76,705 research outputs found
A Framework for Globally Optimizing Mixed-Integer Signomial Programs
Mixed-integer signomial optimization problems have broad applicability in engineering. Extending the Global Mixed-Integer Quadratic Optimizer, GloMIQO (Misener, Floudas in J. Glob. Optim., 2012. doi:10.1007/s10898-012-9874-7), this manuscript documents a computational framework for deterministically addressing mixed-integer signomial optimization problems to Ξ΅-global optimality. This framework generalizes the GloMIQO strategies of (1) reformulating user input, (2) detecting special mathematical structure, and (3) globally optimizing the mixed-integer nonconvex program. Novel contributions of this paper include: flattening an expression tree towards term-based data structures; introducing additional nonconvex terms to interlink expressions; integrating a dynamic implementation of the reformulation-linearization technique into the branch-and-cut tree; designing term-based underestimators that specialize relaxation strategies according to variable bounds in the current tree node. Computational results are presented along with comparison of the computational framework to several state-of-the-art solvers. Β© 2013 Springer Science+Business Media New York
Sequential Predictions based on Algorithmic Complexity
This paper studies sequence prediction based on the monotone Kolmogorov
complexity Km=-log m, i.e. based on universal deterministic/one-part MDL. m is
extremely close to Solomonoff's universal prior M, the latter being an
excellent predictor in deterministic as well as probabilistic environments,
where performance is measured in terms of convergence of posteriors or losses.
Despite this closeness to M, it is difficult to assess the prediction quality
of m, since little is known about the closeness of their posteriors, which are
the important quantities for prediction. We show that for deterministic
computable environments, the "posterior" and losses of m converge, but rapid
convergence could only be shown on-sequence; the off-sequence convergence can
be slow. In probabilistic environments, neither the posterior nor the losses
converge, in general.Comment: 26 pages, LaTe
Differentiable Programming Tensor Networks
Differentiable programming is a fresh programming paradigm which composes
parameterized algorithmic components and trains them using automatic
differentiation (AD). The concept emerges from deep learning but is not only
limited to training neural networks. We present theory and practice of
programming tensor network algorithms in a fully differentiable way. By
formulating the tensor network algorithm as a computation graph, one can
compute higher order derivatives of the program accurately and efficiently
using AD. We present essential techniques to differentiate through the tensor
networks contractions, including stable AD for tensor decomposition and
efficient backpropagation through fixed point iterations. As a demonstration,
we compute the specific heat of the Ising model directly by taking the second
order derivative of the free energy obtained in the tensor renormalization
group calculation. Next, we perform gradient based variational optimization of
infinite projected entangled pair states for quantum antiferromagnetic
Heisenberg model and obtain start-of-the-art variational energy and
magnetization with moderate efforts. Differentiable programming removes
laborious human efforts in deriving and implementing analytical gradients for
tensor network programs, which opens the door to more innovations in tensor
network algorithms and applications.Comment: Typos corrected, discussion and refs added; revised version accepted
for publication in PRX. Source code available at
https://github.com/wangleiphy/tensorgra
A Compilation Target for Probabilistic Programming Languages
Forward inference techniques such as sequential Monte Carlo and particle
Markov chain Monte Carlo for probabilistic programming can be implemented in
any programming language by creative use of standardized operating system
functionality including processes, forking, mutexes, and shared memory.
Exploiting this we have defined, developed, and tested a probabilistic
programming language intermediate representation language we call probabilistic
C, which itself can be compiled to machine code by standard compilers and
linked to operating system libraries yielding an efficient, scalable, portable
probabilistic programming compilation target. This opens up a new hardware and
systems research path for optimizing probabilistic programming systems.Comment: In Proceedings of the 31st International Conference on Machine
Learning (ICML), 201
MCMC-ODPR : primer design optimization using Markov Chain Monte Carlo sampling
Background
Next generation sequencing technologies often require numerous primer designs that require good target coverage that can be financially costly. We aimed to develop a system that would implement primer reuse to design degenerate primers that could be designed around SNPs, thus find the fewest necessary primers and the lowest cost whilst maintaining an acceptable coverage and provide a cost effective solution. We have implemented Metropolis-Hastings Markov Chain Monte Carlo for optimizing primer reuse. We call it the Markov Chain Monte Carlo Optimized Degenerate Primer Reuse (MCMC-ODPR) algorithm.
Results
After repeating the program 1020 times to assess the variance, an average of 17.14% fewer primers were found to be necessary using MCMC-ODPR for an equivalent coverage without implementing primer reuse. The algorithm was able to reuse primers up to five times. We compared MCMC-ODPR with single sequence primer design programs Primer3 and Primer-BLAST and achieved a lower primer cost per amplicon base covered of 0.21 and 0.19 and 0.18 primer nucleotides on three separate gene sequences, respectively. With multiple sequences, MCMC-ODPR achieved a lower cost per base covered of 0.19 than programs BatchPrimer3 and PAMPS, which achieved 0.25 and 0.64 primer nucleotides, respectively.
Conclusions
MCMC-ODPR is a useful tool for designing primers at various melting temperatures at good target coverage. By combining degeneracy with optimal primer reuse the user may increase coverage of sequences amplified by the designed primers at significantly lower costs. Our analyses showed that overall MCMC-ODPR outperformed the other primer-design programs in our study in terms of cost per covered base
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