Benchmark of structured machine learning methods for microbial identification from mass-spectrometry data

Microbial identification is a central issue in microbiology, in particular in the fields of infectious diseases diagnosis and industrial quality control. The concept of species is tightly linked to the concept of biological and clinical classification where the proximity between species is generally measured in terms of evolutionary distances and/or clinical phenotypes. Surprisingly, the information provided by this well-known hierarchical structure is rarely used by machine learning-based automatic microbial identification systems. Structured machine learning methods were recently proposed for taking into account the structure embedded in a hierarchy and using it as additional a priori information, and could therefore allow to improve microbial identification systems. We test and compare several state-of-the-art machine learning methods for microbial identification on a new Matrix-Assisted Laser Desorption/Ionization Time-of-Flight mass spectrometry (MALDI-TOF MS) dataset. We include in the benchmark standard and structured methods, that leverage the knowledge of the underlying hierarchical structure in the learning process. Our results show that although some methods perform better than others, structured methods do not consistently perform better than their "flat" counterparts. We postulate that this is partly due to the fact that standard methods already reach a high level of accuracy in this context, and that they mainly confuse species close to each other in the tree, a case where using the known hierarchy is not helpful

Approximate kernel clustering

In the kernel clustering problem we are given a large $n\times n$ positive semi-definite matrix $A=(a_{ij})$ with $\sum_{i,j=1}^na_{ij}=0$ and a small $k\times k$ positive semi-definite matrix $B=(b_{ij})$. The goal is to find a partition $S_1,...,S_k$ of $\{1,... n\}$ which maximizes the quantity $$\sum_{i,j=1}^k (\sum_{(i,j)\in S_i\times S_j}a_{ij})b_{ij}.$$ We study the computational complexity of this generic clustering problem which originates in the theory of machine learning. We design a constant factor polynomial time approximation algorithm for this problem, answering a question posed by Song, Smola, Gretton and Borgwardt. In some cases we manage to compute the sharp approximation threshold for this problem assuming the Unique Games Conjecture (UGC). In particular, when $B$ is the $3\times 3$ identity matrix the UGC hardness threshold of this problem is exactly $\frac{16\pi}{27}$. We present and study a geometric conjecture of independent interest which we show would imply that the UGC threshold when $B$ is the $k\times k$ identity matrix is $\frac{8\pi}{9}(1-\frac{1}{k})$ for every $k\ge 3$

Discriminative Clustering by Regularized Information Maximization

Is there a principled way to learn a probabilistic discriminative classifier from an unlabeled data set? We present a framework that simultaneously clusters the data and trains a discriminative classifier. We call it Regularized Information Maximization (RIM). RIM optimizes an intuitive information-theoretic objective function which balances class separation, class balance and classifier complexity. The approach can flexibly incorporate different likelihood functions, express prior assumptions about the relative size of different classes and incorporate partial labels for semi-supervised learning. In particular, we instantiate the framework to unsupervised, multi-class kernelized logistic regression. Our empirical evaluation indicates that RIM outperforms existing methods on several real data sets, and demonstrates that RIM is an effective model selection method

Two-Stage Fuzzy Multiple Kernel Learning Based on Hilbert-Schmidt Independence Criterion

© 1993-2012 IEEE. Multiple kernel learning (MKL) is a principled approach to kernel combination and selection for a variety of learning tasks, such as classification, clustering, and dimensionality reduction. In this paper, we develop a novel fuzzy multiple kernel learning model based on the Hilbert-Schmidt independence criterion (HSIC) for classification, which we call HSIC-FMKL. In this model, we first propose an HSIC Lasso-based MKL formulation, which not only has a clear statistical interpretation that minimum redundant kernels with maximum dependence on output labels are found and combined, but also enables the global optimal solution to be computed efficiently by solving a Lasso optimization problem. Since the traditional support vector machine (SVM) is sensitive to outliers or noises in the dataset, fuzzy SVM (FSVM) is used to select the prediction hypothesis once the optimal kernel has been obtained. The main advantage of FSVM is that we can associate a fuzzy membership with each data point such that these data points can have different effects on the training of the learning machine. We propose a new fuzzy membership function using a heuristic strategy based on the HSIC. The proposed HSIC-FMKL is a two-stage kernel learning approach and the HSIC is applied in both stages. We perform extensive experiments on real-world datasets from the UCI benchmark repository and the application domain of computational biology which validate the superiority of the proposed model in terms of prediction accuracy