Support vector machines and kernels for computational biology (2008)
Ben-Hur, A., Ong, C.S., Sonnenburg, S., Schölkopf, B., Rätsch, G.
Support Vector Machines and Kernels for Computational Biology (2008)
Ben-Hur, A., Ong, C.S., Sonnenburg, S., Schölkopf, B., Rätsch, G.
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Support Vector Machines and Kernels for Computational Biology (2008)
Ben-Hur, A., Ong, C.S., Sonnenburg, S., Schölkopf, B., Rätsch, G.
An Automated Combination of Kernels for Predicting Protein Subcellular Localization (2008)
Ong, C.S., Zien, A., Crandall, K. A., Lagergren, J.
Protein subcellular localization is a crucial ingredient to many important inferences about cellular processes, including prediction of protein function and protein interactions. While many...
PALMA: mRNA to genome alignments using large margin algorithms (2007)
Schulze, U., Hepp, B., Ong, C.S., Rätsch, G.
Motivation: Despite many years of research on how to properly align sequences in the presence of sequencing errors, alternative splicing and micro-exons, the correct alignment of mRNA sequences to...
The need for open source software in machine learning (2007)
Sonnenburg, S., Braun, M.L., Ong, C.S., Bengio, S., Bottou, L., Holmes, G., ...
Open source tools have recently reached a level of maturity which makes them suitable for building large-scale real-world systems. At the same time, the field of machine learning has developed a...
The Need for Open Source Software in Machine Learning (2007)
Sonnenburg, S., Braun, M.L., Ong, C.S., Bengio, S., Bottou, L., Holmes, G., ...
Open source tools have recently reached a level of maturity which makes them suitable for building large-scale real-world systems. At the same time, the field of machine learning has developed a...
PALMA: mRNA to Genome Alignments using Large Margin Algorithms (2007)
Schulze, U., Hepp, B., Ong, C.S., Rätsch, G.
Motivation: Despite many years of research on how to properly align sequences in the presence of sequencing errors, alternative splicing and micro-exons, the correct alignment of mRNA sequences to...
Training and Approximation of a Primal Multiclass Support Vector Machine (2007)
We revisit the multiclass support vector machine (SVM) and generalize the formulation to convex loss functions and joint feature maps. Motivated by recent work [Chapelle, 2006] we use logistic loss...
Multiclass Multiple Kernel Learning (2007)
In many applications it is desirable to learn from several kernels. Multiple kernel learning (MKL) allows the practitioner to optimize over linear combinations of kernels. By enforcing sparse...
Upstream of TSS: promoter containing transcription factor (2007)
Petra Philips, Friedrich Miescher, Eberhard Karls, G. Rätsch, C. S. Ong, ...
POL II binds to a rather vague region of ≈ [−20, +20] bp
PALMA: Perfect Alignments using Large Margin Algorithms (2006)
Raetsch, G., Hepp, B., Schulze, U., Ong, C.S.
Despite many years of research on how to properly align sequences in the presence of sequencing errors, alternative splicing and micro-exons, the correct alignment of mRNA sequences to genomic DNA is...
Splines with non positive kernels (2006)
Non parametric regressions methods can be presented in two main clusters. The one of smoothing splines methods requiring positive kernels and the other one known as Nonparametric Kernel Regression...
Learning the Kernel with Hyperkernels (2005)
Ong, C.S., Smola, A., Williamson, R.
This paper addresses the problem of choosing a kernel suitable for estimation with a Support Vector Machine, hence further automating machine learning. This goal is achieved by defining a Reproducing...
Learning with Non-Positive Kernels (2004)
Ong, C.S., Mary, X., Canu, S., Smola, A.
In this paper we show that many kernel methods can be adapted to deal with indefinite kernels, that is, kernels which are not positive semidefinite. They do not satisfy Mercer’s condition and they...
Karanikas, V, Hwang, L A, Pearson, J, Ong, C S, Apostolopoulos, V, Vaughan, H, ...
Mucin 1 (MUC1) is a large complex glycoprotein that is highly expressed in breast cancer, and as such could be a target for immunotherapy. In mice, human MUC1 is highly immunogenic, particularly when...
Karanikas, V, Hwang, L A, Pearson, J, Ong, C S, Apostolopoulos, V, Vaughan, H, ...
Mucin 1 (MUC1) is a large complex glycoprotein that is highly expressed in breast cancer, and as such could be a target for immunotherapy. In mice, human MUC1 is highly immunogenic, particularly when...
Peng, M. M., Xiao, L., Freeman, A. R., Arrowood, M. J., Escalante, A. A., Weltman, A. C., ...
We report the results of molecular analysis of 39 isolates of Cryptosporidium parvum from human and bovine sources in nine human outbreaks and from bovine sources from a wide geographic distribution....