
+from workbench.algorithms.dataframe import smart_aggregator
 
 
 class CachedModel(CachedArtifactMixin, ModelCore):
@@ -85,13 +86,13 @@ class CachedModel(CachedArtifactMixin, ModelCore):
 
     @CachedArtifactMixin.cache_result
     def get_inference_predictions(
-        self, capture_name: str = "full_cross_fold", limit: int = 5000
+        self, capture_name: str = "full_cross_fold", target_rows: int = 1000
     ) -> Union[pd.DataFrame, None]:
         """Retrieve the captured prediction results for this model
 
         Args:
-            capture_name (str, optional): Specific capture_name (default: auto_inference)
-            limit (int, optional): Maximum rows to return (default: 1000)
+            capture_name (str, optional): Specific capture_name (default: full_cross_fold)
+            target_rows (int, optional): Target number of rows to return (default: 1000)
 
         Returns:
             pd.DataFrame: DataFrame of the Captured Predictions (might be None)
@@ -100,7 +101,7 @@ class CachedModel(CachedArtifactMixin, ModelCore):
         if df is None:
             return None
 
-        # Compute residual and do smart sampling based on model type
+        # Compute residual based on model type
         is_regressor = self.model_type in [ModelType.REGRESSOR, ModelType.UQ_REGRESSOR, ModelType.ENSEMBLE_REGRESSOR]
         is_classifier = self.model_type == ModelType.CLASSIFIER
 
@@ -120,21 +121,12 @@ class CachedModel(CachedArtifactMixin, ModelCore):
                     df["prediction"].map(label_to_idx).fillna(-1) - df[target].map(label_to_idx).fillna(-1)
                 )
 
-        # Smart sampling: half high-residual rows, half random from the rest
-        if "residual" in df.columns and len(df) > limit:
-            half_limit = limit // 2
-            self.log.warning(
-                f"{self.name}:{capture_name} Sampling {limit} rows (top {half_limit} residuals + {half_limit} random)"
+        # Use smart_aggregator to aggregate similar rows if we have too many
+        if len(df) > target_rows:
+            self.log.info(
+                f"{self.name}:{capture_name} Using smart_aggregator to reduce {len(df)} rows to ~{target_rows}"
             )
-            top_residuals = df.nlargest(half_limit, "residual")
-            remaining = df.drop(top_residuals.index)
-            random_sample = remaining.sample(min(half_limit, len(remaining)))
-            return pd.concat([top_residuals, random_sample]).reset_index(drop=True)
-
-        # Fallback: just limit rows if no residual computed
-        if len(df) > limit:
-            self.log.warning(f"{self.name}:{capture_name} Sampling to {limit} rows")
-            return df.sample(limit)
+            df = smart_aggregator(df, target_rows=target_rows)
 
         return df
 

{workbench-0.8.228/src/workbench/model_scripts/pytorch_model → workbench-0.8.231/src/workbench/model_script_utils}/model_script_utils.py

@@ -249,6 +249,36 @@ def output_fn(output_df: pd.DataFrame, accept_type: str) -> tuple[str, str]:
         raise RuntimeError(f"{accept_type} accept type is not supported by this script.")
 
 
+def cap_std_outliers(std_array: np.ndarray) -> np.ndarray:
+    """Cap extreme outliers in prediction_std using IQR method.
+
+    Uses the standard IQR fence (Q3 + 1.5*IQR) to cap extreme values.
+    This prevents unreasonably large std values while preserving the
+    relative ordering and keeping meaningful high-uncertainty signals.
+
+    Args:
+        std_array: Array of standard deviations (n_samples,) or (n_samples, n_targets)
+
+    Returns:
+        Array with outliers capped at the upper fence
+    """
+    if std_array.ndim == 1:
+        std_array = std_array.reshape(-1, 1)
+        squeeze = True
+    else:
+        squeeze = False
+
+    capped = std_array.copy()
+    for col in range(capped.shape[1]):
+        col_data = capped[:, col]
+        q1, q3 = np.percentile(col_data, [25, 75])
+        iqr = q3 - q1
+        upper_bound = q3 + 1.5 * iqr
+        capped[:, col] = np.minimum(col_data, upper_bound)
+
+    return capped.squeeze() if squeeze else capped
+
+
 def compute_regression_metrics(y_true: np.ndarray, y_pred: np.ndarray) -> dict[str, float]:
     """Compute standard regression metrics.
 

{workbench-0.8.228 → workbench-0.8.231}/src/workbench/model_scripts/chemprop/chemprop.template

@@ -20,6 +20,7 @@ import torch
 from chemprop import data, models
 
 from model_script_utils import (
+    cap_std_outliers,
     expand_proba_column,
     input_fn,
     output_fn,
@@ -245,6 +246,7 @@ def predict_fn(df: pd.DataFrame, model_dict: dict) -> pd.DataFrame:
     preds_std = np.std(np.stack(all_preds), axis=0)
     if preds.ndim == 1:
         preds, preds_std = preds.reshape(-1, 1), preds_std.reshape(-1, 1)
+    preds_std = cap_std_outliers(preds_std)
 
     print(f"Inference complete: {preds.shape[0]} predictions")
 
@@ -701,6 +703,7 @@ if __name__ == "__main__":
             preds_std = np.std(np.stack(all_ens_preds), axis=0)
             if preds_std.ndim == 1:
                 preds_std = preds_std.reshape(-1, 1)
+            preds_std = cap_std_outliers(preds_std)
 
         print("\n--- Per-target metrics ---")
         for t_idx, t_name in enumerate(target_columns):

{workbench-0.8.228 → workbench-0.8.231}/src/workbench/model_scripts/chemprop/generated_model_script.py

@@ -57,11 +57,11 @@ DEFAULT_HYPERPARAMETERS = {
 
 # Template parameters (filled in by Workbench)
 TEMPLATE_PARAMS = {
-    "model_type": "classifier",
-    "targets": ['class'],
+    "model_type": "uq_regressor",
+    "targets": ['udm_asy_res_value'],
     "feature_list": ['smiles'],
     "id_column": "udm_mol_bat_id",
-    "model_metrics_s3_path": "s3://ideaya-sageworks-bucket/models/logd-value-class-chemprop-1-dt/training",
+    "model_metrics_s3_path": "s3://ideaya-sageworks-bucket/models/logd-value-reg-chemprop-1-dt/training",
     "hyperparameters": {},
 }
 

{workbench-0.8.228/src/workbench/model_script_utils → workbench-0.8.231/src/workbench/model_scripts/chemprop}/model_script_utils.py

@@ -249,6 +249,36 @@ def output_fn(output_df: pd.DataFrame, accept_type: str) -> tuple[str, str]:
         raise RuntimeError(f"{accept_type} accept type is not supported by this script.")
 
 
+def cap_std_outliers(std_array: np.ndarray) -> np.ndarray:
+    """Cap extreme outliers in prediction_std using IQR method.
+
+    Uses the standard IQR fence (Q3 + 1.5*IQR) to cap extreme values.
+    This prevents unreasonably large std values while preserving the
+    relative ordering and keeping meaningful high-uncertainty signals.
+
+    Args:
+        std_array: Array of standard deviations (n_samples,) or (n_samples, n_targets)
+
+    Returns:
+        Array with outliers capped at the upper fence
+    """
+    if std_array.ndim == 1:
+        std_array = std_array.reshape(-1, 1)
+        squeeze = True
+    else:
+        squeeze = False
+
+    capped = std_array.copy()
+    for col in range(capped.shape[1]):
+        col_data = capped[:, col]
+        q1, q3 = np.percentile(col_data, [25, 75])
+        iqr = q3 - q1
+        upper_bound = q3 + 1.5 * iqr
+        capped[:, col] = np.minimum(col_data, upper_bound)
+
+    return capped.squeeze() if squeeze else capped
+
+
 def compute_regression_metrics(y_true: np.ndarray, y_pred: np.ndarray) -> dict[str, float]:
     """Compute standard regression metrics.