34,010 research outputs found
FLASH: Randomized Algorithms Accelerated over CPU-GPU for Ultra-High Dimensional Similarity Search
We present FLASH (\textbf{F}ast \textbf{L}SH \textbf{A}lgorithm for
\textbf{S}imilarity search accelerated with \textbf{H}PC), a similarity search
system for ultra-high dimensional datasets on a single machine, that does not
require similarity computations and is tailored for high-performance computing
platforms. By leveraging a LSH style randomized indexing procedure and
combining it with several principled techniques, such as reservoir sampling,
recent advances in one-pass minwise hashing, and count based estimations, we
reduce the computational and parallelization costs of similarity search, while
retaining sound theoretical guarantees.
We evaluate FLASH on several real, high-dimensional datasets from different
domains, including text, malicious URL, click-through prediction, social
networks, etc. Our experiments shed new light on the difficulties associated
with datasets having several million dimensions. Current state-of-the-art
implementations either fail on the presented scale or are orders of magnitude
slower than FLASH. FLASH is capable of computing an approximate k-NN graph,
from scratch, over the full webspam dataset (1.3 billion nonzeros) in less than
10 seconds. Computing a full k-NN graph in less than 10 seconds on the webspam
dataset, using brute-force (), will require at least 20 teraflops. We
provide CPU and GPU implementations of FLASH for replicability of our results
Machine Learning and Integrative Analysis of Biomedical Big Data.
Recent developments in high-throughput technologies have accelerated the accumulation of massive amounts of omics data from multiple sources: genome, epigenome, transcriptome, proteome, metabolome, etc. Traditionally, data from each source (e.g., genome) is analyzed in isolation using statistical and machine learning (ML) methods. Integrative analysis of multi-omics and clinical data is key to new biomedical discoveries and advancements in precision medicine. However, data integration poses new computational challenges as well as exacerbates the ones associated with single-omics studies. Specialized computational approaches are required to effectively and efficiently perform integrative analysis of biomedical data acquired from diverse modalities. In this review, we discuss state-of-the-art ML-based approaches for tackling five specific computational challenges associated with integrative analysis: curse of dimensionality, data heterogeneity, missing data, class imbalance and scalability issues
Techniques for clustering gene expression data
Many clustering techniques have been proposed for the analysis of gene expression data obtained from microarray experiments. However, choice of suitable method(s) for a given experimental dataset is not straightforward. Common approaches do not translate well and fail to take account of the data profile. This review paper surveys state of the art applications which recognises these limitations and implements procedures to overcome them. It provides a framework for the evaluation of clustering in gene expression analyses. The nature of microarray data is discussed briefly. Selected examples are presented for the clustering methods considered
On Recursive Edit Distance Kernels with Application to Time Series Classification
This paper proposes some extensions to the work on kernels dedicated to
string or time series global alignment based on the aggregation of scores
obtained by local alignments. The extensions we propose allow to construct,
from classical recursive definition of elastic distances, recursive edit
distance (or time-warp) kernels that are positive definite if some sufficient
conditions are satisfied. The sufficient conditions we end-up with are original
and weaker than those proposed in earlier works, although a recursive
regularizing term is required to get the proof of the positive definiteness as
a direct consequence of the Haussler's convolution theorem. The classification
experiment we conducted on three classical time warp distances (two of which
being metrics), using Support Vector Machine classifier, leads to conclude
that, when the pairwise distance matrix obtained from the training data is
\textit{far} from definiteness, the positive definite recursive elastic kernels
outperform in general the distance substituting kernels for the classical
elastic distances we have tested.Comment: 14 page
Large-Scale Online Semantic Indexing of Biomedical Articles via an Ensemble of Multi-Label Classification Models
Background: In this paper we present the approaches and methods employed in
order to deal with a large scale multi-label semantic indexing task of
biomedical papers. This work was mainly implemented within the context of the
BioASQ challenge of 2014. Methods: The main contribution of this work is a
multi-label ensemble method that incorporates a McNemar statistical
significance test in order to validate the combination of the constituent
machine learning algorithms. Some secondary contributions include a study on
the temporal aspects of the BioASQ corpus (observations apply also to the
BioASQ's super-set, the PubMed articles collection) and the proper adaptation
of the algorithms used to deal with this challenging classification task.
Results: The ensemble method we developed is compared to other approaches in
experimental scenarios with subsets of the BioASQ corpus giving positive
results. During the BioASQ 2014 challenge we obtained the first place during
the first batch and the third in the two following batches. Our success in the
BioASQ challenge proved that a fully automated machine-learning approach, which
does not implement any heuristics and rule-based approaches, can be highly
competitive and outperform other approaches in similar challenging contexts
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