Deciphering Network Community Structure by Surprise

The analysis of complex networks permeates all sciences, from biology to sociology. A fundamental, unsolved problem is how to characterize the community structure of a network. Here, using both standard and novel benchmarks, we show that maximization of a simple global parameter, which we call Surprise (S), leads to a very efficient characterization of the community structure of complex synthetic networks. Particularly, S qualitatively outperforms the most commonly used criterion to define communities, Newman and Girvan's modularity (Q). Applying S maximization to real networks often provides natural, well-supported partitions, but also sometimes counterintuitive solutions that expose the limitations of our previous knowledge. These results indicate that it is possible to define an effective global criterion for community structure and open new routes for the understanding of complex networks.Comment: 7 pages, 5 figure

The bootstrap -A review

The bootstrap, extensively studied during the last decade, has become a powerful tool in different areas of Statistical Inference. In this work, we present the main ideas of bootstrap methodology in several contexts, citing the most relevant contributions and illustrating with examples and simulation studies some interesting aspects

公平性下における学習の理論的解析

筑波大学 (University of Tsukuba)201

Estimation of genetic diversity in viral populations from next generation sequencing data with extremely deep coverage

In this paper we propose a method and discuss its computational implementation as an integrated tool for the analysis of viral genetic diversity on data generated by high-throughput sequencing. Most methods for viral diversity estimation proposed so far are intended to take benefit of the longer reads produced by some NGS platforms in order to estimate a population of haplotypes. Our goal here is to take advantage of distinct virtues of a certain kind of NGS platform - the platform SOLiD (Life Technologies) is an example - that has not received much attention due to the short length of its reads, which renders haplotype estimation very difficult. However, this kind of platform has a very low error rate and extremely deep coverage per site and our method is designed to take advantage of these characteristics. We propose to measure the populational genetic diversity through a family of multinomial probability distributions indexed by the sites of the virus genome, each one representing the populational distribution of the diversity per site. The implementation of the method focuses on two main optimization strategies: a read mapping/alignment procedure that aims at the recovery of the maximum possible number of short-reads; the estimation of the multinomial parameters through a Bayesian approach, which, unlike simple frequency counting, allows one to take into account the prior information of the control population within the inference of a posterior experimental condition and provides a natural way to separate signal from noise, since it automatically furnishes Bayesian confidence intervals. The methods described in this paper have been implemented as an integrated tool called Tanden (Tool for Analysis of Diversity in Viral Populations).Comment: 30 pages, 5 figures, 2 tables, Tanden is written in C# (Microsoft), runs on the Windows operating system, and can be downloaded from: http://tanden.url.p

Statistical atlas based registration and planning for ablating bone tumors in minimally invasive interventions

Bone tumor ablation has been a viable treatment in a minimally invasive way compared with surgical resections. In this paper, two key challenges in the computer-Assisted bone tumor ablation have been addressed: 1) establishing the spatial transformation of patient's tumor with respect to a global map of the patient using a minimum number of intra-operative images and 2) optimal treatment planning for large tumors. Statistical atlas is employed to construct the global reference map. The atlas is deformably registered to a pair of intra-operative fluoroscopy images, constructing a patient-specific model, in order to reduce the radiation exposure to the sensitive patients such as pregnant and infants. The optimal treatment planning system incorporates clinical constraints on ablations and trajectories using a multiple objective optimization, which obtains optimal trajectory planning and ablation coverage using integer programming. The proposed system is presented and validated by experiments. © 2012 IEEE.published_or_final_versio

Fairness in Recommendation: Foundations, Methods and Applications

As one of the most pervasive applications of machine learning, recommender systems are playing an important role on assisting human decision making. The satisfaction of users and the interests of platforms are closely related to the quality of the generated recommendation results. However, as a highly data-driven system, recommender system could be affected by data or algorithmic bias and thus generate unfair results, which could weaken the reliance of the systems. As a result, it is crucial to address the potential unfairness problems in recommendation settings. Recently, there has been growing attention on fairness considerations in recommender systems with more and more literature on approaches to promote fairness in recommendation. However, the studies are rather fragmented and lack a systematic organization, thus making it difficult to penetrate for new researchers to the domain. This motivates us to provide a systematic survey of existing works on fairness in recommendation. This survey focuses on the foundations for fairness in recommendation literature. It first presents a brief introduction about fairness in basic machine learning tasks such as classification and ranking in order to provide a general overview of fairness research, as well as introduce the more complex situations and challenges that need to be considered when studying fairness in recommender systems. After that, the survey will introduce fairness in recommendation with a focus on the taxonomies of current fairness definitions, the typical techniques for improving fairness, as well as the datasets for fairness studies in recommendation. The survey also talks about the challenges and opportunities in fairness research with the hope of promoting the fair recommendation research area and beyond.Comment: Accepted by ACM Transactions on Intelligent Systems and Technology (TIST

Combination of direct methods and homotopy in numerical optimal control: application to the optimization of chemotherapy in cancer

We consider a state-constrained optimal control problem of a system of two non-local partial-differential equations, which is an extension of the one introduced in a previous work in mathematical oncology. The aim is to minimize the tumor size through chemotherapy while avoiding the emergence of resistance to the drugs. The numerical approach to solve the problem was the combination of direct methods and continuation on discretization parameters, which happen to be insufficient for the more complicated model, where diffusion is added to account for mutations. In the present paper, we propose an approach relying on changing the problem so that it can theoretically be solved thanks to a Pontryagin Maximum Principle in infinite dimension. This provides an excellent starting point for a much more reliable and efficient algorithm combining direct methods and continuations. The global idea is new and can be thought of as an alternative to other numerical optimal control techniques