Molecular Learning of wDNF Formulae

We introduce a class of generalized DNF formulae called wDNF or weighted disjunctive normal form, and present a molecular algorithm that learns a wDNF formula from training examples. Realized in DNA molecules, the wDNF machines have a natural probabilistic semantics, allowing for their application beyond the pure Boolean logical structure of the standard DNF to real-life problems with uncertainty. The potential of the molecular wDNF machines is evaluated on real-life genomics data in simulation. Our empirical results suggest the possibility of building error-resilient molecular computers that are able to learn from data, potentially from wet DNA data.

[1]  Leslie G. Valiant,et al.  Robust logics , 1999, STOC '99.

[2]  George Shackelford,et al.  Learning k-DNF with noise in the attributes , 1988, Annual Conference Computational Learning Theory.

[3]  E. Shapiro,et al.  An autonomous molecular computer for logical control of gene expression , 2004, Nature.

[4]  J. SantaLucia,et al.  The thermodynamics of DNA structural motifs. , 2004, Annual review of biophysics and biomolecular structure.

[5]  Byoung-Tak Zhang,et al.  Balancing Accuracy and Parsimony in Genetic Programming , 1995, Evolutionary Computation.

[6]  Byoung-Tak Zhang,et al.  A Bayesian Algorithm for In Vitro Molecular Evolution of Pattern Classifiers , 2004, DNA.

[7]  Junghuei Chen,et al.  A DNA-based memory with in vitro learning and associative recall , 2003, Natural Computing.

[8]  R. Deaton,et al.  A DNA-based in vitro Genetic Program , 2005 .

[9]  E B Baum,et al.  Building an associative memory vastly larger than the brain. , 1995, Science.

[10]  J. Downing,et al.  Treatment-specific changes in gene expression discriminate in vivo drug response in human leukemia cells , 2003, Nature Genetics.

[11]  John R. Koza,et al.  Genetic programming - on the programming of computers by means of natural selection , 1993, Complex adaptive systems.

[12]  Bo Guo,et al.  Experimental Construction of Very Large Scale DNA Databases with Associative Search Capability , 2001, DNA.

[13]  Albert S. Benight,et al.  Thermal denaturation of DNA molecules: A comparison of theory with experiment , 1985 .

[14]  Yasubumi Sakakibara.  Solving Computational Learning Problems of Boolean Formulae on DNA Computers , 2000, DNA Computing.

[15]  M Hagiya,et al.  A DNA-based in vitroGenetic Program , 2002, Journal of biological physics.