Merge pull request #477 from OmicsML/fix-doc

JiayuanDing100 · web-flow · commit 735ef4f9a7e0 · 2025-09-16T00:24:16.000-07:00
fix:doc
diff --git a/.gitignore b/.gitignore
@@ -12,6 +12,7 @@ wandb/
 *.egg*
 __pycache__/
 build/
+_build/
 *.log
 
 # =============================================================================
diff --git a/docs/source/DANCE 2.0/Preprocessing Function Parameter Search Space.rst b/docs/source/DANCE 2.0/Preprocessing Function Parameter Search Space.rst
diff --git a/docs/source/DANCE 2.0/Preprocessing Steps and Available Function Candidates.rst b/docs/source/DANCE 2.0/Preprocessing Steps and Available Function Candidates.rst
@@ -1,23 +1,23 @@
-Preprocessing Steps and Their Functions
+Preprocessing Steps and Available Function Candidates
 ====================
 
 This page lists the preprocessing functions included in each step.
 
-filter.gene
+Preprocessing Step: filter.gene
 -----------
 
 - :class:`dance.transforms.FilterGenesPercentile`
 - :class:`dance.transforms.FilterGenesScanpyOrder`
 - :class:`dance.transforms.FilterGenesPlaceHolder`
 
-filter.cell
+Preprocessing Step: filter.cell
 -----------
 
 - :class:`dance.transforms.FilterCellsScanpyOrder`
 - :class:`dance.transforms.FilterCellsPlaceHolder`
 - :class:`dance.transforms.FilterCellsCommonMod`
 
-normalize
+Preprocessing Step: normalize
 ---------
 
 - :class:`dance.transforms.ColumnSumNormalize`
@@ -28,7 +28,7 @@ normalize
 - :class:`dance.transforms.tfidfTransform`
 - :class:`dance.transforms.NormalizePlaceHolder`
 
-filter.gene(highly_variable)
+Preprocessing Step: filter.gene(highly_variable)
 -----------
 
 - :class:`dance.transforms.FilterGenesTopK`
@@ -39,7 +39,7 @@ filter.gene(highly_variable)
 - :class:`dance.transforms.HighlyVariableGenesLogarithmizedByMeanAndDisp`
 - :class:`dance.transforms.FilterGenesNumberPlaceHolder`
 
-feature.cell
+Preprocessing Step: feature.cell
 ------------
 
 - :class:`dance.transforms.CellPCA`
diff --git a/docs/source/DANCE 2.0/Search Space of Preprocessing Function Parameters.rst b/docs/source/DANCE 2.0/Search Space of Preprocessing Function Parameters.rst
@@ -0,0 +1,7 @@
+Search Space of Preprocessing Function Parameters
+========================
+After identifying the optimal preprocessing function in Stage 2, Stage 3 involves parameter tuning for this function. The parameter search is guided by a configuration file that defines the search space, as detailed below. This file is user-editable to allow for customization.
+
+.. literalinclude:: ../../../examples/tuning/step3_default_params.yaml
+   :language: yaml
+   :caption: examples/tuning/step3_default_params.yaml
diff --git a/docs/source/DANCE 2.0/experiments/celltype_annotation/actinn.rst b/docs/source/DANCE 2.0/experiments/celltype_annotation/actinn.rst
@@ -3,6 +3,6 @@ actinn Config
 
 This is the config for actinn.
 
-.. literalinclude:: ../../../../examples/tuning/cta_actinn/328_138/pipeline_params_tuning_config.yaml
+.. literalinclude:: ../../../../../examples/tuning/cta_actinn/328_138/pipeline_params_tuning_config.yaml
    :language: yaml
    :caption: examples/tuning/cta_actinn/328_138/pipeline_params_tuning_config.yaml
diff --git a/docs/source/DANCE 2.0/experiments/celltype_annotation/celltypist.rst b/docs/source/DANCE 2.0/experiments/celltype_annotation/celltypist.rst
@@ -3,6 +3,6 @@ celltypist Config
 
 This is the config for celltypist.
 
-.. literalinclude:: ../../../../examples/tuning/cta_celltypist/328_138/pipeline_params_tuning_config.yaml
+.. literalinclude:: ../../../../../examples/tuning/cta_celltypist/328_138/pipeline_params_tuning_config.yaml
    :language: yaml
    :caption: examples/tuning/cta_celltypist/328_138/pipeline_params_tuning_config.yaml
diff --git a/docs/source/DANCE 2.0/experiments/celltype_annotation/scdeepsort.rst b/docs/source/DANCE 2.0/experiments/celltype_annotation/scdeepsort.rst
@@ -3,6 +3,6 @@ scdeepsort Config
 
 This is the config for scdeepsort.
 
-.. literalinclude:: ../../../../examples/tuning/cta_scdeepsort/328_138/pipeline_params_tuning_config.yaml
+.. literalinclude:: ../../../../../examples/tuning/cta_scdeepsort/328_138/pipeline_params_tuning_config.yaml
    :language: yaml
    :caption: examples/tuning/cta_scdeepsort/328_138/pipeline_params_tuning_config.yaml
diff --git a/docs/source/DANCE 2.0/experiments/celltype_annotation/scheteronet.rst b/docs/source/DANCE 2.0/experiments/celltype_annotation/scheteronet.rst
@@ -3,6 +3,6 @@ scheteronet Config
 
 This is the config for scheteronet.
 
-.. literalinclude:: ../../../../examples/tuning/cta_scheteronet/328_138/pipeline_params_tuning_config.yaml
+.. literalinclude:: ../../../../../examples/tuning/cta_scheteronet/328_138/pipeline_params_tuning_config.yaml
    :language: yaml
    :caption: examples/tuning/cta_scheteronet/328_138/pipeline_params_tuning_config.yaml
diff --git a/docs/source/DANCE 2.0/experiments/celltype_annotation/singlecellnet.rst b/docs/source/DANCE 2.0/experiments/celltype_annotation/singlecellnet.rst
@@ -3,6 +3,6 @@ singlecellnet Config
 
 This is the config for singlecellnet.
 
-.. literalinclude:: ../../../../examples/tuning/cta_singlecellnet/328_138/pipeline_params_tuning_config.yaml
+.. literalinclude:: ../../../../../examples/tuning/cta_singlecellnet/328_138/pipeline_params_tuning_config.yaml
    :language: yaml
    :caption: examples/tuning/cta_singlecellnet/328_138/pipeline_params_tuning_config.yaml
diff --git a/docs/source/DANCE 2.0/experiments/celltype_annotation/svm.rst b/docs/source/DANCE 2.0/experiments/celltype_annotation/svm.rst
@@ -3,6 +3,6 @@ svm Config
 
 This is the config for svm.
 
-.. literalinclude:: ../../../../examples/tuning/cta_svm/328_138/pipeline_params_tuning_config.yaml
+.. literalinclude:: ../../../../../examples/tuning/cta_svm/328_138/pipeline_params_tuning_config.yaml
    :language: yaml
    :caption: examples/tuning/cta_svm/328_138/pipeline_params_tuning_config.yaml
diff --git a/docs/source/DANCE 2.0/experiments/celltype_deconvolution/card.rst b/docs/source/DANCE 2.0/experiments/celltype_deconvolution/card.rst
@@ -3,6 +3,6 @@ card Config
 
 This is the config for card.
 
-.. literalinclude:: ../../../../examples/tuning/deconv_card/hcc_liver/pipeline_params_tuning_config.yaml
+.. literalinclude:: ../../../../../examples/tuning/deconv_card/hcc_liver/pipeline_params_tuning_config.yaml
    :language: yaml
    :caption: examples/tuning/deconv_card/hcc_liver/pipeline_params_tuning_config.yaml
diff --git a/docs/source/DANCE 2.0/experiments/celltype_deconvolution/dstg.rst b/docs/source/DANCE 2.0/experiments/celltype_deconvolution/dstg.rst
@@ -3,6 +3,6 @@ dstg Config
 
 This is the config for dstg.
 
-.. literalinclude:: ../../../../examples/tuning/deconv_dstg/hcc_liver/pipeline_params_tuning_config.yaml
+.. literalinclude:: ../../../../../examples/tuning/deconv_dstg/hcc_liver/pipeline_params_tuning_config.yaml
    :language: yaml
    :caption: examples/tuning/deconv_dstg/hcc_liver/pipeline_params_tuning_config.yaml
diff --git a/docs/source/DANCE 2.0/experiments/celltype_deconvolution/spatialdecon.rst b/docs/source/DANCE 2.0/experiments/celltype_deconvolution/spatialdecon.rst
@@ -3,6 +3,6 @@ spatialdecon Config
 
 This is the config for spatialdecon.
 
-.. literalinclude:: ../../../../examples/tuning/deconv_spatialdecon/hcc_liver/pipeline_params_tuning_config.yaml
+.. literalinclude:: ../../../../../examples/tuning/deconv_spatialdecon/hcc_liver/pipeline_params_tuning_config.yaml
    :language: yaml
    :caption: examples/tuning/deconv_spatialdecon/hcc_liver/pipeline_params_tuning_config.yaml
diff --git a/docs/source/DANCE 2.0/experiments/celltype_deconvolution/spotlight.rst b/docs/source/DANCE 2.0/experiments/celltype_deconvolution/spotlight.rst
@@ -3,6 +3,6 @@ spotlight Config
 
 This is the config for spotlight.
 
-.. literalinclude:: ../../../../examples/tuning/deconv_spotlight/hcc_liver/pipeline_params_tuning_config.yaml
+.. literalinclude:: ../../../../../examples/tuning/deconv_spotlight/hcc_liver/pipeline_params_tuning_config.yaml
    :language: yaml
    :caption: examples/tuning/deconv_spotlight/hcc_liver/pipeline_params_tuning_config.yaml
diff --git a/docs/source/DANCE 2.0/experiments/celltype_deconvolution/stdgcn.rst b/docs/source/DANCE 2.0/experiments/celltype_deconvolution/stdgcn.rst
@@ -3,6 +3,6 @@ stdgcn Config
 
 This is the config for stdgcn.
 
-.. literalinclude:: ../../../../examples/tuning/deconv_stdgcn/hcc_liver/pipeline_params_tuning_config.yaml
+.. literalinclude:: ../../../../../examples/tuning/deconv_stdgcn/hcc_liver/pipeline_params_tuning_config.yaml
    :language: yaml
    :caption: examples/tuning/deconv_stdgcn/hcc_liver/pipeline_params_tuning_config.yaml
diff --git a/docs/source/DANCE 2.0/experiments/cluster/graphsc_config.rst b/docs/source/DANCE 2.0/experiments/cluster/graphsc_config.rst
@@ -3,6 +3,6 @@ graphsc Config
 
 This is the config for graphsc.
 
-.. literalinclude:: ../../../../examples/tuning/cluster_graphsc/human_pbmc2_cell/pipeline_params_tuning_config.yaml
+.. literalinclude:: ../../../../../examples/tuning/cluster_graphsc/human_pbmc2_cell/pipeline_params_tuning_config.yaml
    :language: yaml
    :caption: examples/tuning/cluster_graphsc/human_pbmc2_cell/pipeline_params_tuning_config.yaml
diff --git a/docs/source/DANCE 2.0/experiments/cluster/scdcc_config.rst b/docs/source/DANCE 2.0/experiments/cluster/scdcc_config.rst
@@ -3,6 +3,6 @@ scdcc Config
 
 This is the config for scdcc.
 
-.. literalinclude:: ../../../../examples/tuning/cluster_scdcc/human_pbmc2_cell/pipeline_params_tuning_config.yaml
+.. literalinclude:: ../../../../../examples/tuning/cluster_scdcc/human_pbmc2_cell/pipeline_params_tuning_config.yaml
    :language: yaml
    :caption: examples/tuning/cluster_scdcc/human_pbmc2_cell/pipeline_params_tuning_config.yaml
diff --git a/docs/source/DANCE 2.0/experiments/cluster/scdeepcluster_config.rst b/docs/source/DANCE 2.0/experiments/cluster/scdeepcluster_config.rst
@@ -3,6 +3,6 @@ scdeepcluster Config
 
 This is the config for scdeepcluster.
 
-.. literalinclude:: ../../../../examples/tuning/cluster_scdeepcluster/human_pbmc2_cell/pipeline_params_tuning_config.yaml
+.. literalinclude:: ../../../../../examples/tuning/cluster_scdeepcluster/human_pbmc2_cell/pipeline_params_tuning_config.yaml
    :language: yaml
    :caption: examples/tuning/cluster_scdeepcluster/human_pbmc2_cell/pipeline_params_tuning_config.yaml
diff --git a/docs/source/DANCE 2.0/experiments/cluster/scdsc_config.rst b/docs/source/DANCE 2.0/experiments/cluster/scdsc_config.rst
@@ -3,6 +3,6 @@ scdsc Config
 
 This is the config for scdsc.
 
-.. literalinclude:: ../../../../examples/tuning/cluster_scdsc/human_pbmc2_cell/pipeline_params_tuning_config.yaml
+.. literalinclude:: ../../../../../examples/tuning/cluster_scdsc/human_pbmc2_cell/pipeline_params_tuning_config.yaml
    :language: yaml
    :caption: examples/tuning/cluster_scdsc/human_pbmc2_cell/pipeline_params_tuning_config.yaml
diff --git a/docs/source/DANCE 2.0/experiments/cluster/sctag_config.rst b/docs/source/DANCE 2.0/experiments/cluster/sctag_config.rst
@@ -3,6 +3,6 @@ sctag Config
 
 This is the config for sctag.
 
-.. literalinclude:: ../../../../examples/tuning/cluster_sctag/human_pbmc2_cell/pipeline_params_tuning_config.yaml
+.. literalinclude:: ../../../../../examples/tuning/cluster_sctag/human_pbmc2_cell/pipeline_params_tuning_config.yaml
    :language: yaml
    :caption: examples/tuning/cluster_sctag/human_pbmc2_cell/pipeline_params_tuning_config.yaml
diff --git a/docs/source/DANCE 2.0/experiments/imputation/deepimpute.rst b/docs/source/DANCE 2.0/experiments/imputation/deepimpute.rst
@@ -3,6 +3,6 @@ deepimpute Config
 
 This is the config for deepimpute.
 
-.. literalinclude:: ../../../../examples/tuning/imputation_deepimpute/human_melanoma_data/pipeline_params_tuning_config.yaml
+.. literalinclude:: ../../../../../examples/tuning/imputation_deepimpute/human_melanoma_data/pipeline_params_tuning_config.yaml
    :language: yaml
    :caption: examples/tuning/imputation_deepimpute/human_melanoma_data/pipeline_params_tuning_config.yaml
diff --git a/docs/source/DANCE 2.0/experiments/imputation/graphsci.rst b/docs/source/DANCE 2.0/experiments/imputation/graphsci.rst
@@ -3,6 +3,6 @@ graphsci Config
 
 This is the config for graphsci.
 
-.. literalinclude:: ../../../../examples/tuning/imputation_graphsci/human_melanoma_data/pipeline_params_tuning_config.yaml
+.. literalinclude:: ../../../../../examples/tuning/imputation_graphsci/human_melanoma_data/pipeline_params_tuning_config.yaml
    :language: yaml
    :caption: examples/tuning/imputation_graphsci/human_melanoma_data/pipeline_params_tuning_config.yaml
diff --git a/docs/source/DANCE 2.0/experiments/imputation/scgnn2.rst b/docs/source/DANCE 2.0/experiments/imputation/scgnn2.rst
@@ -3,6 +3,6 @@ scgnn2 Config
 
 This is the config for scgnn2.
 
-.. literalinclude:: ../../../../examples/tuning/imputation_scgnn2/human_melanoma_data/pipeline_params_tuning_config.yaml
+.. literalinclude:: ../../../../../examples/tuning/imputation_scgnn2/human_melanoma_data/pipeline_params_tuning_config.yaml
    :language: yaml
    :caption: examples/tuning/imputation_scgnn2/human_melanoma_data/pipeline_params_tuning_config.yaml
diff --git a/docs/source/DANCE 2.0/experiments/index.rst b/docs/source/DANCE 2.0/experiments/index.rst
@@ -4,7 +4,7 @@ Preprocessing Configuration Library
 This document provides a curated collection of configuration files for data preprocessing in bioinformatics. The configurations are organized by analytical task, such as Cell Type Annotation, Clustering, and Joint Embedding. Each file details a recommended workflow for a specific algorithm, designed to ensure reproducibility and serve as a best-practice starting point for analysis.
 
 .. toctree::
-   :maxdepth: 2
+   :maxdepth: 1
    :caption: Tasks
 
    cluster/index
diff --git a/docs/source/DANCE 2.0/experiments/joint_embedding/dcca.rst b/docs/source/DANCE 2.0/experiments/joint_embedding/dcca.rst
@@ -3,6 +3,6 @@ dcca Config
 
 This is the config for dcca.
 
-.. literalinclude:: ../../../../examples/tuning/joint_embedding_dcca/GSE140203_SKIN_atac2gex/pipeline_params_tuning_config.yaml
+.. literalinclude:: ../../../../../examples/tuning/joint_embedding_dcca/GSE140203_SKIN_atac2gex/pipeline_params_tuning_config.yaml
    :language: yaml
    :caption: examples/tuning/joint_embedding_dcca/GSE140203_SKIN_atac2gex/pipeline_params_tuning_config.yaml
diff --git a/docs/source/DANCE 2.0/experiments/joint_embedding/jae.rst b/docs/source/DANCE 2.0/experiments/joint_embedding/jae.rst
@@ -3,6 +3,6 @@ jae Config
 
 This is the config for jae.
 
-.. literalinclude:: ../../../../examples/tuning/joint_embedding_jae/GSE140203_SKIN_atac2gex/pipeline_params_tuning_config.yaml
+.. literalinclude:: ../../../../../examples/tuning/joint_embedding_jae/GSE140203_SKIN_atac2gex/pipeline_params_tuning_config.yaml
    :language: yaml
    :caption: examples/tuning/joint_embedding_jae/GSE140203_SKIN_atac2gex/pipeline_params_tuning_config.yaml
diff --git a/docs/source/DANCE 2.0/experiments/joint_embedding/scmogcn.rst b/docs/source/DANCE 2.0/experiments/joint_embedding/scmogcn.rst
@@ -3,6 +3,6 @@ scmogcn Config
 
 This is the config for scmogcn.
 
-.. literalinclude:: ../../../../examples/tuning/joint_embedding_scmogcn/GSE140203_SKIN_atac2gex/pipeline_params_tuning_config.yaml
+.. literalinclude:: ../../../../../examples/tuning/joint_embedding_scmogcn/GSE140203_SKIN_atac2gex/pipeline_params_tuning_config.yaml
    :language: yaml
    :caption: examples/tuning/joint_embedding_scmogcn/GSE140203_SKIN_atac2gex/pipeline_params_tuning_config.yaml
diff --git a/docs/source/DANCE 2.0/experiments/joint_embedding/scmvae.rst b/docs/source/DANCE 2.0/experiments/joint_embedding/scmvae.rst
@@ -3,6 +3,6 @@ scmvae Config
 
 This is the config for scmvae.
 
-.. literalinclude:: ../../../../examples/tuning/joint_embedding_scmvae/GSE140203_SKIN_atac2gex/pipeline_params_tuning_config.yaml
+.. literalinclude:: ../../../../../examples/tuning/joint_embedding_scmvae/GSE140203_SKIN_atac2gex/pipeline_params_tuning_config.yaml
    :language: yaml
    :caption: examples/tuning/joint_embedding_scmvae/GSE140203_SKIN_atac2gex/pipeline_params_tuning_config.yaml
diff --git a/docs/source/DANCE 2.0/experiments/spatial_domain/EfNST.rst b/docs/source/DANCE 2.0/experiments/spatial_domain/EfNST.rst
@@ -3,6 +3,6 @@ EfNST Config
 
 This is the config for EfNST.
 
-.. literalinclude:: ../../../../examples/tuning/domain_EfNST/sub_mba/pipeline_params_tuning_config.yaml
+.. literalinclude:: ../../../../../examples/tuning/domain_EfNST/sub_mba/pipeline_params_tuning_config.yaml
    :language: yaml
    :caption: examples/tuning/domain_EfNST/sub_mba/pipeline_params_tuning_config.yaml
diff --git a/docs/source/DANCE 2.0/experiments/spatial_domain/louvain.rst b/docs/source/DANCE 2.0/experiments/spatial_domain/louvain.rst
@@ -3,6 +3,6 @@ louvain Config
 
 This is the config for louvain.
 
-.. literalinclude:: ../../../../examples/tuning/domain_louvain/sub_mba/pipeline_params_tuning_config.yaml
+.. literalinclude:: ../../../../../examples/tuning/domain_louvain/sub_mba/pipeline_params_tuning_config.yaml
    :language: yaml
    :caption: examples/tuning/domain_louvain/sub_mba/pipeline_params_tuning_config.yaml
diff --git a/docs/source/DANCE 2.0/experiments/spatial_domain/spagcn.rst b/docs/source/DANCE 2.0/experiments/spatial_domain/spagcn.rst
@@ -3,6 +3,6 @@ spagcn Config
 
 This is the config for spagcn.
 
-.. literalinclude:: ../../../../examples/tuning/domain_spagcn/sub_mba/pipeline_params_tuning_config.yaml
+.. literalinclude:: ../../../../../examples/tuning/domain_spagcn/sub_mba/pipeline_params_tuning_config.yaml
    :language: yaml
    :caption: examples/tuning/domain_spagcn/sub_mba/pipeline_params_tuning_config.yaml
diff --git a/docs/source/DANCE 2.0/experiments/spatial_domain/stagate.rst b/docs/source/DANCE 2.0/experiments/spatial_domain/stagate.rst
@@ -3,6 +3,6 @@ stagate Config
 
 This is the config for stagate.
 
-.. literalinclude:: ../../../../examples/tuning/domain_stagate/sub_mba/pipeline_params_tuning_config.yaml
+.. literalinclude:: ../../../../../examples/tuning/domain_stagate/sub_mba/pipeline_params_tuning_config.yaml
    :language: yaml
    :caption: examples/tuning/domain_stagate/sub_mba/pipeline_params_tuning_config.yaml
diff --git a/docs/source/DANCE 2.0/experiments/spatial_domain/stlearn.rst b/docs/source/DANCE 2.0/experiments/spatial_domain/stlearn.rst
@@ -3,6 +3,6 @@ stlearn Config
 
 This is the config for stlearn.
 
-.. literalinclude:: ../../../../examples/tuning/domain_stlearn/sub_mba/pipeline_params_tuning_config.yaml
+.. literalinclude:: ../../../../../examples/tuning/domain_stlearn/sub_mba/pipeline_params_tuning_config.yaml
    :language: yaml
    :caption: examples/tuning/domain_stlearn/sub_mba/pipeline_params_tuning_config.yaml
diff --git a/docs/source/DANCE 2.0/index.rst b/docs/source/DANCE 2.0/index.rst
@@ -14,6 +14,6 @@ DANCE 2.0
    experiments/joint_embedding/index
    experiments/spatial_domain/index
    experiments/celltype_deconvolution/index
-   Preprocessing Function Parameter Search Space
-   Preprocessing Steps and Their Functions
+   Search Space of Preprocessing Function Parameters
+   Preprocessing Steps and Available Function Candidates
    tutorials/tutorial.ipynb
diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -54,8 +54,8 @@ some of the experiments from the original papers.
    :caption: DANCE 2.0
 
    DANCE 2.0/tutorials/tutorial.ipynb
-   DANCE 2.0/Preprocessing Steps and Their Functions
-   DANCE 2.0/Preprocessing Function Parameter Search Space
+   DANCE 2.0/Preprocessing Steps and Available Function Candidates
+   DANCE 2.0/Search Space of Preprocessing Function Parameters
    DANCE 2.0/experiments/index
 
 .. note::
diff --git a/examples/tuning/custom-methods/tutorial.ipynb b/examples/tuning/custom-methods/tutorial.ipynb
@@ -4,7 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# Tutorial: Adding and Using a Custom Algorithm in the Auto-Search Framework\n",
+    "# Tutorial: Plugging User-Designed Methods into DANCE 2.0 for Auto-Search\n",
     "\n",
     "In this notebook, we'll walk through how to integrate a new algorithm (specifically an SVM classifier) into the auto-search framework outlined in your documentation. We will:\n",
     "\n",
@@ -17,6 +17,11 @@
     "Before diving in, ensure you have the following directory structure (at least conceptually; your actual project structure can be more extensive):"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": []
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -1770,7 +1775,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## 3. Configuration Files\n",
+    "## 3. Auto-Search Configuration\n",
     "\n",
     "The **configuration files** (e.g., `pipeline_params_tuning_config.yaml`, `pipeline_tuning_config.yaml`, `params_tuning_config.yaml`) guide the auto-search. Each file contains instructions for how to vary your preprocessing pipeline or model hyperparameters (or both). For example:"
    ]
diff --git a/examples/tuning/step3_default_params.yaml b/examples/tuning/step3_default_params.yaml
