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sbi reloaded: a toolkit for simulation-based inference workflows

Authors: Boelts, Jan; Deistler, Michael; Glöckler, Manuel; Tejero-Cantero, Alvaro; Lueckmann, Jan-Matthis; Moss, Guy; Steinbach, Peter; +26 Authors

sbi reloaded: a toolkit for simulation-based inference workflows

Abstract

✨ Highlights 🚀 New Inference Methods MNPE class mixed parameter (similar to MNLE) by @dgedon in https://github.com/sbi-dev/sbi/pull/1362 Implementation of SNPE-B (#199) by @etouron1 in https://github.com/sbi-dev/sbi/pull/1471 🧠 Neural Network Architectures & Embedding Networks Add transformer embedding net by @NicolasRR in https://github.com/sbi-dev/sbi/pull/1494 Add embedding net that uses 1D causal convolutions (#1459) by @Aranka-S in https://github.com/sbi-dev/sbi/pull/1499 Add LRU-backed embedding networks by @famura in https://github.com/sbi-dev/sbi/pull/1512 Add ResNet as embedding model by @StefanWahl in https://github.com/sbi-dev/sbi/pull/1472 Spectral convolution embedding net by @L-in-da in https://github.com/sbi-dev/sbi/pull/1503 ⭐ Major Features & Capabilities Unify flow matching and score-based models by @StarostinV in https://github.com/sbi-dev/sbi/pull/1497 Model misspecification detection based on MMD by @coschroeder in https://github.com/sbi-dev/sbi/pull/1502 Marginal estimator log-prob based test for misspecification by @swag2198 in https://github.com/sbi-dev/sbi/pull/1522 Adding interface for unconditional flow training by @plcrodrigues in https://github.com/sbi-dev/sbi/pull/1470 Support using trained estimators in Pyro models by @sethaxen in https://github.com/sbi-dev/sbi/pull/1491 Add util to generate mcmc samples from user defined potential (#1405) by @hayden-johnson in https://github.com/sbi-dev/sbi/pull/1483 Logit transform by @anastasiakrouglova in https://github.com/sbi-dev/sbi/pull/1485 Log-prob for iid data for score estimators by @Kartik-Sama in https://github.com/sbi-dev/sbi/pull/1508 📚 Documentation & Tutorials Tutorial on new features for score-based methods #1392 by @touronc in https://github.com/sbi-dev/sbi/pull/1489 Docs: Introduce Readthedocs website by @michaeldeistler in https://github.com/sbi-dev/sbi/pull/1463 🐛 Bug Fixes z_score correct order in Zuko by @anastasiakrouglova in https://github.com/sbi-dev/sbi/pull/1492 Minor fix when moving thetas from GPU to CPU by @famura in https://github.com/sbi-dev/sbi/pull/1515 Minor fix while using unconditional density estimator and LRU embedding by @ARna06 in https://github.com/sbi-dev/sbi/pull/1556 fix: replace 'in' operator with '==' for proper classifier comparison by @abelaba in https://github.com/sbi-dev/sbi/pull/1550 flowmatching condition shape fix by @gmoss13 in https://github.com/sbi-dev/sbi/pull/1584 patch for torch bug in tarp, run torch.histogram with cpu-only tensor by @psteinb in https://github.com/sbi-dev/sbi/pull/1596 fix failing tarp test by @janfb in https://github.com/sbi-dev/sbi/pull/1628 fix: cap max_sampling_batch_size to prevent excessive memory by @janfb in https://github.com/sbi-dev/sbi/pull/1624 1561 computation of denoising posterior precision matrix in jac method score fn iid by @manuelgloeckler in https://github.com/sbi-dev/sbi/pull/1636 fix xfail test, fix deprecation warnings by @janfb in https://github.com/sbi-dev/sbi/pull/1642 fix: iid-score device handling by @janfb in https://github.com/sbi-dev/sbi/pull/1650 fix: fmpe singularity on sde sampling by @manuelgloeckler in https://github.com/sbi-dev/sbi/pull/1661 🛠️ Maintenance & Improvements 🔧 Code Quality & Refactoring Refactoring flow and score matching classes and nets by @manuelgloeckler in https://github.com/sbi-dev/sbi/pull/1544 Rename inference trainer classes by @abelaba in https://github.com/sbi-dev/sbi/pull/1605 Rename VectorFieldInference to VectorFieldTrainer by @abelaba in https://github.com/sbi-dev/sbi/pull/1614 Refactor build_posterior to Eliminate Duplication Across Trainers by @abelaba in https://github.com/sbi-dev/sbi/pull/1610 Refactor build posterior method arguments to use Literals by @abelaba in https://github.com/sbi-dev/sbi/pull/1606 Refactor build_posterior Posterior Configuration Using Dataclasses by @abelaba in https://github.com/sbi-dev/sbi/pull/1619 Use TypeAlias and consistent naming for sbi types by @janfb in https://github.com/sbi-dev/sbi/pull/1637 Add protocol for estimator builder by @abelaba in https://github.com/sbi-dev/sbi/pull/1633 Improve abc implementation by @janfb in https://github.com/sbi-dev/sbi/pull/1615 Refactor RatioEstimator to subclass ConditionalEstimator @abelaba in https://github.com/sbi-dev/sbi/pull/1652 🏷️ Type Hints & API Improvements fix: add enum for flow options to fix type hints. by @janfb in https://github.com/sbi-dev/sbi/pull/1562 fix LC2ST kwarg typing by @janfb in https://github.com/sbi-dev/sbi/pull/1565 fix: Update RatioEstimator classifier argument to use a Protocol by @abelaba in https://github.com/sbi-dev/sbi/pull/1582 Update append_simulations return type to Self by @abelaba in https://github.com/sbi-dev/sbi/pull/1622 Deprecation Warnings for build_posterior stringly typed parameters by @abelaba in https://github.com/sbi-dev/sbi/pull/1627 🧪 Testing & CI/CD Testmon by @manuelgloeckler in https://github.com/sbi-dev/sbi/pull/1452 disable testmon for now by @manuelgloeckler in https://github.com/sbi-dev/sbi/pull/1467 chore: Use pytest-split plugin in ci workflow by @schroedk in https://github.com/sbi-dev/sbi/pull/1465 tests: refactor "not slow" tests to be not so slow by @janfb in https://github.com/sbi-dev/sbi/pull/1495 Test for known pytorch distribution transform issue by @dgedon in https://github.com/sbi-dev/sbi/pull/1504 xfail scan test on python 3.13 by @manuelgloeckler in https://github.com/sbi-dev/sbi/pull/1533 Gpu test for VectorFieldPosterior by @jorobledo in https://github.com/sbi-dev/sbi/pull/1542 set vector field iid-tests xfail by @janfb in https://github.com/sbi-dev/sbi/pull/1554 Changed the xfail condition for LRU tests with mode='scan' by @famura in https://github.com/sbi-dev/sbi/pull/1552 Fix/lru test by @Matthijspals in https://github.com/sbi-dev/sbi/pull/1568 refactor sbc funcs and tests by @janfb in https://github.com/sbi-dev/sbi/pull/1578 chore: remove testmon, add codecov test analytics by @janfb in https://github.com/sbi-dev/sbi/pull/1592 chore: reorder setup steps for Python and uv in CI/CD workflows by @janfb in https://github.com/sbi-dev/sbi/pull/1601 Fix/lc2st numpy type fixes by @janfb in https://github.com/sbi-dev/sbi/pull/1613 Fix failing CI on main. by @janfb in https://github.com/sbi-dev/sbi/pull/1618 Fix slow vector field tests by @janfb in https://github.com/sbi-dev/sbi/pull/1657 Add tests for sensitivity analysis by @janfb in https://github.com/sbi-dev/sbi/pull/1662 📖 Documentation & Website Fix tests for new docs by @michaeldeistler in https://github.com/sbi-dev/sbi/pull/1475 Prevent notebook execution upon doc build by @michaeldeistler in https://github.com/sbi-dev/sbi/pull/1477 Fix broken links on website by @michaeldeistler in https://github.com/sbi-dev/sbi/pull/1480 fix: Update documentation folder path by @abelaba in https://github.com/sbi-dev/sbi/pull/1510 fix path to contribute.md by @psteinb in https://github.com/sbi-dev/sbi/pull/1507 Add utils to docs by @sethaxen in https://github.com/sbi-dev/sbi/pull/1520 Update new Readthedocs website by @michaeldeistler in https://github.com/sbi-dev/sbi/pull/1519 fix broken links on new website by @michaeldeistler in https://github.com/sbi-dev/sbi/pull/1538 Fixups for new website landing page by @michaeldeistler in https://github.com/sbi-dev/sbi/pull/1539 Fix: add tutorial page to mkdocs website by @michaeldeistler in https://github.com/sbi-dev/sbi/pull/1540 Fix broken links in some tutorials by @michaeldeistler in https://github.com/sbi-dev/sbi/pull/1541 Add examples to documentation by @jorobledo in https://github.com/sbi-dev/sbi/pull/1548 docs: Add importance_sampling_parameters to build_posterior docstring. by @abelaba in https://github.com/sbi-dev/sbi/pull/1558 Add missing arguments to LikelihoodEstimator and RatioEstimator docstrings. by @abelaba in https://github.com/sbi-dev/sbi/pull/1571 Fixups for new RTD website by @michaeldeistler in https://github.com/sbi-dev/sbi/pull/1573 Tutorial with a more representative training loop by @michaeldeistler in https://github.com/sbi-dev/sbi/pull/1574 Fixups for rendering of HH tutorial notebook by @michaeldeistler in https://github.com/sbi-dev/sbi/pull/1575 fix for colors in Hodgkin-Huxley notebook by @michaeldeistler in https://github.com/sbi-dev/sbi/pull/1576 Add citations to how-to guide by @michaeldeistler in https://github.com/sbi-dev/sbi/pull/1579 Clarify fullscreen view of applications-explorer by @michaeldeistler in https://github.com/sbi-dev/sbi/pull/1580 Fixups for the documentation by @michaeldeistler in https://github.com/sbi-dev/sbi/pull/1585 fixed misrendered bullet list, tested locally by @psteinb in https://github.com/sbi-dev/sbi/pull/1594 Improvements to L-C2ST tutorial by @michaeldeistler in https://github.com/sbi-dev/sbi/pull/1588 docs: Change colortheme in light mode by @michaeldeistler in https://github.com/sbi-dev/sbi/pull/1638 Posterior parameters doc by @abelaba in https://github.com/sbi-dev/sbi/pull/1644 fix contributing links by @janfb in https://github.com/sbi-dev/sbi/pull/1647 docs: add posterior parameters dataclass how to guide by @abelaba in https://github.com/sbi-dev/sbi/pull/1654 🏗️ Infrastructure & Dependencies Add uv support by @abelaba in https://github.com/sbi-dev/sbi/pull/1518 switch to numfocus code of conduct by @janfb in https://github.com/sbi-dev/sbi/pull/1560 Update readme with new JOSS citation by @janfb in https://github.com/sbi-dev/sbi/pull/1564 update numfocus code of conduct by @janfb in https://github.com/sbi-dev/sbi/pull/1602 Added Apache License reference comments to source files + CI bash script check by @nMaax in https://github.com/sbi-dev/sbi/pull/1599 👥 User Experience & Warnings Change xfail to skipif as outcome is not consistent by @gmoss13 in https://github.com/sbi-dev/sbi/pull/1487 Add warning when using append_simulations with exclude_invalid_x=True by @abelaba in https://github.com/sbi-dev/sbi/pull/1486 Batch sampling slow without warning by @dgedon in https://github.com/sbi-dev/sbi/pull/1490 Clarify pbar annotation in sample_batched for DirectPosterior by @StefanWahl in https://github.com/sbi-dev/sbi/pull/1493 🎮 GPU Support & Device Handling Prior to(device) by @jorobledo in https://github.com/sbi-dev/sbi/pull/1505 posterior.to(device) by @jorobledo in https://github.com/sbi-dev/sbi/pull/1527 🔧 Miscellaneous Improvements ref: update tests, add types and docs to marginal trainer by @janfb in https://github.com/sbi-dev/sbi/pull/1516 integrate sbi application eplorer by @lappalainenj in https://github.com/sbi-dev/sbi/pull/1567 fix: update notebook references by @emmanuel-ferdman in https://github.com/sbi-dev/sbi/pull/1563 Update sbiutils.py to use one-dimensional batch by @vivienr in https://github.com/sbi-dev/sbi/pull/1577 fix: remove empty list default argument by @abelaba in https://github.com/sbi-dev/sbi/pull/1608 fix: throw exception on unsupported activation function by @emmanuel-ferdman in https://github.com/sbi-dev/sbi/pull/1609 fix: resolve logger warnings by @emmanuel-ferdman in https://github.com/sbi-dev/sbi/pull/1598 fix paths by @manuelgloeckler in https://github.com/sbi-dev/sbi/pull/1641 🎉 New Contributors @abelaba made their first contribution in https://github.com/sbi-dev/sbi/pull/1486 @dgedon made their first contribution in https://github.com/sbi-dev/sbi/pull/1490 @StefanWahl made their first contribution in https://github.com/sbi-dev/sbi/pull/1493 @touronc made their first contribution in https://github.com/sbi-dev/sbi/pull/1489 @jorobledo made their first contribution in https://github.com/sbi-dev/sbi/pull/1505 @hayden-johnson made their first contribution in https://github.com/sbi-dev/sbi/pull/1483 @sethaxen made their first contribution in https://github.com/sbi-dev/sbi/pull/1491 @etouron1 made their first contribution in https://github.com/sbi-dev/sbi/pull/1471 @Aranka-S made their first contribution in https://github.com/sbi-dev/sbi/pull/1499 @swag2198 made their first contribution in https://github.com/sbi-dev/sbi/pull/1522 @StarostinV made their first contribution in https://github.com/sbi-dev/sbi/pull/1497 @L-in-da made their first contribution in https://github.com/sbi-dev/sbi/pull/1503 @NicolasRR made their first contribution in https://github.com/sbi-dev/sbi/pull/1494 @vivienr made their first contribution in https://github.com/sbi-dev/sbi/pull/1577 Full Changelog: https://github.com/sbi-dev/sbi/compare/v0.24.0...v0.25.0

If you use this software, please cite our article in the Journal of Open Source Software.

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popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
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