Precision-mapping and statistical validation of quantitative trait loci by machine learning

<p>Abstract</p> <p>Background</p> <p>We introduce a QTL-mapping algorithm based on Statistical Machine Learning (SML) that is conceptually quite different to existing methods as there is a strong focus on generalisation ability. Our approach combines ridge regression, recursive feature elimination, and estimation of generalisation performance and marker effects using bootstrap resampling. Model performance and marker effects are determined using independent testing samples (individuals), thus providing better estimates. We compare the performance of SML against Composite Interval Mapping (CIM), Bayesian Interval Mapping (BIM) and single Marker Regression (MR) on synthetic datasets and a multi-trait and multi-environment dataset of the progeny for a cross between two barley cultivars.</p> <p>Results</p> <p>In an analysis of the synthetic datasets, SML accurately predicted the number of QTL underlying a trait while BIM tended to underestimate the number of QTL. The QTL identified by SML for the barley dataset broadly coincided with known QTL locations. SML reported approximately half of the QTL reported by either CIM or MR, not unexpected given that neither CIM nor MR incorporates independent testing. The latter makes these two methods susceptible to producing overly optimistic estimates of QTL effects, as we demonstrate for MR. The QTL resolution (peak definition) afforded by SML was consistently superior to MR, CIM and BIM, with QTL detection power similar to BIM. The precision of SML was underscored by repeatedly identifying, at ≤ 1-cM precision, three QTL for four partially related traits (heading date, plant height, lodging and yield). The set of QTL obtained using a 'raw' and a 'curated' version of the same genotypic dataset were more similar to each other for SML than for CIM or MR.</p> <p>Conclusion</p> <p>The SML algorithm produces better estimates of QTL effects because it eliminates the optimistic bias in the predictive performance of other QTL methods. It produces narrower peaks than other methods (except BIM) and hence identifies QTL with greater precision. It is more robust to genotyping and linkage mapping errors, and identifies markers linked to QTL in the absence of a genetic map.</p

A Reproducible and Realistic Evaluation of Partial Domain Adaptation Methods

Unsupervised Domain Adaptation (UDA) aims at classifying unlabeled target images leveraging source labeled ones. In this work, we consider the Partial Domain Adaptation (PDA) variant, where we have extra source classes not present in the target domain. Most successful algorithms use model selection strategies that rely on target labels to find the best hyper-parameters and/or models along training. However, these strategies violate the main assumption in PDA: only unlabeled target domain samples are available. Moreover, there are also inconsistencies in the experimental settings - architecture, hyper-parameter tuning, number of runs - yielding unfair comparisons. The main goal of this work is to provide a realistic evaluation of PDA methods with the different model selection strategies under a consistent evaluation protocol. We evaluate 7 representative PDA algorithms on 2 different real-world datasets using 7 different model selection strategies. Our two main findings are: (i) without target labels for model selection, the accuracy of the methods decreases up to 30 percentage points; (ii) only one method and model selection pair performs well on both datasets. Experiments were performed with our PyTorch framework, BenchmarkPDA, which we open source.Comment: 17 pages, 13 table

Hadronic interaction of eta and eta-prime mesons with nucleons

Due to their short life-time, flavour-neutral mesons cannot be utilized as free secondary beams or targets, and therefore a study of their interaction with nucleons is not possible via direct scattering experiments. This interaction is, however, accessible via its influence on the energy dependence - and on the phase space distributions of the cross sections for reactions in which these mesons are produced. In case of the p p --> p p eta reaction the experimentally determined distributions of the differential cross sections close to the production threshold cannot be described by taking into account the S-wave proton-proton and proton-eta interaction only. Here we show that the angular distributions determined at the COSY-11 facility reveal some evidence for P-wave admixture in the proton-proton subsystem already at an excess energy as low as Q = 15.5 MeV. We also present that one can estimate the relative strength of the eta-nucleon and eta-prime-nucleon interactions by comparison of the eta and eta-prime production yield.Comment: 4 pages, 3 figures, Talk given at 16th International Conference on Particles and Nuclei (PANIC 02), Osaka, Japan, 30 Sep - 4 Oct 200

Experimental study of the eta-meson interaction with two-nucleons

By means of the COSY-11 detection system, using a stochastically cooled proton beam of the cooler synchrotron COSY and a hydrogen cluster target, we have performed a high statistics measurement of the pp --> pp eta reaction at an excess energy of Q = 15.5 MeV. The experiment was based on the four-momentum determination of both outgoing protons. This permits to identify pp --> pp eta events and to derive the complete kinematical information of the eta-p-p-system allowing for subsequent investigations of the eta-p interaction. The observed spectrum of the invariant mass of the proton-proton system deviates strongly from the phase-space distribution revealing the influence of the final-state-interaction among the outgoing particles or nontrivial features of the primary production mechanism.Comment: 6 pages, 4 figures, Talk presented at Meson 2002, 7th International Workshop on Meson Production, Properties and Interaction, Cracow, Poland, 24-28 May 200

COSY-11: an experimental facility for studying meson production in free and quasi-free nucleon-nucleon collisions

The COSY-11 experimental setup is an internal facility installed at the COoler SYnchrotron COSY in Juelich. It allows to investigate meson production in free and quasi-free nucleon-nucleon collisions, eg. pp --> pp meson and pd --> p_sp np meson reactions. Drift chambers and scintillators permit to measure outgoing protons, separated in magnetic field of COSY-11 dipole. Neutrons are registered in the neutron modular detector installed downstream the beam. Recently, the experimental setup has been extended with spectator detector, deuteron drift chamber and polarization monitoring system, and since then meson production can be investigated also as a function of spin and isospin of colliding nucleons.Comment: Presented at LEAP05: International conference on Low Energy Antiproton Physics, Bonn - Juelich, Germany, May 16-22, 200

Isospin dependence of the eta' meson production in nucleon--nucleon collisions

According to the quark model, the masses of eta and eta' mesons should be almost equal. However, the empirical values of these masses differ by more than the factor of two. Similarly, though the almost the same quark-antiquark content, the total cross section for the creation of these mesons close to the kinematical thresholds in the pp --> ppX reaction differs significantly. Using the COSY-11 detection setup we intend to determine whether this difference will also be so significant in the case of the production of these mesons in the proton-neutron scattering. Additionally, the comparison of the pp --> pp eta' and pn --> pn eta' total cross sections will allow to learn about the production of the eta' meson in the channels of isospin I = 0 and I = 1 and to investigate aspects of the gluonium component of the eta' meson.Comment: Presented at LEAP05: International conference on Low Energy Antiproton Physics, Bonn - Juelich, Germany, May 16-22, 200