10,948 research outputs found
Preparation and characterization of magnetite (Fe3O4) nanoparticles By Sol-Gel method
The magnetite (Fe3O4) nanoparticles were successfully synthesized and annealed under vacuum at different temperature. The Fe3O4 nanoparticles prepared via sol-gel assisted method and annealed at 200-400ºC were characterized by Fourier Transformation Infrared Spectroscopy (FTIR), X-ray Diffraction spectra (XRD), Field Emission Scanning Electron Microscope (FESEM) and Atomic Force Microscopy (AFM). The XRD result indicate the presence of Fe3O4 nanoparticles, and the Scherer`s Formula calculated the mean particles size in range of 2-25 nm. The FESEM result shows that the morphologies of the particles annealed at 400ºC are more spherical and partially agglomerated, while the EDS result indicates the presence of Fe3O4 by showing Fe-O group of elements. AFM analyzed the 3D and roughness of the sample; the Fe3O4 nanoparticles have a minimum diameter of 79.04 nm, which is in agreement with FESEM result. In many cases, the synthesis of Fe3O4 nanoparticles using FeCl3 and FeCl2 has not been achieved, according to some literatures, but this research was able to obtained Fe3O4 nanoparticles base on the characterization 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
A Survey on Soft Subspace Clustering
Subspace clustering (SC) is a promising clustering technology to identify
clusters based on their associations with subspaces in high dimensional spaces.
SC can be classified into hard subspace clustering (HSC) and soft subspace
clustering (SSC). While HSC algorithms have been extensively studied and well
accepted by the scientific community, SSC algorithms are relatively new but
gaining more attention in recent years due to better adaptability. In the
paper, a comprehensive survey on existing SSC algorithms and the recent
development are presented. The SSC algorithms are classified systematically
into three main categories, namely, conventional SSC (CSSC), independent SSC
(ISSC) and extended SSC (XSSC). The characteristics of these algorithms are
highlighted and the potential future development of SSC is also discussed.Comment: This paper has been published in Information Sciences Journal in 201
Inverse Projection Representation and Category Contribution Rate for Robust Tumor Recognition
Sparse representation based classification (SRC) methods have achieved
remarkable results. SRC, however, still suffer from requiring enough training
samples, insufficient use of test samples and instability of representation. In
this paper, a stable inverse projection representation based classification
(IPRC) is presented to tackle these problems by effectively using test samples.
An IPR is firstly proposed and its feasibility and stability are analyzed. A
classification criterion named category contribution rate is constructed to
match the IPR and complete classification. Moreover, a statistical measure is
introduced to quantify the stability of representation-based classification
methods. Based on the IPRC technique, a robust tumor recognition framework is
presented by interpreting microarray gene expression data, where a two-stage
hybrid gene selection method is introduced to select informative genes.
Finally, the functional analysis of candidate's pathogenicity-related genes is
given. Extensive experiments on six public tumor microarray gene expression
datasets demonstrate the proposed technique is competitive with
state-of-the-art methods.Comment: 14 pages, 19 figures, 10 table
Improving average ranking precision in user searches for biomedical research datasets
Availability of research datasets is keystone for health and life science
study reproducibility and scientific progress. Due to the heterogeneity and
complexity of these data, a main challenge to be overcome by research data
management systems is to provide users with the best answers for their search
queries. In the context of the 2016 bioCADDIE Dataset Retrieval Challenge, we
investigate a novel ranking pipeline to improve the search of datasets used in
biomedical experiments. Our system comprises a query expansion model based on
word embeddings, a similarity measure algorithm that takes into consideration
the relevance of the query terms, and a dataset categorisation method that
boosts the rank of datasets matching query constraints. The system was
evaluated using a corpus with 800k datasets and 21 annotated user queries. Our
system provides competitive results when compared to the other challenge
participants. In the official run, it achieved the highest infAP among the
participants, being +22.3% higher than the median infAP of the participant's
best submissions. Overall, it is ranked at top 2 if an aggregated metric using
the best official measures per participant is considered. The query expansion
method showed positive impact on the system's performance increasing our
baseline up to +5.0% and +3.4% for the infAP and infNDCG metrics, respectively.
Our similarity measure algorithm seems to be robust, in particular compared to
Divergence From Randomness framework, having smaller performance variations
under different training conditions. Finally, the result categorization did not
have significant impact on the system's performance. We believe that our
solution could be used to enhance biomedical dataset management systems. In
particular, the use of data driven query expansion methods could be an
alternative to the complexity of biomedical terminologies
Stable Feature Selection for Biomarker Discovery
Feature selection techniques have been used as the workhorse in biomarker
discovery applications for a long time. Surprisingly, the stability of feature
selection with respect to sampling variations has long been under-considered.
It is only until recently that this issue has received more and more attention.
In this article, we review existing stable feature selection methods for
biomarker discovery using a generic hierarchal framework. We have two
objectives: (1) providing an overview on this new yet fast growing topic for a
convenient reference; (2) categorizing existing methods under an expandable
framework for future research and development
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