Updated description and added yaml data for the data viewer

README.md

@@ -1,48 +1,473 @@
 ---
 license: cc-by-4.0
+configs:
+- config_name: raw_complete_data
+  data_files:
+  - split: exploratory
+    path: "exploratory/raw/*-data.parquet"
+  features: &id001
+  - name: subject_id
+    dtype: string
+  - name: datetime
+    dtype: string
+    type: timestamp
+  - name: iob
+    dtype: float32
+  - name: cob
+    dtype: float32
+  - name: ig
+    dtype: float32
+- config_name: raw_complete_labels
+  data_files:
+  - split: exploratory
+    path: "exploratory/raw/*-labels.parquet"
+  features: &id002
+  - name: subject_id
+    dtype: string
+  - name: id
+    dtype: int32
+  - name: start idx
+    dtype: int32
+  - name: end idx
+    dtype: int32
+  - name: length
+    dtype: int32
+  - name: cluster_id
+    dtype: int32
+  - name: correlation to model
+    dtype: string
+  - name: correlation achieved
+    dtype: string
+  - name: correlation achieved with tolerance
+    dtype: string
+  - name: MAE
+    dtype: float32
+  - name: relaxed MAE
+    dtype: float32
+- config_name: raw_complete_badclustering_labels
+  data_files:
+  - split: exploratory
+    path: "exploratory/raw/bad_partitions/*-labels.parquet"
+  features: &id003
+  - name: subject_id
+    dtype: string
+  - name: cluster_desc
+    dtype: string
+  - name: id
+    dtype: int32
+  - name: start idx
+    dtype: int32
+  - name: end idx
+    dtype: int32
+  - name: length
+    dtype: int32
+  - name: cluster_id
+    dtype: int32
+  - name: correlation to model
+    dtype: string
+  - name: correlation achieved
+    dtype: string
+  - name: correlation achieved with tolerance
+    dtype: string
+  - name: MAE
+    dtype: float32
+  - name: relaxed MAE
+    dtype: float32
+- config_name: raw_partial_data
+  data_files:
+  - split: exploratory
+    path: "exploratory/irregular_p30/raw/*-data.parquet"
+  features: *id001
+- config_name: raw_partial_labels
+  data_files:
+  - split: exploratory
+    path: "exploratory/irregular_p30/raw/*-labels.parquet"
+  features: *id002
+- config_name: raw_partial_badclustering_labels
+  data_files:
+  - split: exploratory
+    path: "exploratory/irregular_p30/raw/bad_partitions/*-labels.parquet"
+  features: *id003
+- config_name: raw_sparse_data
+  data_files:
+  - split: exploratory
+    path: "exploratory/irregular_p90/raw/*-data.parquet"
+  features: *id001
+- config_name: raw_sparse_labels
+  data_files:
+  - split: exploratory
+    path: "exploratory/irregular_p90/raw/*-labels.parquet"
+  features: *id002
+- config_name: raw_sparse_badclustering_labels
+  data_files:
+  - split: exploratory
+    path: "exploratory/irregular_p90/raw/bad_partitions/*-labels.parquet"
+  features: *id003
+- config_name: correlated_complete_data
+  data_files:
+  - split: exploratory
+    path: "exploratory/normal/*-data.parquet"
+  features: *id001
+- config_name: correlated_complete_labels
+  data_files:
+  - split: exploratory
+    path: "exploratory/normal/*-labels.parquet"
+  features: *id002
+- config_name: correlated_complete_badclustering_labels
+  data_files:
+  - split: exploratory
+    path: "exploratory/normal/bad_partitions/*-labels.parquet"
+  features: *id003
+- config_name: correlated_partial_data
+  data_files:
+  - split: exploratory
+    path: "exploratory/irregular_p30/normal/*-data.parquet"
+  features: *id001
+- config_name: correlated_partial_labels
+  data_files:
+  - split: exploratory
+    path: "exploratory/irregular_p30/normal/*-labels.parquet"
+  features: *id002
+- config_name: correlated_partial_badclustering_labels
+  data_files:
+  - split: exploratory
+    path: "exploratory/irregular_p30/normal/bad_partitions/*-labels.parquet"
+  features: *id003
+- config_name: correlated_sparse_data
+  data_files:
+  - split: exploratory
+    path: "exploratory/irregular_p90/normal/*-data.parquet"
+  features: *id001
+- config_name: correlated_sparse_labels
+  data_files:
+  - split: exploratory
+    path: "exploratory/irregular_p90/normal/*-labels.parquet"
+  features: *id002
+- config_name: correlated_sparse_badclustering_labels
+  data_files:
+  - split: exploratory
+    path: "exploratory/irregular_p90/normal/bad_partitions/*-labels.parquet"
+  features: *id003
+- config_name: nonnormal_complete_data
+  data_files:
+  - split: exploratory
+    path: "exploratory/non_normal/*-data.parquet"
+  features: *id001
+- config_name: nonnormal_complete_labels
+  data_files:
+  - split: exploratory
+    path: "exploratory/non_normal/*-labels.parquet"
+  features: *id002
+- config_name: nonnormal_complete_badclustering_labels
+  data_files:
+  - split: exploratory
+    path: "exploratory/non_normal/bad_partitions/*-labels.parquet"
+  features: *id003
+- config_name: nonnormal_partial_data
+  data_files:
+  - split: exploratory
+    path: "exploratory/irregular_p30/non_normal/*-data.parquet"
+  features: *id001
+- config_name: nonnormal_partial_labels
+  data_files:
+  - split: exploratory
+    path: "exploratory/irregular_p30/non_normal/*-labels.parquet"
+  features: *id002
+- config_name: nonnormal_partial_badclustering_labels
+  data_files:
+  - split: exploratory
+    path: "exploratory/irregular_p30/non_normal/bad_partitions/*-labels.parquet"
+  features: *id003
+- config_name: nonnormal_sparse_data
+  data_files:
+  - split: exploratory
+    path: "exploratory/irregular_p90/non_normal/*-data.parquet"
+  features: *id001
+- config_name: nonnormal_sparse_labels
+  data_files:
+  - split: exploratory
+    path: "exploratory/irregular_p90/non_normal/*-labels.parquet"
+  features: *id002
+- config_name: nonnormal_sparse_badclustering_labels
+  data_files:
+  - split: exploratory
+    path: "exploratory/irregular_p90/non_normal/bad_partitions/*-labels.parquet"
+  features: *id003
+- config_name: downsampled_complete_data
+  data_files:
+  - split: exploratory
+    path: "exploratory/resampled_1min/*-data.parquet"
+  features: *id001
+- config_name: downsampled_complete_labels
+  data_files:
+  - split: exploratory
+    path: "exploratory/resampled_1min/*-labels.parquet"
+  features: *id002
+- config_name: downsampled_complete_badclustering_labels
+  data_files:
+  - split: exploratory
+    path: "exploratory/resampled_1min/bad_partitions/*-labels.parquet"
+  features: *id003
+- config_name: downsampled_partial_data
+  data_files:
+  - split: exploratory
+    path: "exploratory/irregular_p30/resampled_1min/*-data.parquet"
+  features: *id001
+- config_name: downsampled_partial_labels
+  data_files:
+  - split: exploratory
+    path: "exploratory/irregular_p30/resampled_1min/*-labels.parquet"
+  features: *id002
+- config_name: downsampled_partial_badclustering_labels
+  data_files:
+  - split: exploratory
+    path: "exploratory/irregular_p30/resampled_1min/bad_partitions/*-labels.parquet"
+  features: *id003
+- config_name: downsampled_sparse_data
+  data_files:
+  - split: exploratory
+    path: "exploratory/irregular_p90/resampled_1min/*-data.parquet"
+  features: *id001
+- config_name: downsampled_sparse_labels
+  data_files:
+  - split: exploratory
+    path: "exploratory/irregular_p90/resampled_1min/*-labels.parquet"
+  features: *id002
+- config_name: downsampled_sparse_badclustering_labels
+  data_files:
+  - split: exploratory
+    path: "exploratory/irregular_p90/resampled_1min/bad_partitions/*-labels.parquet"
+  features: *id003
+- config_name: raw_complete_data
+  data_files:
+  - split: confirmatory
+    path: "confirmatory/raw/*-data.parquet"
+  features: *id001
+- config_name: raw_complete_labels
+  data_files:
+  - split: confirmatory
+    path: "confirmatory/raw/*-labels.parquet"
+  features: *id002
+- config_name: raw_complete_badclustering_labels
+  data_files:
+  - split: confirmatory
+    path: "confirmatory/raw/bad_partitions/*-labels.parquet"
+  features: *id003
+- config_name: raw_partial_data
+  data_files:
+  - split: confirmatory
+    path: "confirmatory/irregular_p30/raw/*-data.parquet"
+  features: *id001
+- config_name: raw_partial_labels
+  data_files:
+  - split: confirmatory
+    path: "confirmatory/irregular_p30/raw/*-labels.parquet"
+  features: *id002
+- config_name: raw_partial_badclustering_labels
+  data_files:
+  - split: confirmatory
+    path: "confirmatory/irregular_p30/raw/bad_partitions/*-labels.parquet"
+  features: *id003
+- config_name: raw_sparse_data
+  data_files:
+  - split: confirmatory
+    path: "confirmatory/irregular_p90/raw/*-data.parquet"
+  features: *id001
+- config_name: raw_sparse_labels
+  data_files:
+  - split: confirmatory
+    path: "confirmatory/irregular_p90/raw/*-labels.parquet"
+  features: *id002
+- config_name: raw_sparse_badclustering_labels
+  data_files:
+  - split: confirmatory
+    path: "confirmatory/irregular_p90/raw/bad_partitions/*-labels.parquet"
+  features: *id003
+- config_name: correlated_complete_data
+  data_files:
+  - split: confirmatory
+    path: "confirmatory/normal/*-data.parquet"
+  features: *id001
+- config_name: correlated_complete_labels
+  data_files:
+  - split: confirmatory
+    path: "confirmatory/normal/*-labels.parquet"
+  features: *id002
+- config_name: correlated_complete_badclustering_labels
+  data_files:
+  - split: confirmatory
+    path: "confirmatory/normal/bad_partitions/*-labels.parquet"
+  features: *id003
+- config_name: correlated_partial_data
+  data_files:
+  - split: confirmatory
+    path: "confirmatory/irregular_p30/normal/*-data.parquet"
+  features: *id001
+- config_name: correlated_partial_labels
+  data_files:
+  - split: confirmatory
+    path: "confirmatory/irregular_p30/normal/*-labels.parquet"
+  features: *id002
+- config_name: correlated_partial_badclustering_labels
+  data_files:
+  - split: confirmatory
+    path: "confirmatory/irregular_p30/normal/bad_partitions/*-labels.parquet"
+  features: *id003
+- config_name: correlated_sparse_data
+  data_files:
+  - split: confirmatory
+    path: "confirmatory/irregular_p90/normal/*-data.parquet"
+  features: *id001
+- config_name: correlated_sparse_labels
+  data_files:
+  - split: confirmatory
+    path: "confirmatory/irregular_p90/normal/*-labels.parquet"
+  features: *id002
+- config_name: correlated_sparse_badclustering_labels
+  data_files:
+  - split: confirmatory
+    path: "confirmatory/irregular_p90/normal/bad_partitions/*-labels.parquet"
+  features: *id003
+- config_name: nonnormal_complete_data
+  data_files:
+  - split: confirmatory
+    path: "confirmatory/non_normal/*-data.parquet"
+  features: *id001
+- config_name: nonnormal_complete_labels
+  data_files:
+  - split: confirmatory
+    path: "confirmatory/non_normal/*-labels.parquet"
+  features: *id002
+- config_name: nonnormal_complete_badclustering_labels
+  data_files:
+  - split: confirmatory
+    path: "confirmatory/non_normal/bad_partitions/*-labels.parquet"
+  features: *id003
+- config_name: nonnormal_partial_data
+  data_files:
+  - split: confirmatory
+    path: "confirmatory/irregular_p30/non_normal/*-data.parquet"
+  features: *id001
+- config_name: nonnormal_partial_labels
+  data_files:
+  - split: confirmatory
+    path: "confirmatory/irregular_p30/non_normal/*-labels.parquet"
+  features: *id002
+- config_name: nonnormal_partial_badclustering_labels
+  data_files:
+  - split: confirmatory
+    path: "confirmatory/irregular_p30/non_normal/bad_partitions/*-labels.parquet"
+  features: *id003
+- config_name: nonnormal_sparse_data
+  data_files:
+  - split: confirmatory
+    path: "confirmatory/irregular_p90/non_normal/*-data.parquet"
+  features: *id001
+- config_name: nonnormal_sparse_labels
+  data_files:
+  - split: confirmatory
+    path: "confirmatory/irregular_p90/non_normal/*-labels.parquet"
+  features: *id002
+- config_name: nonnormal_sparse_badclustering_labels
+  data_files:
+  - split: confirmatory
+    path: "confirmatory/irregular_p90/non_normal/bad_partitions/*-labels.parquet"
+  features: *id003
+- config_name: downsampled_complete_data
+  data_files:
+  - split: confirmatory
+    path: "confirmatory/resampled_1min/*-data.parquet"
+  features: *id001
+- config_name: downsampled_complete_labels
+  data_files:
+  - split: confirmatory
+    path: "confirmatory/resampled_1min/*-labels.parquet"
+  features: *id002
+- config_name: downsampled_complete_badclustering_labels
+  data_files:
+  - split: confirmatory
+    path: "confirmatory/resampled_1min/bad_partitions/*-labels.parquet"
+  features: *id003
+- config_name: downsampled_partial_data
+  data_files:
+  - split: confirmatory
+    path: "confirmatory/irregular_p30/resampled_1min/*-data.parquet"
+  features: *id001
+- config_name: downsampled_partial_labels
+  data_files:
+  - split: confirmatory
+    path: "confirmatory/irregular_p30/resampled_1min/*-labels.parquet"
+  features: *id002
+- config_name: downsampled_partial_badclustering_labels
+  data_files:
+  - split: confirmatory
+    path: "confirmatory/irregular_p30/resampled_1min/bad_partitions/*-labels.parquet"
+  features: *id003
+- config_name: downsampled_sparse_data
+  data_files:
+  - split: confirmatory
+    path: "confirmatory/irregular_p90/resampled_1min/*-data.parquet"
+  features: *id001
+- config_name: downsampled_sparse_labels
+  data_files:
+  - split: confirmatory
+    path: "confirmatory/irregular_p90/resampled_1min/*-labels.parquet"
+  features: *id002
+- config_name: downsampled_sparse_badclustering_labels
+  data_files:
+  - split: confirmatory
+    path: "confirmatory/irregular_p90/resampled_1min/bad_partitions/*-labels.parquet"
+  features: *id003
 ---
 # CSTS - Correlation Structures in Time Series
 
 ## Important Notice
-This dataset is published as a pre-publication release. An accompanying research paper is forthcoming on arXiv. **All usage of this dataset must include proper attribution to the original authors as specified below.**
+This dataset is published as a pre-publication release. An accompanying research paper is forthcoming on arXiv. 
+**All usage of this dataset must include proper attribution to the original authors as specified below.**
 
 ## Dataset Description
 CSTS (**C**orrelation **S**tructures in **T**ime **S**eries) is a comprehensive synthetic benchmarking dataset for 
 evaluating correlation structure discovery in time series data. The dataset systematically models known correlation 
 structures between three different time series variates and enables examination of how these structures are affected by
 distribution shifting, sparsification, and downsampling. With its controlled properties and ground truth labels, 
-CSTS provides algorithm developers clean benchmark data that bridges the gap between theoretical models 
+CSTS provides algorithm developers clean benchmark data that bridge the gap between theoretical models 
 and messy real-world data.
 
 ### Key Applications
-- Evaluating the ability of time series clustering algorithms to segment and group by correlation structures
-- Assessing clustering validation methods for correlation-based clusters
-- Investigating how data preprocessing affects correlation structure discovery
-- Establishing performance thresholds for high-quality clustering result
+- Evaluating the ability of **time series clustering algorithms** to segment and group segments by correlation structures
+- Assessing **clustering validation** methods for correlation-based clusters
+- Investigating how **data preprocessing** affects correlation structure discovery
+- Establishing **performance thresholds** for high-quality clustering result
 
 ### Dataset Structure
 CSTS provides **two main splits** (exploratory and confirmatory) with **30 subjects** each, enabling proper statistical validation.
 The dataset structure includes:
-- **12 data variants** across four generation stages × three completeness levels for each split
-- **Generation stages**: raw (unstructured), correlated (normal-distributed), non-normal distribution shifts, downsampled (1s→1min)
-- **Completeness levels**: complete (100%), partial (70%), sparse (10%) of observations retained
+- **12 data variants**: 4 generation stages × 3 completeness levels for each split
+- **Generation stages**: raw (unstructured data), correlated (normal-distributed data), nonnormal (extreme value and negative binomial distribution shifts), downsampled (1s→1min)
+- **Completeness levels**: complete (100% of observations), partial (70% of observations), sparse (10% of observations)
 
 ### Subjects
-Each subject contains 100 segments of varying lengths and each segment encodes one of the 23 specific correlation 
-structures. Each subject uses all 23 patterns 4-5 times.
+Each subject contains 100 segments of varying lengths (900-36000) and each segment encodes one of the 23 specific correlation 
+structures. Each subject uses all 23 patterns 4-5 times. For the complete data variants each subject consists of ~1.26 mio
+observations.
 
-For each subject, CSTS includes:
-- a time series **data file** with three variates
+Subjects each have the following information, accessible as subsets:
+- a time series **data file** with three variates (iob, cob, ig) and time stamps (datetime)
 - a **label file** specifying the ground truth segmentation and clustering
-- 67 **bad clustering label files** with controlled degradations (varying numbers of segmentations and/or cluster assignment mistakes) spanning the full Jaccard Index range [0,1]
+- 67 **bad clustering label files** with controlled degradations (varying numbers of segmentations and/or cluster assignment mistakes) spanning the entire Jaccard Index range [0,1]
 
 ### Additional Splits
-CSTS also includes versions (configured as splits) that allow exploration of how cluster and segment counts affect 
-algorithm performance. They follow the same structure as above and are:
-- Reduced clusters (11 or 6 instead of 23)
-- Reduced segments (50 or 25 instead of 100)
+CSTS also includes versions (configured as splits) that allow exploring how cluster and segment counts affect 
+algorithm performance. They follow the same dataset structure (exploratory and confirmatory splits with each 12 data variants subset with each 3 information file subsets).
+These versions are:
+- Reduced cluster count: 11 or 6 instead of 23
+- Reduced segment count: 50 or 25 instead of 100
 
-Our accompanying paper provides complete methodological details, baseline findings, and usage guidance.
+Our accompanying paper provides complete methodological details, baseline findings, and usage guidance. Our
+GitHub codebase includes the generation, validation and use case code and is configured to automatically load the data.
+
+## Usage Guidance
+... coming soon
 
 ## Authors
 - Isabella Degen, University of Bristol
@@ -50,7 +475,6 @@ Our accompanying paper provides complete methodological details, baseline findin
 - Henry W J Reeve, University of Nanjing
 - Kate Robson Brown, University College Dublin
 
-
 ## Pre-Publication Release Details
 - **Release Date:** 29 Apr 2024
 - **Version:** 1.0-pre
@@ -79,5 +503,5 @@ Please use the following temporary citation until our paper is published:
 Once our paper is published on arXiv, we will update this README with the proper citation information.
 **Please check back for updates.**
 
-## Dataset Details
-...coming soon
+## Acknowledgements
+... coming soon