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+---
+title: "TSGap: Reproducible missingness simulation for time-series benchmarks"
+date: "2026-11-09"
+type: blog
+url: "/blog/tsgap-time-series-missingness.html"
+excerpt: >-
+  TSGap is a NumPy-native Python package for creating reproducible artificial
+  missingness scenarios for time-series imputation benchmarks.
+author: "Feruz Oripov"
+blog_topic: software
+toc: true
+lastmod: "2026-11-09"
+image:
+  src: "images/blog/2026/tsgap-before-after.png"
+  alt: >-
+    A complete multivariate time series beside six examples with missing values
+    highlighted in red: pointwise, block, monotone, decay, Markov, and
+    Gilbert-Elliott patterns.
+tags:
+  - time series
+  - missing data
+  - imputation
+  - scientific Python
+show_author: true
+learn_more:
+  - title: "TSGap documentation"
+    url: "https://feruzoripov.github.io/tsgap/"
+  - title: "TSGap on GitHub"
+    url: "https://github.com/feruzoripov/tsgap"
+  - title: "TSGap on PyPI"
+    url: "https://pypi.org/project/tsgap/"
+comments: true
+---
+
+Evaluating a time-series imputation method requires known values that can be
+hidden and reconstructed. The way those values are hidden matters: isolated
+missing points, sensor outages, dropout near the end of a recording, and bursty
+packet loss create very different reconstruction problems.
+
+[TSGap](https://github.com/feruzoripov/tsgap) is a lightweight, NumPy-native
+Python package for creating these artificial missingness scenarios. It was
+recently [peer reviewed and accepted by
+pyOpenSci](https://github.com/pyOpenSci/software-submission/issues/354).
+
+## Why separate mechanism from pattern
+
+TSGap describes a scenario using two ideas:
+
+* The **mechanism** describes why a value is selected for masking. TSGap
+  supports missing completely at random (MCAR), missing at random (MAR), and
+  missing not at random (MNAR).
+* The **pattern** describes how missing values are arranged over time.
+  Available patterns include pointwise, block, monotone, decay, Markov, and
+  Gilbert-Elliott burst loss.
+
+Separating these concepts makes experiments easier to describe and reproduce.
+For example, researchers can compare isolated MCAR gaps with contiguous MCAR
+outages while keeping the requested missing rate fixed.
+
+There is an important interpretation detail. Pointwise MAR and MNAR preserve a
+direct relationship between the mechanism score and each masked value.
+Non-pointwise patterns reshape a mechanism-informed missingness budget into a
+temporal structure. They should therefore be described as structured,
+mechanism-informed masks rather than automatically treated as strict MAR or
+MNAR data-generating processes.
+
+## Create a block-missingness scenario
+
+Install TSGap from PyPI:
+
+```bash
+pip install tsgap
+```
+
+The following example masks 20% of the eligible values in a two-feature time
+series. Each block spans between 2% and 10% of the series length.
+
+```python
+import numpy as np
+
+from tsgap import simulate_missingness
+
+rng = np.random.default_rng(42)
+X = rng.normal(size=(1_000, 2))
+
+X_missing, observed_mask = simulate_missingness(
+    X,
+    mechanism="mcar",
+    pattern="block",
+    missing_rate=0.20,
+    block_frac=(0.02, 0.10),
+    seed=42,
+)
+
+artificially_missing = ~observed_mask & np.isfinite(X)
+achieved_rate = artificially_missing.sum() / np.isfinite(X).sum()
+
+print(f"Artificial missingness rate: {achieved_rate:.1%}")
+```
+
+`X_missing` contains `NaN` at the newly hidden positions. The Boolean
+`observed_mask` is `False` at those positions and `True` where data remain
+observed. The same seed produces the same mask, which supports reproducible
+benchmarking.
+
+The missing-rate denominator is the number of originally observed, eligible
+entries in the selected target dimensions. Existing `NaN` values are preserved
+but do not count toward the requested artificial missingness rate. This
+distinction is useful when working with real sensor recordings that already
+contain gaps.
+
+## From simulation to evaluation
+
+A typical benchmark can use TSGap in four steps:
+
+1. Start with complete data, or record which values were originally observed.
+2. Generate a missingness scenario with a fixed seed.
+3. Run an imputation method on `X_missing`.
+4. Evaluate predictions only at positions that TSGap artificially masked.
+
+TSGap supports both two-dimensional arrays shaped as time by features and
+three-dimensional arrays shaped as samples by time by features. Target
+dimensions can be selected so that auxiliary variables remain available while
+another variable is masked.
+
+Deterministic patterns aim for exact rate control among eligible entries.
+Stochastic state models such as Markov and Gilbert-Elliott masks can vary
+between seeds, so studies using them should report achieved rates and aggregate
+results across multiple seeds.
+
+## Try TSGap
+
+TSGap is available under the MIT license:
+
+* [Documentation](https://feruzoripov.github.io/tsgap/)
+* [Source code](https://github.com/feruzoripov/tsgap)
+* [PyPI package](https://pypi.org/project/tsgap/)
+* [Version 0.8.0
+  release](https://github.com/feruzoripov/tsgap/releases/tag/v0.8.0)
+
+Bug reports, feature requests, and contributions are welcome through the
+[TSGap issue tracker](https://github.com/feruzoripov/tsgap/issues).
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