14,745 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
SNPredict: A Machine Learning Approach for Detecting Low Frequency Variants in Cancer
Cancer is a genetic disease caused by the accumulation of DNA variants such as single nucleotide changes or insertions/deletions in DNA. DNA variants can cause silencing of tumor suppressor genes or increase the activity of oncogenes. In order to come up with successful therapies for cancer patients, these DNA variants need to be identified accurately. DNA variants can be identified by comparing DNA sequence of tumor tissue to a non-tumor tissue by using Next Generation Sequencing (NGS) technology. But the problem of detecting variants in cancer is hard because many of these variant occurs only in a small subpopulation of the tumor tissue. It becomes a challenge to distinguish these low frequency variants from sequencing errors, which are common in today\u27s NGS methods. Several algorithms have been made and implemented as a tool to identify such variants in cancer. However, it has been previously shown that there is low concordance in the results produced by these tools. Moreover, the number of false positives tend to significantly increase when these tools are faced with low frequency variants. This study presents SNPredict, a single nucleotide polymorphism (SNP) detection pipeline that aims to utilize the results of multiple variant callers to produce a consensus output with higher accuracy than any of the individual tool with the help of machine learning techniques. By extracting features from the consensus output that describe traits associated with an individual variant call, it creates binary classifiers that predict a SNP’s true state and therefore help in distinguishing a sequencing error from a true variant
Speculative Approximations for Terascale Analytics
Model calibration is a major challenge faced by the plethora of statistical
analytics packages that are increasingly used in Big Data applications.
Identifying the optimal model parameters is a time-consuming process that has
to be executed from scratch for every dataset/model combination even by
experienced data scientists. We argue that the incapacity to evaluate multiple
parameter configurations simultaneously and the lack of support to quickly
identify sub-optimal configurations are the principal causes. In this paper, we
develop two database-inspired techniques for efficient model calibration.
Speculative parameter testing applies advanced parallel multi-query processing
methods to evaluate several configurations concurrently. The number of
configurations is determined adaptively at runtime, while the configurations
themselves are extracted from a distribution that is continuously learned
following a Bayesian process. Online aggregation is applied to identify
sub-optimal configurations early in the processing by incrementally sampling
the training dataset and estimating the objective function corresponding to
each configuration. We design concurrent online aggregation estimators and
define halting conditions to accurately and timely stop the execution. We apply
the proposed techniques to distributed gradient descent optimization -- batch
and incremental -- for support vector machines and logistic regression models.
We implement the resulting solutions in GLADE PF-OLA -- a state-of-the-art Big
Data analytics system -- and evaluate their performance over terascale-size
synthetic and real datasets. The results confirm that as many as 32
configurations can be evaluated concurrently almost as fast as one, while
sub-optimal configurations are detected accurately in as little as a
fraction of the time
Adapt or perish? How parties respond to party system saturation in 21 Western democracies, 1945–2011
This study examines whether (and how) parties adapt to party system saturation (PSS). A party system is oversaturated when a higher effective number of parties contests elections than predicted. Previous research has shown that parties are more likely to exit when party systems are oversaturated. This article examines whether parties will adapt by increasing the nicheness of their policy platform, by forming electoral alliances or by merging. Based on time-series analyses of 522 parties contesting 357 elections in twenty-one established Western democracies between 1945 and 2011, the study finds that parties are more likely to enter – and less likely to leave – electoral alliances if PSS increases. Additionally, a small share of older parties will merge. The results highlight parties’ limited capacity to adapt to their environments, which has important implications for the literature on party (system) change and models of electoral competition
MIRACLE-FI at ImageCLEFphoto 2008: Experiences in merging text-based and content-based retrievals
This paper describes the participation of the MIRACLE consortium at the ImageCLEF Photographic Retrieval task of ImageCLEF 2008. In this is new participation of the group, our first purpose is to evaluate our own tools for text-based retrieval and for content-based retrieval using different similarity metrics and the aggregation OWA operator to fuse the three topic images. From the MIRACLE last year experience, we implemented a new merging module combining the text-based and the content-based information in three different ways: FILTER-N, ENRICH and TEXT-FILTER. The former approaches try to improve the text-based baseline results using the content-based results lists. The last one was used to select the relevant images to the content-based module. No clustering strategies were analyzed. Finally, 41 runs were submitted: 1 for the text-based baseline, 10 content-based runs, and 30 mixed experiments merging text and content-based results. Results in general can be considered nearly acceptable comparing with the best results of other groups. Obtained results from textbased retrieval are better than content-based. Merging both textual and visual retrieval we improve the text-based baseline when applying the ENRICH merging algorithm although visual results are lower than textual ones. From these results we were going to try to improve merged results by clustering methods applied to this image collection
Reliable ABC model choice via random forests
Approximate Bayesian computation (ABC) methods provide an elaborate approach
to Bayesian inference on complex models, including model choice. Both
theoretical arguments and simulation experiments indicate, however, that model
posterior probabilities may be poorly evaluated by standard ABC techniques. We
propose a novel approach based on a machine learning tool named random forests
to conduct selection among the highly complex models covered by ABC algorithms.
We thus modify the way Bayesian model selection is both understood and
operated, in that we rephrase the inferential goal as a classification problem,
first predicting the model that best fits the data with random forests and
postponing the approximation of the posterior probability of the predicted MAP
for a second stage also relying on random forests. Compared with earlier
implementations of ABC model choice, the ABC random forest approach offers
several potential improvements: (i) it often has a larger discriminative power
among the competing models, (ii) it is more robust against the number and
choice of statistics summarizing the data, (iii) the computing effort is
drastically reduced (with a gain in computation efficiency of at least fifty),
and (iv) it includes an approximation of the posterior probability of the
selected model. The call to random forests will undoubtedly extend the range of
size of datasets and complexity of models that ABC can handle. We illustrate
the power of this novel methodology by analyzing controlled experiments as well
as genuine population genetics datasets. The proposed methodologies are
implemented in the R package abcrf available on the CRAN.Comment: 39 pages, 15 figures, 6 table
Multiple Retrieval Models and Regression Models for Prior Art Search
This paper presents the system called PATATRAS (PATent and Article Tracking,
Retrieval and AnalysiS) realized for the IP track of CLEF 2009. Our approach
presents three main characteristics: 1. The usage of multiple retrieval models
(KL, Okapi) and term index definitions (lemma, phrase, concept) for the three
languages considered in the present track (English, French, German) producing
ten different sets of ranked results. 2. The merging of the different results
based on multiple regression models using an additional validation set created
from the patent collection. 3. The exploitation of patent metadata and of the
citation structures for creating restricted initial working sets of patents and
for producing a final re-ranking regression model. As we exploit specific
metadata of the patent documents and the citation relations only at the
creation of initial working sets and during the final post ranking step, our
architecture remains generic and easy to extend
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