# Bims

### Bayesian Inference of Model Structure.

Bims constructs Markov chains over model structures defined by Dlps (Distributional Logic Programming programs).
The main intuition is that a DLP program can define the space of all possible
models and also assign a probability which reflects our
prior belief that a particular model explains the data. In addition to
composing such a program, the user must provide a function for calculating
the likelihood of the data given a model.

### install

#### SWI

Bims can be installed from within SWI using its
package manager.

?- pack_install(bims).

And then load by :

?- [library(bims)].

To install a source distribution:

?- pack_install( 'the_source.tgz' ).

#### Yap

Copy the sources from
bims

and install locally.
To use load the file

?- ['prolog/bims.pl']

### examples

There are 2 main prepared examples.

?- bims([]).

Runs 3 short example chains that learn classifications trees for the BCW dataset.

?- bims([models(bns)]).

Runs chains that learn Bayesian networks.
### docs

Also available in distribution directory doc/

### sources

packed sources: bims

sources on github bims

### authors

Nicos Angelopoulos

James Cussens

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#### Invited talk

Invited talk at PLP 2015 (September 2015, Cork, Ireland)

Bayesian inference of model structure

#### Publications

##### When citing Bims use the following:

Nicos Angelopoulos and James Cussens.
Distributional Logic Programming for Bayesian Knowledge Representation.

International Journal of Approximate Reasoning (IJAR).
To appear in Volume 80, January 2017, pages 52-66.

Available on-line August 26th, 2016.

##### Inference and Sampling

Nicos Angelopoulos, Sampling and probabilistic inference in D/Slps

In 10th Workshop in Probabilistic Logic Programming (PLP'23)

July 9th, 2023, London UK (slides: 23.07-PLP-Presentation-Nicos.pdf)
##### Papers using Bims

Nicos Angelopoulos and Lodewyk Wessels.
Effective priors over model structures applied to DNA binding assay data
.

AIME'11 Workshop on
Probabilistic Problem Solving in Biomedicine
Bled, Slovenia, July 2011.

Nicos Angelopoulos, Andreas Hadjiprocopis and Malcolm D. Walkinshaw.
Learning binding affinity from augmented high throuput screening data.
Chapter in "Chemoinformatics and Advanced Machine Learning Perspectives: Complex Computational Methods and Collaborative Techniques".
IGI Book Series on Chemoinformatics. Huma Lodhi and Yoshihiro Yamanishi (Eds).
212-234, 2011.

Nicos Angelopoulos, Andreas Hadjiprocopis and Malcolm D. Walkinshaw.
Bayesian ligand discovery from high dimensional descriptor data.
ACS Journal of Chemical Information and Modeling
,
49(6), 1547-1557, 2009.
##### Earlier papers explaining technical aspects of Bims

Nicos Angelopoulos and James Cussens
Bayesian learning of Bayesian Networks with informative priors.
Special issue on BN learning. Journal of Annals of Mathematics and Artificial Intelligence
,
54(1-3), 53-98, 2008.

Nicos Angelopoulos and James Cussens.
Tempering for Bayesian C&RTs.
Proceedings of the 2nd International Conference on Machine Learning (ICML05), Bonn, 2005.

Nicos Angelopoulos and James Cussens.
Exploiting Informative Priors for Bayesian Classification and Regression Trees.
Proceedings of the Nineteenth International Joint Conference on
Artificial Intelligence , Edinburgh, Scotland, UK, July - August 2005.

Nicos Angelopoulos and James Cussens.
Extended stochastic logic programs for informative priors over C&RTs.
In Rui Camacho, Ross King, and Ashwin Srinivasan, editors, Proceedings of
the work-in-progress track of the Fourteenth International Conference on
Inductive Logic Programming (ILP04), pages 7-11, Porto, September
2004.

Nicos Angelopoulos and James Cussens.
On the implementation of MCMC proposals over stochastic logic programs.
In Colloquium on Implementation of Constraint and LOgic
Programming Systems. Satellite workshop to ICLP'04, Saint-Malo, France,
2004.

Nicos Angelopoulos and James Cussens. Markov
chain Monte Carlo using tree-based priors on model structure. In Jack
Breese and Daphne Koller, editors, Proceedings of the Seventeenth
Annual Conference on Uncertainty in Artificial Intelligence (UAI-2001), Seattle, August 2001. Morgan Kaufmann.

Nicos Angelopoulos,

London, April, 2017 - May 2023