## Modeling Genome Evolution with a DSEL for Probabilistic Programming (2006)

### Cached

### Download Links

- [web.engr.oregonstate.edu]
- [www.cs.orst.edu]
- [eecs.oregonstate.edu]
- [cs.oregonstate.edu]
- [web.engr.orst.edu]
- DBLP

### Other Repositories/Bibliography

Venue: | In 8th Int. Symp. on Practical Aspects of Declarative Languages |

Citations: | 1 - 1 self |

### BibTeX

@INPROCEEDINGS{Erwig06modelinggenome,

author = {Martin Erwig and Steve Kollmansberger},

title = {Modeling Genome Evolution with a DSEL for Probabilistic Programming},

booktitle = {In 8th Int. Symp. on Practical Aspects of Declarative Languages},

year = {2006}

}

### OpenURL

### Abstract

Abstract. Many scientific applications benefit from simulation. However, programming languages used in simulation, such as C++ or Matlab, approach problems from a deterministic procedural view, which seems to differ, in general, from many scientists ’ mental representation. We apply a domain-specific language for probabilistic programming to the biological field of gene modeling, showing how the mental-model gap may be bridged. Our system assisted biologists in developing a model for genome evolution by separating the concerns of model and simulation and providing implicit probabilistic non-determinism.

### Citations

168 |
Shapiro: BioAmbients – An Abstraction for Biological Compartments
- Regev, Panina, et al.
(Show Context)
Citation Context ...y, such as Fortran or C. Later simulations were also written in mathematical packages such at MatLab. Recently, some researchers have developed domain-specific modeling tools for biological processes =-=[9, 11, 15, 4, 3]-=-. Many of these approaches, however, are merely speculation and have not been used in an actual research application. In addition, many of them are limited to only the particular given model, and so g... |

125 |
A probabilistic powerdomain of evaluations
- Jones, Plotkin
- 1989
(Show Context)
Citation Context ...ity distributions form a monad is not new [6]. However, previous work was mainly concerned with extending languages by offering probabilistic expressions as primitives and defining suitable semantics =-=[7, 10, 14, 12]-=-. Consider the case where we take a sum, roll a die and add its value to the sum. We may wish to repeat this process several times. We can employ a transition which takes the current sum s and adds ea... |

117 |
Circuit simulation of genetic networks
- McAdams, Shapiro
- 1995
(Show Context)
Citation Context ...y, such as Fortran or C. Later simulations were also written in mathematical packages such at MatLab. Recently, some researchers have developed domain-specific modeling tools for biological processes =-=[9, 11, 15, 4, 3]-=-. Many of these approaches, however, are merely speculation and have not been used in an actual research application. In addition, many of them are limited to only the particular given model, and so g... |

107 | Probabilistic predicate transformers
- Morgan, McIver, et al.
- 1996
(Show Context)
Citation Context ...ity distributions form a monad is not new [6]. However, previous work was mainly concerned with extending languages by offering probabilistic expressions as primitives and defining suitable semantics =-=[7, 10, 14, 12]-=-. Consider the case where we take a sum, roll a die and add its value to the sum. We may wish to repeat this process several times. We can employ a transition which takes the current sum s and adds ea... |

91 | 2001. Parameter learning of logic programs for symbolicstatistical modeling
- Sato, Kameya
(Show Context)
Citation Context ...circuits noting that, like electrical circuits, biological systems operate in parallel and switches may describe activation or repression of either electricity or biological function. Sato and Kameya =-=[17]-=- introduce a statistical logic learning language called PRISM based on Prolog. This language is designed for modeling uncertainty at a high level and can also infer parameters based on a set of given ... |

76 |
Modelling Biological Populations in Space and Time
- Renshaw
- 1991
(Show Context)
Citation Context ...peaks develop, suggesting that using probabilities in modeling has more effect than simply attempting to average the values and retain a deterministic approach. This conclusion is verified by Renshaw =-=[16]-=-, who notes that stochastic predator-prey models almost always experience extinction after several generations. 4 Model Prototyping In this section, we report on the gradual development of the genome ... |

56 | Stochastic lambda calculus and monads of probability distributions
- Ramsey, Pfeffer
- 2002
(Show Context)
Citation Context ...ity distributions form a monad is not new [6]. However, previous work was mainly concerned with extending languages by offering probabilistic expressions as primitives and defining suitable semantics =-=[7, 10, 14, 12]-=-. Consider the case where we take a sum, roll a die and add its value to the sum. We may wish to repeat this process several times. We can employ a transition which takes the current sum s and adds ea... |

40 |
A categorical approach to probability theory
- Giry
- 1982
(Show Context)
Citation Context ... and a transition, threads the values in the first distribution through the transition and combines the resultant distributions. The observation that probability distributions form a monad is not new =-=[6]-=-. However, previous work was mainly concerned with extending languages by offering probabilistic expressions as primitives and defining suitable semantics [7, 10, 14, 12]. Consider the case where we t... |

26 | A probabilistic language based upon sampling functions
- Park, Pfenning, et al.
- 2005
(Show Context)
Citation Context |

14 | Probabilistic functional programming in Haskell
- Erwig, Kollmansberger
(Show Context)
Citation Context ...ce microRNAs are an essential regulatory mechanism for controlling gene expressiveness. The model is realized with the help of a domain-specific embedded language (DSEL) for probabilistic programming =-=[5]-=-. This paper reports on our process as well as results applicable to modeling a wide variety of scientific domains. We have chosen a DSEL approach because it yields a language that offers constructs g... |

11 |
The growth of mixed populations: two species competing for a common food supply
- Lotka
- 1932
(Show Context)
Citation Context ... be imagined as a three dimensional plane showing a slightly different distribution at each z value. type Space a = [Dist a] 3 Probabilistic Modeling in Biology The Lotka-Volterra predator-prey model =-=[8]-=- states that the population of predators and of prey can be described with mutually dependent equations. In particular, given the victims’ growth factor (g), the predators’ death factor (d), the searc... |

8 |
Sonmez K: Pathway logic: symbolic analysis of biological signaling
- Eker, Knapp, et al.
(Show Context)
Citation Context ...y, such as Fortran or C. Later simulations were also written in mathematical packages such at MatLab. Recently, some researchers have developed domain-specific modeling tools for biological processes =-=[9, 11, 15, 4, 3]-=-. Many of these approaches, however, are merely speculation and have not been used in an actual research application. In addition, many of them are limited to only the particular given model, and so g... |

3 |
Using Modelica for Modeling of Discrete, Continuous and Hybrid Biological and Biochemical Systems
- Nilsson, Fritzson
- 2003
(Show Context)
Citation Context |

2 |
Computational Modeling of microRNA Formation and Target Differentiation in Plants
- Allen, Carrington, et al.
- 2005
(Show Context)
Citation Context ...ms [4]. We approach the problem driven by a specific application: In conjunctionswith the Center for Gene Research at Oregon State University, we have developed a model for the evolution of microRNAs =-=[2, 1]-=-, which has enabled scientists to predict what types of genome sequences are most likely to exhibit active microRNAs. This result is important since microRNAs are an essential regulatory mechanism for... |

2 |
Chang and Manu Sridharan. PML: Toward a High-Level Formal Language for Biological Systems
- Evan
- 2003
(Show Context)
Citation Context |