14,959 research outputs found
CleanML: A Study for Evaluating the Impact of Data Cleaning on ML Classification Tasks
Data quality affects machine learning (ML) model performances, and data
scientists spend considerable amount of time on data cleaning before model
training. However, to date, there does not exist a rigorous study on how
exactly cleaning affects ML -- ML community usually focuses on developing ML
algorithms that are robust to some particular noise types of certain
distributions, while database (DB) community has been mostly studying the
problem of data cleaning alone without considering how data is consumed by
downstream ML analytics. We propose a CleanML study that systematically
investigates the impact of data cleaning on ML classification tasks. The
open-source and extensible CleanML study currently includes 14 real-world
datasets with real errors, five common error types, seven different ML models,
and multiple cleaning algorithms for each error type (including both commonly
used algorithms in practice as well as state-of-the-art solutions in academic
literature). We control the randomness in ML experiments using statistical
hypothesis testing, and we also control false discovery rate in our experiments
using the Benjamini-Yekutieli (BY) procedure. We analyze the results in a
systematic way to derive many interesting and nontrivial observations. We also
put forward multiple research directions for researchers.Comment: published in ICDE 202
Foundational principles for large scale inference: Illustrations through correlation mining
When can reliable inference be drawn in the "Big Data" context? This paper
presents a framework for answering this fundamental question in the context of
correlation mining, with implications for general large scale inference. In
large scale data applications like genomics, connectomics, and eco-informatics
the dataset is often variable-rich but sample-starved: a regime where the
number of acquired samples (statistical replicates) is far fewer than the
number of observed variables (genes, neurons, voxels, or chemical
constituents). Much of recent work has focused on understanding the
computational complexity of proposed methods for "Big Data." Sample complexity
however has received relatively less attention, especially in the setting when
the sample size is fixed, and the dimension grows without bound. To
address this gap, we develop a unified statistical framework that explicitly
quantifies the sample complexity of various inferential tasks. Sampling regimes
can be divided into several categories: 1) the classical asymptotic regime
where the variable dimension is fixed and the sample size goes to infinity; 2)
the mixed asymptotic regime where both variable dimension and sample size go to
infinity at comparable rates; 3) the purely high dimensional asymptotic regime
where the variable dimension goes to infinity and the sample size is fixed.
Each regime has its niche but only the latter regime applies to exa-scale data
dimension. We illustrate this high dimensional framework for the problem of
correlation mining, where it is the matrix of pairwise and partial correlations
among the variables that are of interest. We demonstrate various regimes of
correlation mining based on the unifying perspective of high dimensional
learning rates and sample complexity for different structured covariance models
and different inference tasks
Engineering simulations for cancer systems biology
Computer simulation can be used to inform in vivo and in vitro experimentation, enabling rapid, low-cost hypothesis generation and directing experimental design in order to test those hypotheses. In this way, in silico models become a scientific instrument for investigation, and so should be developed to high standards, be carefully calibrated and their findings presented in such that they may be reproduced. Here, we outline a framework that supports developing simulations as scientific instruments, and we select cancer systems biology as an exemplar domain, with a particular focus on cellular signalling models. We consider the challenges of lack of data, incomplete knowledge and modelling in the context of a rapidly changing knowledge base. Our framework comprises a process to clearly separate scientific and engineering concerns in model and simulation development, and an argumentation approach to documenting models for rigorous way of recording assumptions and knowledge gaps. We propose interactive, dynamic visualisation tools to enable the biological community to interact with cellular signalling models directly for experimental design. There is a mismatch in scale between these cellular models and tissue structures that are affected by tumours, and bridging this gap requires substantial computational resource. We present concurrent programming as a technology to link scales without losing important details through model simplification. We discuss the value of combining this technology, interactive visualisation, argumentation and model separation to support development of multi-scale models that represent biologically plausible cells arranged in biologically plausible structures that model cell behaviour, interactions and response to therapeutic interventions
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