Changepoint detection is a central problem in time series and genomic data. For some applications, it is natural to impose constraints on the directions of changes. One example is ChIP-seq data, for which adding an up-down constraint improves peak detection accuracy, but makes the optimization problem more complicated. We show how a recently proposed functional pruning technique can be adapted to solve such constrained changepoint detection problems. This leads to a new algorithm which can solve problems with arbitrary affine constraints on adjacent segment means, and which has empirical time complexity that is log-linear in the amount of data. This algorithm achieves state-of-the-art accuracy in a benchmark of several genomic data sets, and is orders of magnitude faster than existing algorithms that have similar accuracy. Our implementation is available as the PeakSegPDPA function in the coseg R package, https://github.com/tdhock/coseg

This text is a survey on cross-validation. We define all classical cross-validation procedures, and we study their properties for two different goals: estimating the risk of a given estimator, and selecting the best estimator among a given family. For the risk estimation problem, we compute the bias (which can also be corrected) and the variance of cross-validation methods. For estimator selection, we first provide a first-order analysis (based on expectations). Then, we explain how to take into account second-order terms (from variance computations, and by taking into account the usefulness of overpenalization). This allows, in the end, to provide some guidelines for choosing the best cross-validation method for a given learning problem.

We envision that algorithm such as ours could improve the efficiency and consistency of pathologists,

This paper is a tutorial on Formal Concept Analysis (FCA) and its applications. FCA is an applied branch of Lattice Theory, a mathematical discipline which enables formalisation of concepts as basic units of human thinking and analysing data in the object-attribute form. Originated in early 80s, during the last three decades, it became a popular human-centred tool for knowledge representation and data analysis with numerous applications. Since the tutorial was specially prepared for RuSSIR 2014, the covered FCA topics include Information Retrieval with a focus on visualisation aspects, Machine Learning, Data Mining and Knowledge Discovery, Text Mining and several others.

Automated data-driven decision making systems are increasingly being used to assist, or even replace humans in many settings. These systems function by learning from historical decisions, often taken by humans. In order to maximize the utility of these systems (or, classifiers), their training involves minimizing the errors (or, misclassifications) over the given historical data. However, it is quite possible that the optimally trained classifier makes decisions for people belonging to different social groups with different misclassification rates (e.g., misclassification rates for females are higher than for males), thereby placing these groups at an unfair disadvantage. To account for and avoid such unfairness, in this paper, we introduce a new notion of unfairness, disparate mistreatment, which is defined in terms of misclassification rates. We then propose intuitive measures of disparate mistreatment for decision boundary-based classifiers, which can be easily incorporated into their formulation as convex-concave constraints. Experiments on synthetic as well as real world datasets show that our methodology is effective at avoiding disparate mistreatment, often at a small cost in terms of accuracy.

For an autonomous agent, executing a poor policy may be costly or even dangerous. For such agents, it is desirable to determine confidence interval lower bounds on the performance of any given policy without executing said policy. Current methods for exact high confidence off-policy evaluation that use importance sampling require a substantial amount of data to achieve a tight lower bound. Existing model-based methods only address the problem in discrete state spaces. Since exact bounds are intractable for many domains we trade off strict guarantees of safety for more data-efficient approximate bounds. In this context, we propose two bootstrapping off-policy evaluation methods which use learned MDP transition models in order to estimate lower confidence bounds on policy performance with limited data in both continuous and discrete state spaces. Since direct use of a model may introduce bias, we derive a theoretical upper bound on model bias for when the model transition function is estimated with i.i.d. trajectories. This bound broadens our understanding of the conditions under which model-based methods have high bias. Finally, we empirically evaluate our proposed methods and analyze the settings in which different bootstrapping off-policy confidence interval methods succeed and fail.

Several diseases related to cell proliferation are characterized by the accumulation of somatic DNA changes, with respect to wildtype conditions. Cancer and HIV are two common examples of such diseases, where the mutational load in the cancerous/viral population increases over time. In these cases, selective pressures are often observed along with competition, cooperation and parasitism among distinct cellular clones. Recently, we presented a mathematical framework to model these phenomena, based on a combination of Bayesian inference and Suppes' theory of probabilistic causation, depicted in graphical structures dubbed Suppes-Bayes Causal Networks (SBCNs). SBCNs are generative probabilistic graphical models that recapitulate the potential ordering of accumulation of such DNA changes during the progression of the disease. Such models can be inferred from data by exploiting likelihood-based model-selection strategies with regularization. In this paper we discuss the theoretical foundations of our approach and we investigate in depth the influence on the model-selection task of: (i) the poset based on Suppes' theory and (ii) different regularization strategies. Furthermore, we provide an example of application of our framework to HIV genetic data highlighting the valuable insights provided by the inferred.

In Machine Learning, Cross-validation is a resampling method used for model evaluation to avoid testing a model on the same dataset on which it was trained. This is a common mistake, especially that a separate testing dataset is not always available. However, this usually leads to inaccurate performance measures (as the model will have an almost perfect score since it is being tested on the same data it was trained on). To avoid this kind of mistakes, cross validation is usually preferred. The concept of cross-validation is actually simple: Instead of using the whole dataset to train and then test on same data, we could randomly divide our data into training and testing datasets.

Many complex ecosystems, such as those formed by multiple microbial taxa, involve intricate interactions amongst various sub-communities. The most basic relationships are frequently modeled as co-occurrence networks in which the nodes represent the various players in the community and the weighted edges encode levels of interaction. In this setting, the composition of a community may be viewed as a probability distribution on the nodes of the network. This paper develops methods for modeling the organization of such data, as well as their Euclidean counterparts, across spatial scales. Using the notion of diffusion distance, we introduce diffusion Frechet functions and diffusion Frechet vectors associated with probability distributions on Euclidean space and the vertex set of a weighted network, respectively. We prove that these functional statistics are stable with respect to the Wasserstein distance between probability measures, thus yielding robust descriptors of their shapes. We apply the methodology to investigate bacterial communities in the human gut, seeking to characterize divergence from intestinal homeostasis in patients with Clostridium difficile infection (CDI) and the effects of fecal microbiota transplantation, a treatment used in CDI patients that has proven to be significantly more effective than traditional treatment with antibiotics. The proposed method proves useful in deriving a biomarker that might help elucidate the mechanisms that drive these processes.

Each year, roughly 30% of first-year students at US baccalaureate institutions do not return for their second year and over $9 billion is spent educating these students. Yet, little quantitative research has analyzed the causes and possible remedies for student attrition. Here, we describe initial efforts to model student dropout using the largest known dataset on higher education attrition, which tracks over 32,500 students' demographics and transcript records at one of the nation's largest public universities. Our results highlight several early indicators of student attrition and show that dropout can be accurately predicted even when predictions are based on a single term of academic transcript data. These results highlight the potential for machine learning to have an impact on student retention and success while pointing to several promising directions for future work.