New metric implementations for Alpha Precision and Entropic Relevance

Feature release with fixes and improvements across Stochastic Play-out Log Generation, new metric implementations, metric capture in experiments, and analysis scripts.

New Metrics

• Alpha Precision implementations. See Depaire et al (2022) - Alpha Precision: Estimating the Significant System Behavior in a Model
• Existential Precision, a measure inspired by Alpha Precision, but with tolerance of differences across domains / logs. Alpha precision depends on a domain-specific alpha constant.
• Entropic Relevance implementations. See Alkhammash et al (2022) - Entropic relevance: A mechanism for measuring stochastic process models discovered from event data. All three variants are implemented. The SDFA constraint on input models is relaxed by using stochastic playout logs
• Fix rare bug in Generalization by Trace Difference which allows negative measure when TraceFreq is scaled down
• • This can happen when the model playout size greater than log size

Stochastic Play-out Log Generation

• During stochastic playout log generation surplus allocation, sort silent transitions before other transitions, using the invisible() method on the net transition

Metric Collection

• Collect various new metrics on all experiment runs, including model entity counts, entropic relevance, and existential precision
• Allow genetic miner runs to have observer metrics collected that are not part of the survival function

Experiment Runner

• Allow calculation of some metrics post-hoc, using the run file and model as input
• Change metrics collected during experiments
• • Removed collection of Trace Probability Mass Overlap (TMO)
• • Removed collection of Generalization by Trace Floor 1 and 10

Analysis

• New paradigm cases to further illustrate dimensional extremes
• 3D plots and more selective biplots of PCA space in dimchoice.R

Environment and Lifecycle

• Now requires Java 11 or later
• Remove the deprecated PPT implementation in package qut.pm.spm.ppt.legacy
• Upgrade Earth Movers to latest API

Upgrade EarthMovers plugin

• Upgrade Earth Movers to latest API
• Small updates to stats scripts to improve visualizations
• Reorganize results directories

Performance and PPT semantics improvements

• Improved Stochastic Playout Log Generator performance
• • spg size can now vary independently of event log size
• Fixed bug in PPT loops and conversion
• Update to dedicated prob-process-tree library
• Entropy measures
• • New entropy trace projection measures for fitness and precision
• • Force entropy intersection measures to be bound to [0,1]
• Performance improvement for Random PPT generation

First public version

v1.0

Merge branch 'master' of https://github.com/adamburkegh/spm_dim into …