Joachim M. Buhmann

Distortion invariant object recognition in the dynamic link architecture

An object recognition system based on the dynamic link architecture, an extension to classical artificial neural networks (ANNs), is presented. The dynamic link architecture exploits correlations in the fine-scale temporal structure of cellular signals to group neurons dynamically into higher-order entities. These entities represent a rich structure and can code for high-level objects. To demonstrate the capabilities of the dynamic link architecture, a program was implemented that can recognize human faces and other objects from video images. Memorized objects are represented by sparse graphs, whose vertices are labeled by a multiresolution description in terms of a local power spectrum, and whose edges are labeled by geometrical distance vectors. Object recognition can be formulated as elastic graph matching, which is performed here by stochastic optimization of a matching cost function. The implementation on a transputer network achieved recognition of human faces and office objects from gray-level camera images. The performance of the program is evaluated by a statistical analysis of recognition results from a portrait gallery comprising images of 87 persons. >

Empirical evaluation of dissimilarity measures for color and texture

This paper empirically compares nine image dissimilarity measures that are based on distributions of color and texture features summarizing over 1,000 CPU hours of computational experiments. Ground truth is collected via a novel random sampling scheme for color and via an image partitioning method for texture. Quantitative performance evaluations are given for classification, image retrieval, and segmentation tasks, and for a wide variety of dissimilarity measures. It is demonstrated how the selection of a measure, based on large scale evaluation, substantially improves the quality of classification, retrieval, and unsupervised segmentation of color and texture images.

Pairwise data clustering by deterministic annealing

Partitioning a data set and extracting hidden structure from the data arises in different application areas of pattern recognition, speech and image processing. Pairwise data clustering is a combinatorial optimization method for data grouping which extracts hidden structure from proximity data. We describe a deterministic annealing approach to pairwise clustering which shares the robustness properties of maximum entropy inference. The resulting Gibbs probability distributions are estimated by mean-field approximation. A new structure-preserving algorithm to cluster dissimilarity data and to simultaneously embed these data in a Euclidian vector space is discussed which can be used for dimensionality reduction and data visualization. The suggested embedding algorithm which outperforms conventional approaches has been implemented to analyze dissimilarity data from protein analysis and from linguistics. The algorithm for pairwise data clustering is used to segment textured images.

Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry

Mass cytometry enables high-dimensional, single-cell analysis of cell type and state. In mass cytometry, rare earth metals are used as reporters on antibodies. Analysis of metal abundances using the mass cytometer allows determination of marker expression in individual cells. Mass cytometry has previously been applied only to cell suspensions. To gain spatial information, we have coupled immunohistochemical and immunocytochemical methods with high-resolution laser ablation to CyTOF mass cytometry. This approach enables the simultaneous imaging of 32 proteins and protein modifications at subcellular resolution; with the availability of additional isotopes, measurement of over 100 markers will be possible. We applied imaging mass cytometry to human breast cancer samples, allowing delineation of cell subpopulations and cell-cell interactions and highlighting tumor heterogeneity. Imaging mass cytometry complements existing imaging approaches. It will enable basic studies of tissue heterogeneity and function and support the transition of medicine toward individualized molecularly targeted diagnosis and therapies.

Stability-based validation of clustering solutions

Data clustering describes a set of frequently employed techniques in exploratory data analysis to extract natural group structure in data. Such groupings need to be validated to separate the signal in the data from spurious structure. In this context, finding an appropriate number of clusters is a particularly important model selection question. We introduce a measure of cluster stability to assess the validity of a cluster model. This stability measure quantifies the reproducibility of clustering solutions on a second sample, and it can be interpreted as a classification risk with regard to class labels produced by a clustering algorithm. The preferred number of clusters is determined by minimizing this classification risk as a function of the number of clusters. Convincing results are achieved on simulated as well as gene expression data sets. Comparisons to other methods demonstrate the competitive performance of our method and its suitability as a general validation tool for clustering solutions in real-world problems.

Empirical Evaluation of Dissimilarity Measures for Color and Texture

This paper empirically compares nine families of image dissimilarity measures that are based on distributions of color and texture features summarizing over 1000 CPU hours of computational experiments. Ground truth is collected via a novel random sampling scheme for color, and by an image partitioning method for texture. Quantitative performance evaluations are given for classification, image retrieval, and segmentation tasks, and for a wide variety of dissimilarity measure parameters. It is demonstrated how the selection of a measure, based on large scale evaluation, substantially improves the quality of classification, retrieval, and unsupervised segmentation of color and texture images.

The Balanced Accuracy and Its Posterior Distribution

Evaluating the performance of a classification algorithm critically requires a measure of the degree to which unseen examples have been identified with their correct class labels. In practice, generalizability is frequently estimated by averaging the accuracies obtained on individual cross-validation folds. This procedure, however, is problematic in two ways. First, it does not allow for the derivation of meaningful confidence intervals. Second, it leads to an optimistic estimate when a biased classifier is tested on an imbalanced dataset. We show that both problems can be overcome by replacing the conventional point estimate of accuracy by an estimate of the posterior distribution of the balanced accuracy.

Non-parametric similarity measures for unsupervised texture segmentation and image retrieval

In this paper we propose and examine non-parametric statistical tests to define similarity and homogeneity measures for textures. The statistical tests are applied to the coefficients of images filtered by a multi-scale Gabor filter bank. We demonstrate that these similarity measures are useful for both, texture based image retrieval and for unsupervised texture segmentation, and hence offer a unified approach to these closely related tasks. We present results on Brodatz-like micro-textures and a collection of real-word images.

Sensory segmentation with coupled neural oscillators

We present a model of sensory segmentation that is based on the generation and processing of temporal tags in the form of oscillations, as suggested by the Dynamic Link Architecture. The model forms the basis for a natural solution to the sensory segmentation problem. It can deal with multiple segments, can integrate different cues and has the potential for processing hierarchical structures. Temporally tagged segments can easily be utilized in neural systems and form a natural basis for object recognition and learning. The model consists of a “cortical” circuit, an array of units that act as local feature detectors. Units are formulated as neural oscillators. Knowledge relevant to segmentation is encoded by connections. In accord with simple Gestalt laws, our concrete model has intracolumnar connections, between all units with overlapping receptive fields, and intercolumnar connections, between units responding to the same quality in different positions. An inhibitory connection system prevents total correlation and controls the grain of the segmentation. In simulations with synthetic input data we show the performance of the circuit, which produces signal correlation within segments and anticorrelation between segments.

Protein Identification False Discovery Rates for Very Large Proteomics Data Sets Generated by Tandem Mass Spectrometry

Comprehensive characterization of a proteome is a fundamental goal in proteomics. To achieve saturation coverage of a proteome or specific subproteome via tandem mass spectrometric identification of tryptic protein sample digests, proteomics data sets are growing dramatically in size and heterogeneity. The trend toward very large integrated data sets poses so far unsolved challenges to control the uncertainty of protein identifications going beyond well established confidence measures for peptide-spectrum matches. We present MAYU, a novel strategy that reliably estimates false discovery rates for protein identifications in large scale data sets. We validated and applied MAYU using various large proteomics data sets. The data show that the size of the data set has an important and previously underestimated impact on the reliability of protein identifications. We particularly found that protein false discovery rates are significantly elevated compared with those of peptide-spectrum matches. The function provided by MAYU is critical to control the quality of proteome data repositories and thereby to enhance any study relying on these data sources. The MAYU software is available as standalone software and also integrated into the Trans-Proteomic Pipeline.