10,093 research outputs found
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
Online Tool Condition Monitoring Based on Parsimonious Ensemble+
Accurate diagnosis of tool wear in metal turning process remains an open
challenge for both scientists and industrial practitioners because of
inhomogeneities in workpiece material, nonstationary machining settings to suit
production requirements, and nonlinear relations between measured variables and
tool wear. Common methodologies for tool condition monitoring still rely on
batch approaches which cannot cope with a fast sampling rate of metal cutting
process. Furthermore they require a retraining process to be completed from
scratch when dealing with a new set of machining parameters. This paper
presents an online tool condition monitoring approach based on Parsimonious
Ensemble+, pENsemble+. The unique feature of pENsemble+ lies in its highly
flexible principle where both ensemble structure and base-classifier structure
can automatically grow and shrink on the fly based on the characteristics of
data streams. Moreover, the online feature selection scenario is integrated to
actively sample relevant input attributes. The paper presents advancement of a
newly developed ensemble learning algorithm, pENsemble+, where online active
learning scenario is incorporated to reduce operator labelling effort. The
ensemble merging scenario is proposed which allows reduction of ensemble
complexity while retaining its diversity. Experimental studies utilising
real-world manufacturing data streams and comparisons with well known
algorithms were carried out. Furthermore, the efficacy of pENsemble was
examined using benchmark concept drift data streams. It has been found that
pENsemble+ incurs low structural complexity and results in a significant
reduction of operator labelling effort.Comment: this paper has been published by IEEE Transactions on Cybernetic
An Incremental Construction of Deep Neuro Fuzzy System for Continual Learning of Non-stationary Data Streams
Existing FNNs are mostly developed under a shallow network configuration
having lower generalization power than those of deep structures. This paper
proposes a novel self-organizing deep FNN, namely DEVFNN. Fuzzy rules can be
automatically extracted from data streams or removed if they play limited role
during their lifespan. The structure of the network can be deepened on demand
by stacking additional layers using a drift detection method which not only
detects the covariate drift, variations of input space, but also accurately
identifies the real drift, dynamic changes of both feature space and target
space. DEVFNN is developed under the stacked generalization principle via the
feature augmentation concept where a recently developed algorithm, namely
gClass, drives the hidden layer. It is equipped by an automatic feature
selection method which controls activation and deactivation of input attributes
to induce varying subsets of input features. A deep network simplification
procedure is put forward using the concept of hidden layer merging to prevent
uncontrollable growth of dimensionality of input space due to the nature of
feature augmentation approach in building a deep network structure. DEVFNN
works in the sample-wise fashion and is compatible for data stream
applications. The efficacy of DEVFNN has been thoroughly evaluated using seven
datasets with non-stationary properties under the prequential test-then-train
protocol. It has been compared with four popular continual learning algorithms
and its shallow counterpart where DEVFNN demonstrates improvement of
classification accuracy. Moreover, it is also shown that the concept drift
detection method is an effective tool to control the depth of network structure
while the hidden layer merging scenario is capable of simplifying the network
complexity of a deep network with negligible compromise of generalization
performance.Comment: This paper has been published in IEEE Transactions on Fuzzy System
Methods for protein complex prediction and their contributions towards understanding the organization, function and dynamics of complexes
Complexes of physically interacting proteins constitute fundamental
functional units responsible for driving biological processes within cells. A
faithful reconstruction of the entire set of complexes is therefore essential
to understand the functional organization of cells. In this review, we discuss
the key contributions of computational methods developed till date
(approximately between 2003 and 2015) for identifying complexes from the
network of interacting proteins (PPI network). We evaluate in depth the
performance of these methods on PPI datasets from yeast, and highlight
challenges faced by these methods, in particular detection of sparse and small
or sub- complexes and discerning of overlapping complexes. We describe methods
for integrating diverse information including expression profiles and 3D
structures of proteins with PPI networks to understand the dynamics of complex
formation, for instance, of time-based assembly of complex subunits and
formation of fuzzy complexes from intrinsically disordered proteins. Finally,
we discuss methods for identifying dysfunctional complexes in human diseases,
an application that is proving invaluable to understand disease mechanisms and
to discover novel therapeutic targets. We hope this review aptly commemorates a
decade of research on computational prediction of complexes and constitutes a
valuable reference for further advancements in this exciting area.Comment: 1 Tabl
Data-driven Soft Sensors in the Process Industry
In the last two decades Soft Sensors established themselves as a valuable alternative to the traditional means for the acquisition of critical process variables, process monitoring and other tasks which are related to process control. This paper discusses characteristics of the process industry data which are critical for the development of data-driven Soft Sensors. These characteristics are common to a large number of process industry fields, like the chemical industry, bioprocess industry, steel industry, etc. The focus of this work is put on the data-driven Soft Sensors because of their growing popularity, already demonstrated usefulness and huge, though yet not completely realised, potential. A comprehensive selection of case studies covering the three most important Soft Sensor application fields, a general introduction to the most popular Soft Sensor modelling techniques as well as a discussion of some open issues in the Soft Sensor development and maintenance and their possible solutions are the main contributions of this work
A Reinforcement Learning Approach to Weaning of Mechanical Ventilation in Intensive Care Units
The management of invasive mechanical ventilation, and the regulation of
sedation and analgesia during ventilation, constitutes a major part of the care
of patients admitted to intensive care units. Both prolonged dependence on
mechanical ventilation and premature extubation are associated with increased
risk of complications and higher hospital costs, but clinical opinion on the
best protocol for weaning patients off of a ventilator varies. This work aims
to develop a decision support tool that uses available patient information to
predict time-to-extubation readiness and to recommend a personalized regime of
sedation dosage and ventilator support. To this end, we use off-policy
reinforcement learning algorithms to determine the best action at a given
patient state from sub-optimal historical ICU data. We compare treatment
policies from fitted Q-iteration with extremely randomized trees and with
feedforward neural networks, and demonstrate that the policies learnt show
promise in recommending weaning protocols with improved outcomes, in terms of
minimizing rates of reintubation and regulating physiological stability
Deep Learning Models For Biomedical Data Analysis
The field of biomedical data analysis is a vibrant area of research dedicated to extracting valuable insights from a wide range of biomedical data sources, including biomedical images and genomics data. The emergence of deep learning, an artificial intelligence approach, presents significant prospects for enhancing biomedical data analysis and knowledge discovery. This dissertation focused on exploring innovative deep-learning methods for biomedical image processing and gene data analysis.
During the COVID-19 pandemic, biomedical imaging data, including CT scans and chest x-rays, played a pivotal role in identifying COVID-19 cases by categorizing patient chest x-ray outcomes as COVID-19-positive or negative. While supervised deep learning methods have effectively recognized COVID-19 patterns in chest x-ray datasets, the availability of annotated training data remains limited. To address this challenge, the thesis introduced a semi-supervised deep learning model named ssResNet, built upon the Residual Neural Network (ResNet) architecture. The model combines supervised and unsupervised paths, incorporating a weighted supervised loss function to manage data imbalance. The strategies to diminish prediction uncertainty in deep learning models for critical applications like medical image processing is explore. It achieves this through an ensemble deep learning model, integrating bagging deep learning and model calibration techniques. This ensemble model not only boosts biomedical image segmentation accuracy but also reduces prediction uncertainty, as validated on a comprehensive chest x-ray image segmentation dataset.
Furthermore, the thesis introduced an ensemble model integrating Proformer and ensemble learning methodologies. This model constructs multiple independent Proformers for predicting gene expression, their predictions are combined through weighted averaging to generate final predictions. Experimental outcomes underscore the efficacy of this ensemble model in enhancing prediction performance across various metrics.
In conclusion, this dissertation advances biomedical data analysis by harnessing the potential of deep learning techniques. It devises innovative approaches for processing biomedical images and gene data. By leveraging deep learning\u27s capabilities, this work paves the way for further progress in biomedical data analytics and its applications within clinical contexts.
Index Terms- biomedical data analysis, COVID-19, deep learning, ensemble learning, gene data analytics, medical image segmentation, prediction uncertainty, Proformer, Residual Neural Network (ResNet), semi-supervised learning
Mal-Netminer: Malware Classification Approach based on Social Network Analysis of System Call Graph
As the security landscape evolves over time, where thousands of species of
malicious codes are seen every day, antivirus vendors strive to detect and
classify malware families for efficient and effective responses against malware
campaigns. To enrich this effort, and by capitalizing on ideas from the social
network analysis domain, we build a tool that can help classify malware
families using features driven from the graph structure of their system calls.
To achieve that, we first construct a system call graph that consists of system
calls found in the execution of the individual malware families. To explore
distinguishing features of various malware species, we study social network
properties as applied to the call graph, including the degree distribution,
degree centrality, average distance, clustering coefficient, network density,
and component ratio. We utilize features driven from those properties to build
a classifier for malware families. Our experimental results show that
influence-based graph metrics such as the degree centrality are effective for
classifying malware, whereas the general structural metrics of malware are less
effective for classifying malware. Our experiments demonstrate that the
proposed system performs well in detecting and classifying malware families
within each malware class with accuracy greater than 96%.Comment: Mathematical Problems in Engineering, Vol 201
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