On The Stability of Interpretable Models

Interpretable classification models are built with the purpose of providing a comprehensible description of the decision logic to an external oversight agent. When considered in isolation, a decision tree, a set of classification rules, or a linear model, are widely recognized as human-interpretable. However, such models are generated as part of a larger analytical process. Bias in data collection and preparation, or in model's construction may severely affect the accountability of the design process. We conduct an experimental study of the stability of interpretable models with respect to feature selection, instance selection, and model selection. Our conclusions should raise awareness and attention of the scientific community on the need of a stability impact assessment of interpretable models

Real-time human ambulation, activity, and physiological monitoring:taxonomy of issues, techniques, applications, challenges and limitations

Automated methods of real-time, unobtrusive, human ambulation, activity, and wellness monitoring and data analysis using various algorithmic techniques have been subjects of intense research. The general aim is to devise effective means of addressing the demands of assisted living, rehabilitation, and clinical observation and assessment through sensor-based monitoring. The research studies have resulted in a large amount of literature. This paper presents a holistic articulation of the research studies and offers comprehensive insights along four main axes: distribution of existing studies; monitoring device framework and sensor types; data collection, processing and analysis; and applications, limitations and challenges. The aim is to present a systematic and most complete study of literature in the area in order to identify research gaps and prioritize future research directions

Characterizing Exoplanets in the Visible and Infrared: A Spectrometer Concept for the EChO Space Mission

Transit-spectroscopy of exoplanets is one of the key observational techniques to characterize the extrasolar planet and its atmosphere. The observational challenges of these measurements require dedicated instrumentation and only the space environment allows an undisturbed access to earth-like atmospheric features such as water or carbon-dioxide. Therefore, several exoplanet-specific space missions are currently being studied. One of them is EChO, the Exoplanet Characterization Observatory, which is part of ESA's Cosmic Vision 2015-2025 program, and which is one of four candidates for the M3 launch slot in 2024. In this paper we present the results of our assessment study of the EChO spectrometer, the only science instrument onboard this spacecraft. The instrument is a multi-channel all-reflective dispersive spectrometer, covering the wavelength range from 400 nm to 16 microns simultaneously with a moderately low spectral resolution. We illustrate how the key technical challenge of the EChO mission - the high photometric stability - influences the choice of spectrometer concept and drives fundamentally the instrument design. First performance evaluations underline the fitness of the elaborated design solution for the needs of the EChO mission.Comment: 20 pages, 8 figures, accepted for publication in the Journal of Astronomical Instrumentatio

Inferential stability in systems biology

The modern biological sciences are fraught with statistical difficulties. Biomolecular stochasticity, experimental noise, and the “large p, small n” problem all contribute to the challenge of data analysis. Nevertheless, we routinely seek to draw robust, meaningful conclusions from observations. In this thesis, we explore methods for assessing the effects of data variability upon downstream inference, in an attempt to quantify and promote the stability of the inferences we make. We start with a review of existing methods for addressing this problem, focusing upon the bootstrap and similar methods. The key requirement for all such approaches is a statistical model that approximates the data generating process. We move on to consider biomarker discovery problems. We present a novel algorithm for proposing putative biomarkers on the strength of both their predictive ability and the stability with which they are selected. In a simulation study, we find our approach to perform favourably in comparison to strategies that select on the basis of predictive performance alone. We then consider the real problem of identifying protein peak biomarkers for HAM/TSP, an inflammatory condition of the central nervous system caused by HTLV-1 infection. We apply our algorithm to a set of SELDI mass spectral data, and identify a number of putative biomarkers. Additional experimental work, together with known results from the literature, provides corroborating evidence for the validity of these putative biomarkers. Having focused on static observations, we then make the natural progression to time course data sets. We propose a (Bayesian) bootstrap approach for such data, and then apply our method in the context of gene network inference and the estimation of parameters in ordinary differential equation models. We find that the inferred gene networks are relatively unstable, and demonstrate the importance of finding distributions of ODE parameter estimates, rather than single point estimates

Iterative Random Forests to detect predictive and stable high-order interactions

Genomics has revolutionized biology, enabling the interrogation of whole transcriptomes, genome-wide binding sites for proteins, and many other molecular processes. However, individual genomic assays measure elements that interact in vivo as components of larger molecular machines. Understanding how these high-order interactions drive gene expression presents a substantial statistical challenge. Building on Random Forests (RF), Random Intersection Trees (RITs), and through extensive, biologically inspired simulations, we developed the iterative Random Forest algorithm (iRF). iRF trains a feature-weighted ensemble of decision trees to detect stable, high-order interactions with same order of computational cost as RF. We demonstrate the utility of iRF for high-order interaction discovery in two prediction problems: enhancer activity in the early Drosophila embryo and alternative splicing of primary transcripts in human derived cell lines. In Drosophila, among the 20 pairwise transcription factor interactions iRF identifies as stable (returned in more than half of bootstrap replicates), 80% have been previously reported as physical interactions. Moreover, novel third-order interactions, e.g. between Zelda (Zld), Giant (Gt), and Twist (Twi), suggest high-order relationships that are candidates for follow-up experiments. In human-derived cells, iRF re-discovered a central role of H3K36me3 in chromatin-mediated splicing regulation, and identified novel 5th and 6th order interactions, indicative of multi-valent nucleosomes with specific roles in splicing regulation. By decoupling the order of interactions from the computational cost of identification, iRF opens new avenues of inquiry into the molecular mechanisms underlying genome biology

Network Model Selection Using Task-Focused Minimum Description Length

Networks are fundamental models for data used in practically every application domain. In most instances, several implicit or explicit choices about the network definition impact the translation of underlying data to a network representation, and the subsequent question(s) about the underlying system being represented. Users of downstream network data may not even be aware of these choices or their impacts. We propose a task-focused network model selection methodology which addresses several key challenges. Our approach constructs network models from underlying data and uses minimum description length (MDL) criteria for selection. Our methodology measures efficiency, a general and comparable measure of the network's performance of a local (i.e. node-level) predictive task of interest. Selection on efficiency favors parsimonious (e.g. sparse) models to avoid overfitting and can be applied across arbitrary tasks and representations. We show stability, sensitivity, and significance testing in our methodology

Data-driven Localization and Estimation of Disturbance in the Interconnected Power System

Identifying the location of a disturbance and its magnitude is an important component for stable operation of power systems. We study the problem of localizing and estimating a disturbance in the interconnected power system. We take a model-free approach to this problem by using frequency data from generators. Specifically, we develop a logistic regression based method for localization and a linear regression based method for estimation of the magnitude of disturbance. Our model-free approach does not require the knowledge of system parameters such as inertia constants and topology, and is shown to achieve highly accurate localization and estimation performance even in the presence of measurement noise and missing data