5,729 research outputs found
Unconventional machine learning of genome-wide human cancer data
Recent advances in high-throughput genomic technologies coupled with
exponential increases in computer processing and memory have allowed us to
interrogate the complex aberrant molecular underpinnings of human disease from
a genome-wide perspective. While the deluge of genomic information is expected
to increase, a bottleneck in conventional high-performance computing is rapidly
approaching. Inspired in part by recent advances in physical quantum
processors, we evaluated several unconventional machine learning (ML)
strategies on actual human tumor data. Here we show for the first time the
efficacy of multiple annealing-based ML algorithms for classification of
high-dimensional, multi-omics human cancer data from the Cancer Genome Atlas.
To assess algorithm performance, we compared these classifiers to a variety of
standard ML methods. Our results indicate the feasibility of using
annealing-based ML to provide competitive classification of human cancer types
and associated molecular subtypes and superior performance with smaller
training datasets, thus providing compelling empirical evidence for the
potential future application of unconventional computing architectures in the
biomedical sciences
Interpretable multiclass classification by MDL-based rule lists
Interpretable classifiers have recently witnessed an increase in attention
from the data mining community because they are inherently easier to understand
and explain than their more complex counterparts. Examples of interpretable
classification models include decision trees, rule sets, and rule lists.
Learning such models often involves optimizing hyperparameters, which typically
requires substantial amounts of data and may result in relatively large models.
In this paper, we consider the problem of learning compact yet accurate
probabilistic rule lists for multiclass classification. Specifically, we
propose a novel formalization based on probabilistic rule lists and the minimum
description length (MDL) principle. This results in virtually parameter-free
model selection that naturally allows to trade-off model complexity with
goodness of fit, by which overfitting and the need for hyperparameter tuning
are effectively avoided. Finally, we introduce the Classy algorithm, which
greedily finds rule lists according to the proposed criterion. We empirically
demonstrate that Classy selects small probabilistic rule lists that outperform
state-of-the-art classifiers when it comes to the combination of predictive
performance and interpretability. We show that Classy is insensitive to its
only parameter, i.e., the candidate set, and that compression on the training
set correlates with classification performance, validating our MDL-based
selection criterion
Mental distress detection and triage in forum posts: the LT3 CLPsych 2016 shared task system
This paper describes the contribution of LT3 for the CLPsych 2016 Shared Task on automatic triage of mental health forum posts. Our systems use multiclass Support Vector Machines (SVM), cascaded binary SVMs and ensembles with a rich feature set. The best systems obtain macro-averaged F-scores of 40% on the full task and 80% on the green versus alarming distinction. Multiclass SVMs with all features score best in terms of F-score, whereas feature filtering with bi-normal separation and classifier ensembling are found to improve recall of alarming posts
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