diff --git a/docs/index.rst b/docs/index.rst index cebc531..cc6727a 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -51,6 +51,11 @@ explanations. Their run metadata identifies the source revision, parameters, seed, and pinned dependencies. +When using these examples in research, follow the +`software and algorithm citation guidelines +`_ for Sequince and +any additional packages and methods used. + For background and the full interface reference, see Sequince's `user guide `_ and `API reference `_. diff --git a/examples/ns-smc/README.rst b/examples/ns-smc/README.rst index 5d73873..6a1f592 100644 --- a/examples/ns-smc/README.rst +++ b/examples/ns-smc/README.rst @@ -3,6 +3,12 @@ NS-SMC Nested sampling via sequential Monte Carlo (NS-SMC) estimates evidence and posterior expectations by sampling through successive likelihood shells. +The method is described by `Salomone et al. (2025) +`_ in *Unbiased and consistent nested +sampling via sequential Monte Carlo*. The paper distinguishes fixed-threshold +NS-SMC from adaptive NS-SMC (ANS-SMC). Sequince's helper uses adaptive +thresholds by default; these do not inherit fixed-schedule unbiasedness +guarantees. Start with the Gaussian example for basic usage. The spike-and-slab example compares nested and tempered SMC on a model with a phase transition. diff --git a/examples/persistent_sampling/README.rst b/examples/persistent_sampling/README.rst index b70a8c2..0ebd5ac 100644 --- a/examples/persistent_sampling/README.rst +++ b/examples/persistent_sampling/README.rst @@ -4,7 +4,10 @@ Persistent sampling This example demonstrates how to use persistent sampling in ``sequince`` to sample an n-dimensional Rosenbrock target. -Persistent sampling is a variation of SMC proposed by `Karamanis 2025`_. +Persistent sampling is a variation of SMC proposed by +`Karamanis and Seljak (2025)`_ in *Persistent sampling: enhancing the efficiency +of sequential Monte Carlo*. It retains and reweights populations from previous +stages. Run the example from the repository root: @@ -43,7 +46,9 @@ Preconditioning First read :doc:`../preconditioning/README` for an explicit flow-transform setup. This example also shows how to use the normalizing-flow-based preconditioning -described in `Karamanis 2022`_ and `Karamanis 2025`_. +described in `Karamanis et al. (2022)`_, *Accelerating astronomical and +cosmological inference with Preconditioned Monte Carlo*, combined with +persistent sampling from `Karamanis and Seljak (2025)`_. The ``--flow`` option enables learned normalizing-flow preconditioning: @@ -54,8 +59,8 @@ The ``--flow`` option enables learned normalizing-flow preconditioning: The flow option requires ``sequince-density`` and its flow dependencies. -.. _Karamanis 2022: https://arxiv.org/abs/2207.05660 -.. _Karamanis 2025: https://arxiv.org/abs/2407.20722 +.. _Karamanis et al. (2022): https://doi.org/10.1093/mnras/stac2272 +.. _Karamanis and Seljak (2025): https://doi.org/10.1007/s11222-025-10682-y Example plots ------------- diff --git a/examples/preconditioning/README.rst b/examples/preconditioning/README.rst index c5293b1..fba2cb6 100644 --- a/examples/preconditioning/README.rst +++ b/examples/preconditioning/README.rst @@ -74,4 +74,4 @@ Example plots :language: python :linenos: -.. _Karamanis et al. (2022): https://arxiv.org/abs/2207.05652 +.. _Karamanis et al. (2022): https://doi.org/10.1093/mnras/stac2272 diff --git a/examples/waste_free_smc/README.rst b/examples/waste_free_smc/README.rst index 29ad57c..a3bb9cb 100644 --- a/examples/waste_free_smc/README.rst +++ b/examples/waste_free_smc/README.rst @@ -2,7 +2,8 @@ Waste-free sequential Monte Carlo ================================= :download:`run_waste_free_smc.py ` demonstrates waste-free -sequential Monte Carlo (SMC), as described by `Dau & Chopin`_, alongside a +sequential Monte Carlo (SMC), as described by `Dau and Chopin (2022)`_ +in *Waste-free sequential Monte Carlo*, alongside a standard resample-move SMC run. Both sample a four-dimensional correlated Gaussian likelihood with a uniform prior on ``[-10, 10]^4``. @@ -82,4 +83,4 @@ The target densities and complete sampler setup are shown below: :language: python :linenos: -.. _Dau & Chopin: https://arxiv.org/abs/2011.02328 +.. _Dau and Chopin (2022): https://doi.org/10.1111/rssb.12475