De novo Sequencing of peptides is a challenging task in proteome research. While there exist reliable DNAsequencing methods, the highthroughput de novo sequencing of proteins by mass spectrometry is still an open problem. Current approaches suffer from a lack in precision to detect mass peaks in the spectrograms. In this paper we present a novel method for de novo peptide sequencing based on a hidden Markov model. Experiments effectively demonstrate that this new method significantly outperforms standard approaches in matching quality.

We introduce a computationally efficient method to estimate the validity of the BP method as a function of graph topology, the connectivity strength, frustration and network size. We present numerical results that demonstrate the correctness of our estimates for the uniform random model and for a real-world network ("C.

We describe an algorithm for support vector machines (SVM) that can be parallelized efficiently and scales to very large problems with hundreds of thousands of training vectors. Instead of analyzing the whole training set in one optimization step, the data are split into subsets and optimized separately with multiple SVMs. The partial results are combined and filtered again in a'Cascade' of SVMs, until the global optimum is reached. The Cascade SVM can be spread over multiple processors with minimal communication overhead and requires far less memory, since the kernel matrices are much smaller than for a regular SVM. Convergence to the global optimum is guaranteed with multiple passes th rough the Cascade, but already a single pass provides good generalization. A single pass is 5x - 10x faster than a regular SVM for problems of 100,000 vectors when implemented on a single processor. Parallel implementations on a cluster of 16 processors were tested with over 1 million vectors (2-class problems), converging in a day or two, while a regular SVM never converged in over a week.

We give a fast rejection scheme that is based on image segments and demonstrate it on the canonical example of face detection. However, instead of focusing on the detection step we focus on the rejection step and show that our method is simple and fast to be learned, thus making it an excellent pre-processing step to accelerate standard machine learning classifiers, such as neural-networks, Bayes classifiers or SVM. We decompose a collection of face images into regions of pixels with similar behavior over the image set. The relationships between the mean and variance of image segments are used to form a cascade of rejectors that can reject over 99.8% of image patches, thus only a small fraction of the image patches must be passed to a full-scale classifier. Moreover, the training time for our method is much less than an hour, on a standard PC.

We propose a novel a framework for deriving approximations for intractable probabilistic models. This framework is based on a free energy (negative log marginal likelihood) and can be seen as a generalization of adaptive TAP [1, 2, 3] and expectation propagation (EP) [4, 5]. The free energy is constructed from two approximating distributions which encode different aspects of the intractable model such a single node constraints and couplings and are by construction consistent on a chosen set of moments. We test the framework on a difficult benchmark problem with binary variables on fully connected graphs and 2D grid graphs. We find good performance using sets of moments which either specify factorized nodes or a spanning tree on the nodes (structured approximation). Surprisingly, the Bethe approximation gives very inferior results even on grids.

This paper investigates the effect of Kernel Principal Component Analysis (KPCA) within the classification framework, essentially the regularization properties of this dimensionality reduction method. KPCA has been previously used as a pre-processing step before applying an SVM but we point out that this method is somewhat redundant from a regularization point of view and we propose a new algorithm called Kernel Projection Machine to avoid this redundancy, based on an analogy with the statistical framework of regression for a Gaussian white noise model. Preliminary experimental results show that this algorithm reaches the same performances as an SVM.

We describe methods for computing an implicit model of a hypersurface that is given only by a finite sampling. The methods work by mapping the sample points into a reproducing kernel Hilbert space and then determining regions in terms of hyperplanes.

We describe a method that can make a scanned, handwritten mediaeval latin manuscript accessible to full text search. A generalized HMM is fitted, using transcribed latin to obtain a transition model and one example each of 22 letters to obtain an emission model. We show results for unigram, bigram and trigram models.

We present a graphical model for beat tracking in recorded music. Using a probabilistic graphical model allows us to incorporate local information and global smoothness constraints in a principled manner. We evaluate our model on a set of varied and difficult examples, and achieve impressive results. By using a fast dual-tree algorithm for graphical model inference, our system runs in less time than the duration of the music being processed.

We propose a gossip-based distributed algorithm for Gaussian mixture learning, Newscast EM. The algorithm operates on network topologies where each node observes a local quantity and can communicate with other nodes in an arbitrary point-to-point fashion. The main difference between Newscast EM and the standard EM algorithm is that the M-step in our case is implemented in a decentralized manner: (random) pairs of nodes repeatedly exchange their local parameter estimates and combine them by (weighted) averaging. We provide theoretical evidence and demonstrate experimentally that, under this protocol, nodes converge exponentially fast to the correct estimates in each M-step of the EM algorithm.