4,427 research outputs found
Parallel Implementation of Efficient Search Schemes for the Inference of Cancer Progression Models
The emergence and development of cancer is a consequence of the accumulation
over time of genomic mutations involving a specific set of genes, which
provides the cancer clones with a functional selective advantage. In this work,
we model the order of accumulation of such mutations during the progression,
which eventually leads to the disease, by means of probabilistic graphic
models, i.e., Bayesian Networks (BNs). We investigate how to perform the task
of learning the structure of such BNs, according to experimental evidence,
adopting a global optimization meta-heuristics. In particular, in this work we
rely on Genetic Algorithms, and to strongly reduce the execution time of the
inference -- which can also involve multiple repetitions to collect
statistically significant assessments of the data -- we distribute the
calculations using both multi-threading and a multi-node architecture. The
results show that our approach is characterized by good accuracy and
specificity; we also demonstrate its feasibility, thanks to a 84x reduction of
the overall execution time with respect to a traditional sequential
implementation
Efficient computational strategies to learn the structure of probabilistic graphical models of cumulative phenomena
Structural learning of Bayesian Networks (BNs) is a NP-hard problem, which is
further complicated by many theoretical issues, such as the I-equivalence among
different structures. In this work, we focus on a specific subclass of BNs,
named Suppes-Bayes Causal Networks (SBCNs), which include specific structural
constraints based on Suppes' probabilistic causation to efficiently model
cumulative phenomena. Here we compare the performance, via extensive
simulations, of various state-of-the-art search strategies, such as local
search techniques and Genetic Algorithms, as well as of distinct regularization
methods. The assessment is performed on a large number of simulated datasets
from topologies with distinct levels of complexity, various sample size and
different rates of errors in the data. Among the main results, we show that the
introduction of Suppes' constraints dramatically improve the inference
accuracy, by reducing the solution space and providing a temporal ordering on
the variables. We also report on trade-offs among different search techniques
that can be efficiently employed in distinct experimental settings. This
manuscript is an extended version of the paper "Structural Learning of
Probabilistic Graphical Models of Cumulative Phenomena" presented at the 2018
International Conference on Computational Science
A Profile Likelihood Analysis of the Constrained MSSM with Genetic Algorithms
The Constrained Minimal Supersymmetric Standard Model (CMSSM) is one of the
simplest and most widely-studied supersymmetric extensions to the standard
model of particle physics. Nevertheless, current data do not sufficiently
constrain the model parameters in a way completely independent of priors,
statistical measures and scanning techniques. We present a new technique for
scanning supersymmetric parameter spaces, optimised for frequentist profile
likelihood analyses and based on Genetic Algorithms. We apply this technique to
the CMSSM, taking into account existing collider and cosmological data in our
global fit. We compare our method to the MultiNest algorithm, an efficient
Bayesian technique, paying particular attention to the best-fit points and
implications for particle masses at the LHC and dark matter searches. Our
global best-fit point lies in the focus point region. We find many
high-likelihood points in both the stau co-annihilation and focus point
regions, including a previously neglected section of the co-annihilation region
at large m_0. We show that there are many high-likelihood points in the CMSSM
parameter space commonly missed by existing scanning techniques, especially at
high masses. This has a significant influence on the derived confidence regions
for parameters and observables, and can dramatically change the entire
statistical inference of such scans.Comment: 47 pages, 8 figures; Fig. 8, Table 7 and more discussions added to
Sec. 3.4.2 in response to referee's comments; accepted for publication in
JHE
Automating biomedical data science through tree-based pipeline optimization
Over the past decade, data science and machine learning has grown from a
mysterious art form to a staple tool across a variety of fields in academia,
business, and government. In this paper, we introduce the concept of tree-based
pipeline optimization for automating one of the most tedious parts of machine
learning---pipeline design. We implement a Tree-based Pipeline Optimization
Tool (TPOT) and demonstrate its effectiveness on a series of simulated and
real-world genetic data sets. In particular, we show that TPOT can build
machine learning pipelines that achieve competitive classification accuracy and
discover novel pipeline operators---such as synthetic feature
constructors---that significantly improve classification accuracy on these data
sets. We also highlight the current challenges to pipeline optimization, such
as the tendency to produce pipelines that overfit the data, and suggest future
research paths to overcome these challenges. As such, this work represents an
early step toward fully automating machine learning pipeline design.Comment: 16 pages, 5 figures, to appear in EvoBIO 2016 proceeding
The Optimisation of Stochastic Grammars to Enable Cost-Effective Probabilistic Structural Testing
The effectiveness of probabilistic structural testing depends on the characteristics of the probability distribution from which test inputs are sampled at random. Metaheuristic search has been shown to be a practical method of optimis- ing the characteristics of such distributions. However, the applicability of the existing search-based algorithm is lim- ited by the requirement that the software’s inputs must be a fixed number of numeric values. In this paper we relax this limitation by means of a new representation for the probability distribution. The repre- sentation is based on stochastic context-free grammars but incorporates two novel extensions: conditional production weights and the aggregation of terminal symbols represent- ing numeric values. We demonstrate that an algorithm which combines the new representation with hill-climbing search is able to effi- ciently derive probability distributions suitable for testing software with structurally-complex input domains
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