Posts Tagged ‘i0kdd’

markov logic network from KDD 2014, might be good for netessay

August 31, 2014

[[DW: very large-scale models (vs. VLSI): markov logic network on customer networks, Innovation Award Talk by Pedro Domingos, KDD 2014 ]]

http://homes.cs.washington.edu/~pedrod/803

also, it has biological applications like:
Markov Logic Networks in the Analysis of Genetic Data
https://www.systemsbiology.org/markov-logic-networks-analysis-genetic-data

My public notes from KDD 2014

August 31, 2014

https://storify.com/markgerstein/tweets-related-to-kdd-2014-i0kdd-kdd2014

https://www.flickr.com/photos/mbgmbg/tags/seriesspacyworldofbloombergbldg

https://linkstream2.gerstein.info/tag/i0kdd/

http://archive.gersteinlab.org/meetings/s/2014/08.28/kdd2014-i0kdd-meeting-materials/ (need password)

http://www.kdd.org/kdd2014/

Google’s fact-checking bots build vast knowledge bank – tech – 20 August 2014 – New Scientist

August 31, 2014

http://www.newscientist.com/article/mg22329832.700-googles-factchecking-bots-build-vast-knowledge-bank.html#.VAPjsWRdVCB

PLOS Computational Biology: Improving Breast Cancer Survival Analysis through Competition-Based Multidimensional Modeling

August 31, 2014

– apply to metabric consortium
– 17K clin feat. + ~50K gene exp. + ~30K CNVs ==to-predict==> 10yr survival – uses CI instead of AUC for real valued predictions
– combine collaboration & competition to beat the baseline (cox regression on only clinical features)
– mol. feat. on their own don’t work well due to the curse of dimensionality – features more important than the learning method

http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003047

Pandey mentions: Cancer Survival Analysis through
Competition-Based…Modeling, using Human #Ensembles
http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003047 #kdd2014

CPTAC – Office of Cancer Clinical Proteomics Research – National Cancer Institute

August 31, 2014

contains proteomics on some of the TCGA samples
http://proteomics.cancer.gov/programs/cptacnetwork

Laboratory of Computational Proteomics – Tools – Quilts

August 31, 2014

http://www.fenyolab.org/tools/tools.html

QT:{{”
QUILTS is a tools for creating sample specific protein sequence databased. It uses genomic and transcriptomic information to create comprehensive sample specific protein database that supports the identification of novel proteins, resulting from single nucleotide variants, splice variants and fusion genes.
“}}

Similar to the alleleseq personal genome for proteomics

Fenyo: Nice discussion of Quilts Tools for making up sample specific protein databases to identify novel proteins in cancer. Similar to personal genome construction #kdd2014 #biokdd

Fenyo: Quilts Tools for sample-specific DBs to identify novel proteins in cancer. Similar to personal genome construction #kdd2014 #biokdd

The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups : Nature : Nature Publishing Group

August 31, 2014

metabric consortium

gene expression & copy number data available and survival data (on request) for the 4 main breast cancer types (basal, her2 , luma, lumb)

similar to TCGA but from the UK

Allows construction of discovery & validation sets to compare segregation of survival with mRNA level

compare segreg. of survival with inferred protein activity v mRNA level

BMC Bioinformatics | Full text | BicSPAM: flexible biclustering using sequential patterns

August 31, 2014

Related to BIP KDD talk, dealing with overlapping biclusters http://www.biomedcentral.com/1471-2105/15/130

BMC Bioinformatics | Full text | BicSPAM: flexible biclustering using sequential patterns

August 31, 2014

http://www.biomedcentral.com/1471-2105/15/130

Dr Fenyo in NYU Proteomic talks

August 31, 2014

http://www.fenyolab.org/presentations/presentations.html
https://www.youtube.com/watch?v=wviPWfF5bdw