Evaluating Microarray-based Classifiers: An Overview

For the last eight years, microarray-based class prediction has been the subject of numerous publications in medicine, bioinformatics and statistics journals. However, in many articles, the assessment of classification accuracy is carried out using suboptimal procedures and is not paid much attention. In this paper, we carefully review various statistical aspects of classifier evaluation and validation from a practical point of view. The main topics addressed are accuracy measures, error rate estimation procedures, variable selection, choice of classifiers and validation strategy

An AUC-based Permutation Variable Importance Measure for Random Forests

The random forest (RF) method is a commonly used tool for classification with high dimensional data as well as for ranking candidate predictors based on the so-called random forest variable importance measures (VIMs). However the classification performance of RF is known to be suboptimal in case of strongly unbalanced data, i.e. data where response class sizes differ considerably. Suggestions were made to obtain better classification performance based either on sampling procedures or on cost sensitivity analyses. However to our knowledge the performance of the VIMs has not yet been examined in the case of unbalanced response classes. In this paper we explore the performance of the permutation VIM for unbalanced data settings and introduce an alternative permutation VIM based on the area under the curve (AUC) that is expected to be more robust towards class imbalance. We investigated the performance of the standard permutation VIM and of our novel AUC-based permutation VIM for different class imbalance levels using simulated data and real data. The results suggest that the standard permutation VIM loses its ability to discriminate between associated predictors and predictors not associated with the response for increasing class imbalance. It is outperformed by our new AUC-based permutation VIM for unbalanced data settings, while the performance of both VIMs is very similar in the case of balanced classes. The new AUC-based VIM is implemented in the R package party for the unbiased RF variant based on conditional inference trees. The codes implementing our study are available from the companion website: http://www.ibe.med.uni-muenchen.de/organisation/mitarbeiter/070_drittmittel/janitza/index.html

Simulation of the d.c. critical current in superconducting sintered ceramics

The new superconducting high-Tc sintered ceramics can be described in some case as a lattice of interconnected rods, in other cases as a more or less random packing of parallelepiped crystallites ; their size is about a few microns. The d.c. critical current at zero voltage of such a material is not related to the critical current of the bulk material, but to its granular structure. Indeed, the critical current between two adjacent cells is governed by the critical current of the weak link between them ; this link behaves within some limits as a Josephson junction, the critical current of which is known. For our present problem, the system can be modeled as a lattice of Josephson junctions. We present here results for the d.c. critical current at zero voltage of lattices of identical Josephson junctions in two dimensions. The influence of the finiteness of size of the sample is examined. The relationship with normal conductivity simulations and percolation is discussed

The Compact Group of Galaxies HCG 31 is in an early phase of merging

We have obtained high spectral resolution (R = 45900) Fabry-Perot velocity maps of the Hickson Compact Group HCG 31 in order to revisit the important problem of the merger nature of the central object A+C and to derive the internal kinematics of the candidate tidal dwarf galaxies in this group. Our main findings are: (1) double kinematic components are present throughout the main body of A+C, which strongly suggests that this complex is an ongoing merger (2) regions $A2$ and E, to the east and south of complex A+C, present rotation patterns with velocity amplitudes of $\sim 25 km s^{-1}$ and they counterrotate with respect to A+C, (3) region F, which was previously thought to be the best example of a tidal dwarf galaxy in HCG 31, presents no rotation and negligible internal velocity dispersion, as is also the case for region $A1$. HCG 31 presents an undergoing merger in its center (A+C) and it is likely that it has suffered additional perturbations due to interactions with the nearby galaxies B, G and Q.Comment: 5 pages + figures - Accepted to ApJ Lette

Clusters of Extragalactic Ultra Compact HII Regions

We report on the detection of optically thick free-free radio sources in the galaxies M33, NGC 253, and NGC 6946 using data in the literature. We interpret these sources as being young, embedded star birth regions, which are likely to be clusters of ultracompact HII regions. All 35 of the sources presented in this article have positive radio spectral indices alpha>0 suggesting an optically thick thermal bremsstrahlung emission arising in the HII region surrounding hot stars. Energy requirements indicate a range of a several to >500 O7V star equivalents powering each HII region. Assuming a Salpeter IMF, this corresponds to integrated stellar masses of 0.1--60,000 Msun. For roughly half of the sources in our sample, there is no obvious optical counterpart, giving further support for their deeply embedded nature. Their luminosities and radio spectral energy distributions are consistent with HII regions having electron densities from 1500 cm^-3 to 15000 cm^-3 and radii of 1 - 7 pc. We suggest that the less luminous of these sources are extragalactic ultracompact HII region complexes, those of intermediate luminosity are similar to W49 in the Galaxy, while the brightest will be counterparts to 30 Doradus. These objects constitute the lower mass range of extragalactic ``ultradense HII regions'' which we argue are the youngest stages of massive star cluster formation yet observed. This sample is beginning to fill in the continuum of objects between small associations of ultracompact HII regions and the massive extragalactic clusters that may evolve into globular clusters.Comment: 37 pages, uses AASTeX; scheduled to appear in ApJ v. 559 October 2001. Full postscript version available from http://www.astro.wisc.edu/~chip/Papers/Johnson_Kobulnicky_etal_ApJ559.ps.g

Extented ionized gas emission and kinematics of the compact group galaxies in HCG 16: Signatures of mergers

We report on kinematic observations of Ha emission line from four late-type galaxies of Hickson Compact Group 16 (H16a,b,c and d) obtained with a scanning Fabry-Perot interferometer and samplings of 16 km/s and 1". The velocity fields show kinematic peculiarities for three of the four galaxies: H16b, c and d. Misalignments between the kinematic and photometric axes of gas and stellar components (H16b,c,d), double gas systems (H16c) and severe warping of the kinematic major axis (H16b and c) were some of the peculiarities detected. We conclude that major merger events have taken place in at least two of the galaxies group. H16c and d, based on their significant kinematic peculiarities, their double nuclei and high infrared luminosities. Their Ha gas content is strongly spatially concentred - H16d contains a peculiar bar-like structure confined to the inner $\sim$ 1 h^-1 kpc region. These observations are in agreement with predictions of simulations, namely that the gas flows towards the galaxy nucleus during mergers, forms bars and fuel the central activity. Galaxy H16b, and Sb galaxy, also presents some of the kinematic evidences for past accretion events. Its gas content, however, is very spare, limiting our ability to find other kinematic merging indicators, if they are present. We find that isolated mergers, i.e., they show an anormorphous morphology and no signs of tidal tails. Tidal arms and tails formed during the mergers may have been stripped by the group potential (Barnes & Hernquist 1992) ar alternatively they may have never been formed. Our observations suggest that HCG 16 may be a young compact group in formation throught the merging of close-by objects in a dense environment.Comment: Accepted for publication in ApJ. 35 pages, 13 figures. tar file gzipped and uuencode

The kinematics of the warm gas in Hickson compact group of galaxies HCG 90

We present kinematic observations of H$\alpha$ emission for two early-type galaxies and one disk system, members of the Hickson compact group 90 (HCG 90) obtained with a scanning Fabry-Perot interferometer and samplings of 16 $km$ $s^{-1}$ and 1\arcsec. Mapping of the gas kinematics was possible to $\sim$ 2 r$_{eff}$ for the disk galaxy N7174 and to $\sim$ 1.3 r$_{eff}$ and $\sim$ 1.7 r$_{eff}$ for the early-type galaxies N7176 and N7173 respectively. Evidence for ongoing interaction was found in the properties of the warm gas of the three galaxies, some of which do not have stellar counterparts. We suggest the following evolutionary scenario for the system. H90d is the warm gas reservoir of the group in process of fueling H90b with gas. H90c and d have experienced past interaction with gas exchange. The gas acquired by H90c has already settled and relaxed but the effects of the interaction can still be visible in the morphology of the two galaxies and their stellar kinematics. This process will possibly result in a major merger.Comment: 32 pages - 10 figures, Accepted for publication in Astronomical Journa

A Virgo high-resolution Halpha kinematical survey

We have completed a survey of 30 Virgo cluster galaxies in the Halpha emission-line using Fabry-Perot interferometry. The goal of the survey is to obtain a high angular resolution sample of velocity fields of spirals and to study the environmental effects on their kinematics and dynamics.Comment: 2 pages, 1 figure, Proceedings SF2A 2004, eds.: F. Combes, D. Barret, T. Contini, F. Meynadier and L. Pagan

Environmental Effects on the Kinematics of Virgo Cluster Galaxies

We present results from an ongoing survey dedicated to the ionized gas kinematics of Virgo cluster spiral galaxies using Fabry-Perot interferometry. Our goal is to study the environmental effects on galaxy evolution in the Virgo cluster. We report here on the Halpha distribution map and velocity field of NGC 4438, the prototype of an interacting galaxy near the centre of the cluster.Comment: 2 pages, 1 figure, to be published in "IAU Symposium 217, Recycling intergalactic and interstellar matter", ASP Conf Serie