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1mikelove/awesome-multi-omics: List of software packages for multi-omics analysis
https://github.com/mikelove/awesome-multi-omics
6 years ago by @becker
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multiomics
multi
omics
nalab
bio
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collection
multiomicsmultiomicsnalabbiopapersoverviewcollection
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1DmitryUlyanov/Multicore-TSNE: Parallel t-SNE implementation with Python and Torch wrappers.
https://github.com/DmitryUlyanov/Multicore-TSNE
6 years ago by @becker
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tsne
multi
core
parallel
multicore
python
py
py3
python3
sklearn
scikit
learn
tsnemulticoreparallelmulticorepythonpypy3python3sklearnscikitlearn
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1ratschlab/RGAN: Recurrent (conditional) generative adversarial networks for generating real-valued time series data.
https://github.com/ratschlab/RGAN
6 years ago by @becker
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real
valued
time
series
multi
dim
dimensional
gan
recurrent
neural
network
conditional
realvaluedtimeseriesmultidimdimensionalganrecurrentneuralnetworkconditional
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1Multi-Omics Data Sharing
https://www.nature.com/collections/hbchcddagg/
5 years ago by @becker
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multi
omics
multiomics
multi-omics
data
dataset
datasets
sets
sharing
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multiomicsmultiomicsmulti-omicsdatadatasetdatasetssetssharingrepositoryoverview
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1Overview of mvlearn — mvlearn alpha documentation
https://mvlearn.neurodata.io/index.html
4 years ago by @becker
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python
multi
view
learning
ml
multiomics
omics
multiview
nalab
butterfly
learn
py
pythonmultiviewlearningmlmultiomicsomicsmultiviewnalabbutterflylearnpy
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1MULTI-VIEW LEARNING | Papers With Code
https://paperswithcode.com/task/multi-view-learning/
4 years ago by @becker
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python
multi
view
learning
ml
multiomics
omics
multiview
nalab
butterfly
learn
py
overview
code
list
pythonmultiviewlearningmlmultiomicsomicsmultiviewnalabbutterflylearnpyoverviewcodelist
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1GFLASSO: Graph-Guided Fused LASSO in R - DataCamp
https://www.datacamp.com/community/tutorials/gflasso-R
4 years ago by @becker
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graph
guided
lasso
machine
learning
r
multilabel
multi
label
graphguidedlassomachinelearningrmultilabelmultilabel
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1HipGraph/Force2Vec: Implementation of Force2Vec method for ICDM 2020 paper titled "Force2Vec: Parallel force-directed graph embedding"
https://github.com/HipGraph/Force2Vec
4 years ago by @becker
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force
graph
network
embeddng
layout
efficient
parallel
python
multicore
multi
core
directed
forcegraphnetworkembeddnglayoutefficientparallelpythonmulticoremulticoredirected
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1LinkedOmics :: Login
http://www.linkedomics.org/login.php
4 years ago by @becker
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paper:fastcor
data
dataset
datasets
cancer
multi
omics
multiomics
paper:fastcordatadatasetdatasetscancermultiomicsmultiomics
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1Discovery of time-series motif from multi-dimensional data based on MDL principle
Y. Tanaka, K. Iwamoto, and K. Uehara. Machine Learning, 58 (2-3): 269--300 (2005)
11 years ago by @becker
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MDL
anomaly
detection
dimensional
motif
multi
s:2013-12-10_anomaly
series
time
MDLanomalydetectiondimensionalmotifmultis:2013-12-10_anomalyseriestime
(0)
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2Multi-dimensional regression analysis of time-series data streams
Y. Chen, G. Dong, J. Han, B. Wah, and J. Wang. Proceedings of the 28th international conference on Very Large Data Bases, page 323--334. VLDB Endowment, (2002)
11 years ago by @becker
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analysis
dimensional
mining
multi
regression
s:2013-12-18_time-series-mining
series
time
analysisdimensionalminingmultiregressions:2013-12-18_time-series-miningseriestime
(0)
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3Optimal multi-scale patterns in time series streams
S. Papadimitriou, and P. Yu. Proceedings of the 2006 ACM SIGMOD international conference on Management of data, page 647--658. ACM, (2006)
11 years ago by @becker
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mining
multi
pattern
s:2013-12-18_time-series-mining
scale
series
stream
time
miningmultipatterns:2013-12-18_time-series-miningscaleseriesstreamtime
(0)
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2Streaming pattern discovery in multiple time-series
S. Papadimitriou, J. Sun, and C. Faloutsos. Proceedings of the 31st international conference on Very large data bases, page 697--708. VLDB Endowment, (2005)
11 years ago by @becker
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discovery
mining
multi
pattern
s:2013-12-18_time-series-mining
series
stream
time
discoveryminingmultipatterns:2013-12-18_time-series-miningseriesstreamtime
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2Multidimensional data modeling for complex data
T. Pedersen, and C. Jensen. Data Engineering, 1999. Proceedings., 15th International Conference on, page 336--345. IEEE, (1999)
11 years ago by @becker
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complex
data
dimensional
model
multi
s:2013-08-23_sensorplatforms
complexdatadimensionalmodelmultis:2013-08-23_sensorplatforms
(0)
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2Testing the Predictive Power of Variable History Web Usage
J. Borges, and M. Levene. Soft Computing, 11 (8): 717--727 (2007)
8 years ago by @becker
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chain
diss
inthesis
length
markov
multi
order
prediction
variable
chaindissinthesislengthmarkovmultiorderpredictionvariable
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3Pre-Deployment Testing, Augmentation and Calibration of Cross-Sensitive Sensors.
B. Maag, O. Saukh, D. Hasenfratz, and L. Thiele. EWSN, page 169--180. (2016)
8 years ago by @becker
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airprobe
neural
networks
multi
linear
regression
calibration
sensor
air
quality
citedby:scholar:count:3
citedby:scholar:timestamp:2017-5-12
airprobeneuralnetworksmultilinearregressioncalibrationsensorairqualitycitedby:scholar:count:3citedby:scholar:timestamp:2017-5-12
(0)
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3Mapping urban air quality in near real-time using observations from low-cost sensors and model information
P. Schneider, N. Castell, M. Vogt, F. Dauge, W. Lahoz, and A. Bartonova. Environment International, (2017)
7 years ago by @becker
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air
calibration
co2
eva
everyaware
multi
p2map
quality
sensor
aircalibrationco2evaeveryawaremultip2mapqualitysensor
(0)
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4SCAN: Multi-Hop Calibration for Mobile Sensor Arrays
B. Maag, Z. Zhou, O. Saukh, and L. Thiele. Proc. ACM Interact. Mob. Wearable Ubiquitous Technol., 1 (2): 19:1--19:21 (June 2017)
6 years ago by @becker
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array
box
calibration
eva
everyaware
hop
multi
no2
p2map
sensor
arrayboxcalibrationevaeveryawarehopmultino2p2mapsensor
(0)
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4Multimodal generative models for scalable weakly-supervised learning
M. Wu, and N. Goodman. Advances in Neural Information Processing Systems, page 5575--5585. (2018)
5 years ago by @becker
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autoencoder
generative
modal
model
multi
multimodal
nips
vae
variational
autoencodergenerativemodalmodelmultimultimodalnipsvaevariational
(0)
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2DIABLO: an integrative approach for identifying key molecular drivers from multi-omics assays
A. Singh, C. Shannon, B. Gautier, F. Rohart, M. Vacher, S. Tebbutt, and K. Lê Cao. Bioinformatics, (2019)
5 years ago by @becker
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bio
immune
integration
mchri
multi
multiomics
omics
prediction
preterm
system
bioimmuneintegrationmchrimultimultiomicsomicspredictionpretermsystem
(0)
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1Multiomics modeling of the immunome, transcriptome, microbiome, proteome and metabolome adaptations during human pregnancy
M. Ghaemi, D. DiGiulio, K. Contrepois, B. Callahan, T. Ngo, B. Lee-McMullen, B. Lehallier, A. Robaczewska, D. Mcilwain, Y. Rosenberg-Hasson and 1 other author(s). Bioinformatics, 35 (1): 95--103 (2019)
5 years ago by @becker
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elastic
generalization
mchri
multi
multiomics
net
omics
paper:cordis
paper:fastcor
paper:milkreview:selected
paper:stressmulti
pregnancy
preterm
stacked
elasticgeneralizationmchrimultimultiomicsnetomicspaper:cordispaper:fastcorpaper:milkreview:selectedpaper:stressmultipregnancypretermstacked
(0)
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1Learning important features from multi-view data to predict drug side effects
X. Liang, P. Zhang, J. Li, Y. Fu, L. Qu, Y. Chen, and Z. Chen. Journal of Cheminformatics, 11 (1): 1--17 (2019)
4 years ago by @becker
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multi
view
learning
machine
laplacian
laplace
matrix
constrained
lasso
constraint
drug
effect
side
effects
graph
network
correlation
cordis
overlap
citedby:scholar:count:1
citedby:scholar:timestamp:2020-7-8
multiviewlearningmachinelaplacianlaplacematrixconstrainedlassoconstraintdrugeffectsideeffectsgraphnetworkcorrelationcordisoverlapcitedby:scholar:count:1citedby:scholar:timestamp:2020-7-8
(0)
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1Causal integration of multi-omics data with prior knowledge to generate mechanistic hypotheses
A. Dugourd, C. Kuppe, M. Sciacovelli, E. Gjerga, K. Emdal, D. Bekker-Jensen, J. Kranz, E. Bindels, A. Costa, J. Olsen and 3 other author(s). bioRxiv, (2020)
4 years ago by @becker
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causal
causality
multi
multiomics
omics
toread
causalcausalitymultimultiomicsomicstoread
(0)
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1Multiview learning for understanding functional multiomics
N. Nguyen, and D. Wang. PLOS Computational Biology, 16 (4): e1007677 (2020)
4 years ago by @becker
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citedby:scholar:count:4
citedby:scholar:timestamp:2020-7-29
learning
multi
multiomics
multiview
omics
paper:milkreview:selected
view
citedby:scholar:count:4citedby:scholar:timestamp:2020-7-29learningmultimultiomicsmultiviewomicspaper:milkreview:selectedview
(0)
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1A review on machine learning principles for multi-view biological data integration
Y. Li, F. Wu, and A. Ngom. Briefings in bioinformatics, 19 (2): 325--340 (2018)
4 years ago by @becker
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biology
citedby:scholar:count:143
citedby:scholar:timestamp:2020-7-29
multi
multiomics
multiview
omics
p21
paper:milkreview:selected
relatedwork
review
view
biologycitedby:scholar:count:143citedby:scholar:timestamp:2020-7-29multimultiomicsmultiviewomicsp21paper:milkreview:selectedrelatedworkreviewview
(0)
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1A survey of multi-view machine learning
S. Sun. Neural computing and applications, 23 (7-8): 2031--2038 (2013)
4 years ago by @becker
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multiview
multi
view
survey
review
learning
citedby:scholar:count:576
citedby:scholar:timestamp:2020-7-29
multiviewmultiviewsurveyreviewlearningcitedby:scholar:count:576citedby:scholar:timestamp:2020-7-29
(0)
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1Evaluation of colorectal cancer subtypes and cell lines using deep learning
J. Ronen, S. Hayat, and A. Akalin. Life science alliance, (2019)
4 years ago by @becker
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autoencoder
citedby:scholar:count:6
citedby:scholar:timestamp:2020-7-29
deep
integration
learning
multi
multiomics
omics
paper:milkreview:selected
autoencodercitedby:scholar:count:6citedby:scholar:timestamp:2020-7-29deepintegrationlearningmultimultiomicsomicspaper:milkreview:selected
(0)
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1Network-Based Approaches for Multi-omics Integration
G. Zhou, S. Li, and J. Xia. Computational Methods and Data Analysis for Metabolomics, Springer, (2020)
4 years ago by @becker
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anlaysis
citedby:scholar:count:2
citedby:scholar:timestamp:2020-7-29
graph
integration
multi
multiomics
network
omics
p21
relatedwork
anlaysiscitedby:scholar:count:2citedby:scholar:timestamp:2020-7-29graphintegrationmultimultiomicsnetworkomicsp21relatedwork
(0)
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2mixOmics: An R package for ‘omics feature selection and multiple data integration
F. Rohart, B. Gautier, A. Singh, and K. Lê Cao. PLOS Computational Biology, 13 (11): 1-19 (November 2017)
4 years ago by @becker
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cross
data
dataset
integration
merging
multi
multiomics
n
omics
p
set
crossdatadatasetintegrationmergingmultimultiomicsnomicspset
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1Personal Omics for Precision Health
R. Kellogg, J. Dunn, and M. Snyder. Circulation Research, 122 (9): 1169--1171 (April 2018)
4 years ago by @becker
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medicine
multi
multiomics
omics
precision
medicinemultimultiomicsomicsprecision
(0)
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1Convolutional neural networks for structured omics: OmicsCNN and the OmicsConv layer
G. Jurman, V. Maggio, D. Fioravanti, Y. Giarratano, I. Landi, M. Francescatto, C. Agostinelli, M. Chierici, M. De Domenico, and C. Furlanello. arXiv preprint arXiv:1710.05918, (2017)
4 years ago by @becker
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multi
multiomics
structure
background
knowledge
omics
graph
cnn
convolutional
neural
network
citedby:scholar:count:2
citedby:scholar:timestamp:2020-8-31
multimultiomicsstructurebackgroundknowledgeomicsgraphcnnconvolutionalneuralnetworkcitedby:scholar:count:2citedby:scholar:timestamp:2020-8-31
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1OmicsMapNet: Transforming omics data to take advantage of Deep Convolutional Neural Network for discovery
S. Ma, and Z. Zhang. arXiv preprint arXiv:1804.05283, (2018)
4 years ago by @becker
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convoluational
nn
neural
network
cnn
multi
omics
multiomics
deep
map
tree
citedby:scholar:count:5
citedby:scholar:timestamp:2020-8-31
convoluationalnnneuralnetworkcnnmultiomicsmultiomicsdeepmaptreecitedby:scholar:count:5citedby:scholar:timestamp:2020-8-31
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6Community structure in time-dependent, multiscale, and multiplex networks
P. Mucha, T. Richardson, K. Macon, M. Porter, and J. Onnela. science, 328 (5980): 876--878 (2010)
4 years ago by @becker
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citedby:scholar:count:1565
citedby:scholar:timestamp:2020-9-15
cluster
clustering
community
cordis
dependent
dis
funcdis
graph
multi
multiplex
multiscale
network
project:bmbf
scale
structure
time
citedby:scholar:count:1565citedby:scholar:timestamp:2020-9-15clusterclusteringcommunitycordisdependentdisfuncdisgraphmultimultiplexmultiscalenetworkproject:bmbfscalestructuretime
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1LinkedOmics: analyzing multi-omics data within and across 32 cancer types
S. Vasaikar, P. Straub, J. Wang, and B. Zhang. Nucleic acids research, 46 (D1): D956--D963 (2018)
4 years ago by @becker
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paper:fastcor
data
omics
dataset
cancer
multi
citedby:scholar:count:325
citedby:scholar:timestamp:2020-12-4
paper:fastcordataomicsdatasetcancermulticitedby:scholar:count:325citedby:scholar:timestamp:2020-12-4
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1Multi-omics data integration, interpretation, and its application
I. Subramanian, S. Verma, S. Kumar, A. Jere, and K. Anamika. Bioinformatics and biology insights, (2020)
4 years ago by @becker
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application
citedby:scholar:count:57
citedby:scholar:timestamp:2021-2-14
data
integration
multi
multiomics
omics
p21
paper:fastcor
paper:milkreview:selected
relatedwork
review
survey
applicationcitedby:scholar:count:57citedby:scholar:timestamp:2021-2-14dataintegrationmultimultiomicsomicsp21paper:fastcorpaper:milkreview:selectedrelatedworkreviewsurvey
(0)
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1Multiomics Characterization of Preterm Birth in Low- and Middle-Income Countries
F. Jehan, S. Sazawal, A. Baqui, M. Nisar, U. Dhingra, R. Khanam, M. Ilyas, A. Dutta, D. Mitra, U. Mehmood and 68 other author(s). JAMA Network Open, (2020)
4 years ago by @becker
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birth
cohort
lmic
multi
multiomucs
myown
p21
paper:milkreview:selected
pregnancy
preterm
project:bmbf
site
birthcohortlmicmultimultiomucsmyownp21paper:milkreview:selectedpregnancypretermproject:bmbfsite
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1Multi-omics approaches to disease
Y. Hasin, M. Seldin, and A. Lusis. Genome biology, 18 (1): 1--15 (2017)
4 years ago by @becker
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citedby:scholar:count:683
citedby:scholar:timestamp:2021-5-12
fastcor
multi
multiomics
omics
paper
paper:fastcor
paper:milkreview
citedby:scholar:count:683citedby:scholar:timestamp:2021-5-12fastcormultimultiomicsomicspaperpaper:fastcorpaper:milkreview
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1Challenges in the integration of omics and non-omics data
E. López de Maturana, L. Alonso, P. Alarcón, I. Mart\'ın-Antoniano, S. Pineda, L. Piorno, M. Calle, and N. Malats. Genes, 10 (3): 238 (2019)
4 years ago by @becker
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citedby:scholar:count:31
citedby:scholar:timestamp:2021-5-28
clinical
data
ehr
integration
multi
multiomics
non
omics
paper:milkreview
paper:milkreview:selected
citedby:scholar:count:31citedby:scholar:timestamp:2021-5-28clinicaldataehrintegrationmultimultiomicsnonomicspaper:milkreviewpaper:milkreview:selected
(0)
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1Machine learning and integrative analysis of biomedical big data
B. Mirza, W. Wang, J. Wang, H. Choi, N. Chung, and P. Ping. Genes, 10 (2): 87 (2019)
4 years ago by @becker
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challenges
citedby:scholar:count:67
citedby:scholar:timestamp:2021-5-29
integration
issues
multi
multiomics
omics
paper:milkreview
paper:milkreview:selected
challengescitedby:scholar:count:67citedby:scholar:timestamp:2021-5-29integrationissuesmultimultiomicsomicspaper:milkreviewpaper:milkreview:selected
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1Multimodal machine learning: A survey and taxonomy
T. Baltrusaitis, C. Ahuja, and L. Morency. IEEE transactions on pattern analysis and machine intelligence, 41 (2): 423--443 (2018)
4 years ago by @becker
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paper:milkreview:selected
multi
model
machine
learning
multimodal
survey
taxonomy
citedby:scholar:count:842
citedby:scholar:timestamp:2021-5-29
paper:milkreview:selectedmultimodelmachinelearningmultimodalsurveytaxonomycitedby:scholar:count:842citedby:scholar:timestamp:2021-5-29
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