Most network-based protein (or gene) function prediction methods are based on the assumption that the labels of two adjacent proteins in the network are likely to be the same. However, assuming the pairwise relationship between proteins or genes is not complete, the information a group of genes that show very similar patterns of expression and tend to have similar functions (i.e. the functional modules) is missed. The natural way overcoming the information loss of the above assumption is to represent the gene expression data as the hypergraph. Thus, in this paper, the three un-normalized, random walk, and symmetric normalized hypergraph Laplacian based semi-supervised learning methods applied to hypergraph constructed from the gene expression data in order to predict the functions of yeast proteins are introduced. Experiment results show that the average accuracy performance measures of these three hypergraph Laplacian based semi-supervised learning methods are the same. However, their average accuracy performance measures of these three methods are much greater than the average accuracy performance measures of un-normalized graph Laplacian based semi-supervised learning method (i.e. the baseline method of this paper) applied to gene co-expression network created from the gene expression data.

Extracting important relations between biological components and semantic events involving genes or proteins from literature has become a focus for the biomedical text mining community. In this paper, we review a subgraph matching-based approach proposed in our previous work for mining relations and events in the biomedical literature. Our subgraph matching algorithm is formally presented, along with a detailed analysis of its complexity. We present three different relation/event extraction tasks in which our approach has been successfully applied. Our approach is of considerable value in extracting highly precise, binary relations when appropriate training data is available.

We address the problem of general supervised learning when data can only be accessed through an (indefinite) similarity function between data points. Existing work on learning with indefinite kernels has concentrated solely on binary/multi-class classification problems. We propose a model that is generic enough to handle any supervised learning task and also subsumes the model previously proposed for classification. We give a "goodness" criterion for similarity functions w.r.t. a given supervised learning task and then adapt a well-known landmarking technique to provide efficient algorithms for supervised learning using "good" similarity functions. We demonstrate the effectiveness of our model on three important super-vised learning problems: a) real-valued regression, b) ordinal regression and c) ranking where we show that our method guarantees bounded generalization error. Furthermore, for the case of real-valued regression, we give a natural goodness definition that, when used in conjunction with a recent result in sparse vector recovery, guarantees a sparse predictor with bounded generalization error. Finally, we report results of our learning algorithms on regression and ordinal regression tasks using non-PSD similarity functions and demonstrate the effectiveness of our algorithms, especially that of the sparse landmark selection algorithm that achieves significantly higher accuracies than the baseline methods while offering reduced computational costs.

We introduce a method to learn a mixture of submodular "shells" in a large-margin setting. A submodular shell is an abstract submodular function that can be instantiated with a ground set and a set of parameters to produce a submodular function. A mixture of such shells can then also be so instantiated to produce a more complex submodular function. What our algorithm learns are the mixture weights over such shells. We provide a risk bound guarantee when learning in a large-margin structured-prediction setting using a projected subgradient method when only approximate submodular optimization is possible (such as with submodular function maximization). We apply this method to the problem of multi-document summarization and produce the best results reported so far on the widely used NIST DUC-05 through DUC-07 document summarization corpora.

Agents learning to act autonomously in real-world domains must acquire a model of the dynamics of the domain in which they operate. Learning domain dynamics can be challenging, especially where an agent only has partial access to the world state, and/or noisy external sensors. Even in standard STRIPS domains, existing approaches cannot learn from noisy, incomplete observations typical of real-world domains. We propose a method which learns STRIPS action models in such domains, by decomposing the problem into first learning a transition function between states in the form of a set of classifiers, and then deriving explicit STRIPS rules from the classifiers' parameters. We evaluate our approach on simulated standard planning domains from the International Planning Competition, and show that it learns useful domain descriptions from noisy, incomplete observations.

This paper introduces a novel, well-founded, betweenness measure, called the Bag-of-Paths (BoP) betweenness, as well as its extension, the BoP group betweenness, to tackle semisupervised classification problems on weighted directed graphs. The objective of semi-supervised classification is to assign a label to unlabeled nodes using the whole topology of the graph and the labeled nodes at our disposal. The BoP betweenness relies on a bag-of-paths framework assigning a Boltzmann distribution on the set of all possible paths through the network such that long (high-cost) paths have a low probability of being picked from the bag, while short (low-cost) paths have a high probability of being picked. Within that context, the BoP betweenness of node j is defined as the sum of the a posteriori probabilities that node j lies in-between two arbitrary nodes i, k, when picking a path starting in i and ending in k. Intuitively, a node typically receives a high betweenness if it has a large probability of appearing on paths connecting two arbitrary nodes of the network. This quantity can be computed in closed form by inverting a n x n matrix where n is the number of nodes. For the group betweenness, the paths are constrained to start and end in nodes within the same class, therefore defining a group betweenness for each class. Unlabeled nodes are then classified according to the class showing the highest group betweenness. Experiments on various real-world data sets show that BoP group betweenness outperforms all the tested state of-the-art methods. The benefit of the BoP betweenness is particularly noticeable when only a few labeled nodes are available.

We present a system that enables rapid model experimentation for tera-scale machine learning with trillions of non-zero features, billions of training examples, and millions of parameters. Our contribution to the literature is a new method (SA L-BFGS) for changing batch L-BFGS to perform in near real-time by using statistical tools to balance the contributions of previous weights, old training examples, and new training examples to achieve fast convergence with few iterations. The result is, to our knowledge, the most scalable and flexible linear learning system reported in the literature, beating standard practice with the current best system (Vowpal Wabbit and AllReduce). Using the KDD Cup 2012 data set from Tencent, Inc. we provide experimental results to verify the performance of this method.

In the supervised learning setting termed Multiple-Instance Learning (MIL), the examples are bags of instances, and the bag label is a function of the labels of its instances. Typically, this function is the Boolean OR. The learner observes a sample of bags and the bag labels, but not the instance labels that determine the bag labels. The learner is then required to emit a classification rule for bags based on the sample. MIL has numerous applications, and many heuristic algorithms have been used successfully on this problem, each adapted to specific settings or applications. In this work we provide a unified theoretical analysis for MIL, which holds for any underlying hypothesis class, regardless of a specific application or problem domain. We show that the sample complexity of MIL is only poly-logarithmically dependent on the size of the bag, for any underlying hypothesis class. In addition, we introduce a new PAC-learning algorithm for MIL, which uses a regular supervised learning algorithm as an oracle. We prove that efficient PAC-learning for MIL can be generated from any efficient non-MIL supervised learning algorithm that handles one-sided error. The computational complexity of the resulting algorithm is only polynomially dependent on the bag size.

Structured prediction tasks pose a fundamental trade-off between the need for model complexity to increase predictive power and the limited computational resources for inference in the exponentially-sized output spaces such models require. We formulate and develop the Structured Prediction Cascade architecture: a sequence of increasingly complex models that progressively filter the space of possible outputs. The key principle of our approach is that each model in the cascade is optimized to accurately filter and refine the structured output state space of the next model, speeding up both learning and inference in the next layer of the cascade. We learn cascades by optimizing a novel convex loss function that controls the trade-off between the filtering efficiency and the accuracy of the cascade, and provide generalization bounds for both accuracy and efficiency. We also extend our approach to intractable models using tree-decomposition ensembles, and provide algorithms and theory for this setting. We evaluate our approach on several large-scale problems, achieving state-of-the-art performance in handwriting recognition and human pose recognition. We find that structured prediction cascades allow tremendous speedups and the use of previously intractable features and models in both settings.

The method of conformal prediction produces set predictions that are automatically valid in the sense that their unconditional coverage probability is equal to or exceeds a preset confidence level ([14], Chapter 2). A more computationally efficient method of this kind is that of inductive conformal prediction ([12], [14], Section 4.1, [1]). However, inductive conformal predictors are typically less predictively efficient, in the sense of producing larger prediction sets as compared with conformal predictors. Motivated by the method of cross-validation [11, 13], this note explores a hybrid method, which we call cross-conformal prediction. We are mainly interested in the problems of classification and regression, in which we are given a training set consisting of examples, each example consisting of an object and a label, and asked to predict the label of a new test object; in the problem of classification labels are elements of a given finite set, and in the problem of regression labels are real numbers. If we are asked to predict labels for more than one test objects, the same prediction procedure can be applied to each test object separately. In this introductory section and in our empirical studies we consider the problem of binary classification, in which labels can take only two values, which we will encode as 0 and 1. We always assume that the examples (both the training examples and the test examples, consisting of given objects and unknown labels) are generated independently from the same probability measure; this assumption will be called the assumption of randomness.