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arthegall + research-article   578

Zhu, et al. "Inferring Taxi Status Using GPS Trajectories"
If I had a million free hours, I'd be thinking of spending some of them on applying this to MBTA buses ("Inferring bus fullness using GPS trajectories.") Maybe someday.
mbta  idea  gps  arxiv  research-article  inference 
3 days ago by arthegall
Van Durme, Lall, "Probabilistic Counting with Randomized Storage" ICJAI, 2009.
I like the "TOMB Counter" name -- this is a reasonably important technique, and this is the first place I've found it referenced in the literature.
probabilistic-methods  morris-counter  bloom-filters  research-article  big-data  to-re-read 
4 days ago by arthegall
Zhu, Schadt, et al. "Stitching together Multiple Data Dimensions Reveals Interacting Metabolomic and Transcriptomic Networks That Modulate Cell Regulation" (PLoS Biology)
Someone on twitter posted a link to this as an example of actual "data integration." Mmm... color me skeptical (here "data integration" reads to me as a synonym for "ad hoc systems biology,") but I need to read it more closely.
data-integration  bioinformatics  eric-schadt  plos-biology  research-article  systems-biology 
6 days ago by arthegall
Frasconi et al. "kLog: A Language for Logical and Relational Learning with Kernels" (arXiv)
Also reading this morning -- unforch, the refs in their PDF are messed up, and their source-code is missing some import, so I can't recompile it (from .tex source) unaided. GRrrrr.
machinelearning  arxiv  research-article  learning  programminglanguage  to-read 
9 days ago by arthegall
DROPS - Algorithmic Differentiation Through Automatic Graph Elimination Ordering (ADTAGEO)
"Algorithmic Differentiation Through Automatic Graph Elimination Ordering (ADTAGEO) is based on the principle of Instant Elimination: At runtime we dynamically maintain a DAG representing only active variables that are alive at any time. Whenever an active variable is deallocated or its value is overwritten the corresponding vertex in the Live-DAG will be eliminated immediately by the well known vertex elimination rule [1]. Consequently, the total memory requirement is equal to that of the sparse forward mode."
automatic-differentiation  research-article  numerical-methods  algorithms 
9 days ago by arthegall
Phipps, Pawlowski, "Efficient Expression Templates for Operator Overloading-based Automatic Differentiation"
I'd via:chl this, if I didn't already have it open in my tabs. :-)
automatic-differentiation  arxiv  research-article  symbolic-methods  nudged  humor 
9 days ago by arthegall
Goodarzi et al. "Systematic discovery of structural elements governing stability of mammalian messenger RNAs" (Nature)
I'll be honest, I still shudder when I see the name "Saeed Tavazoie". (cf. http://www.ncbi.nlm.nih.gov/pubmed/15084257 )
saeed-tavazoie  genomics  expression-from-sequence  nature  research-article  personal 
10 days ago by arthegall
Need, Shashi et al. "Clinical application of exome sequencing in undiagnosed genetic conditions," Journal of Medical Genetics (2012)
"This study provides evidence that next-generation sequencing can have high success rates in a clinical setting, but also highlights key challenges. It further suggests that the presentation of known Mendelian conditions may be considerably broader than currently recognised." -- Looks like the authors are from Duke Medical School...
research-article  sequencing  exomes  clinical-genetics  biology  genetics  genomics  mendelian-disease 
11 days ago by arthegall
Fiskerstrand et al. "Familial Diarrhea Syndrome Caused by an Activating GUCY2C Mutation" NEJM (2012)
"Other causes include inflammatory bowel disease, infections, paraneoplastic hormones, celiac disease, malabsorption syndromes, and bacterial overgrowth in the small intestine. In addition to organic causes, psychological factors have an important effect on bowel function."
celiac-disease  genetics  disease  research-article  medicine  nejm 
13 days ago by arthegall
Stahl etl al. "Bayesian inference analyses of the polygenic architecture of rheumatoid arthritis," Nature Genetics (2012)
"Our results are consistent with simulated genetic models in which hundreds of associated loci harbor common causal variants and a smaller number of loci harbor multiple rare causal variants. These analyses suggest that GWAS will continue to be highly productive for the discovery of additional susceptibility loci for common diseases."
gwas  genetic-testing  arthritis  genetics  genomics  research-article  nature-genetics 
13 days ago by arthegall
Jones, Ruzzo, Peng, Katze, "A new approach to bias correction in RNA-Seq" (Bioinformatics, 2012)
"We present a new method to measure and correct for these influences using a simple graphical model. Our model does not rely on existing gene annotations, and model selection is performed automatically making it applicable with few assumptions."
bioinformatics  research-article  rna-seq  bias-correction  graphical-models  normalization 
16 days ago by arthegall
Kroenke, Spitzer, and Williams "The PHQ-9: Validity of a Brief Depression Severity Measure"
depression  psychology  measurement  statistics  medicine  research-article 
17 days ago by arthegall
Gal Elidan, "Inference-less Density Estimation using Copula Bayesian Networks" (arXiv)
arxiv  research-article  copula  bayesian-networks  graphical-models  machinelearning 
17 days ago by arthegall
[1203.3473] Lifted Inference for Relational Continuous Models
machinelearning  arxiv  graphical-models  research-article  lifted-inference 
17 days ago by arthegall
[1203.3494] Negative Tree Reweighted Belief Propagation
belief-propagation  research-article  machinelearning  arxiv  graphical-models 
17 days ago by arthegall
Judea Pearl, "On Measurement Bias in Causal Inference" (arXiv)
by:judea-pearl  arxiv  research-article  measurement  causality  inference 
17 days ago by arthegall
[1203.3534] Invariant Gaussian Process Latent Variable Models and Application in Causal Discovery
via:probably-cshalizi  arxiv  research-article  gaussian-processes  machinelearning  causality  graphical-models 
17 days ago by arthegall
Identifying differentially expressed transcripts from RNA-seq data with biological variation
<sigh> (cf. http://online.liebertpub.com/doi/abs/10.1089/cmb.2010.0267 -- which is, fwiw, a nearly-identical model, evaluated in an identical way. )
nothing-new-under-the-sun  citations  research-article  bioinformatics  sequencing  personal 
20 days ago by arthegall
[1203.3496] Dirichlet Process Mixtures of Generalized Mallows Models
machinelearning  arxiv  research-article  harr-chen  dirichlet-processes  mallows-models  ranking 
23 days ago by arthegall
A Maxent-Stress Model for Graph Layout: Some Examples
More graph-layouts.
via:?  graph-layout  graphs  visualization  ieee  research-article 
4 weeks ago by arthegall
Bachwerk, Vogel, "Modelling Social Structures and Hierarchies in Language Evolution" (arXiv)
language  arxiv  research-article  linguistics  social-networks  social-science  evolution 
4 weeks ago by arthegall
Blech, "On Compositional Reasoning for Guaranteeing Probabilistic Properties" (arXiv)
The title alone is enough to put it in my "to read" queue.
to-read  probabilistic-methods  arxiv  research-article  logic 
4 weeks ago by arthegall
[1204.3941] A Log-Linear Graphical Model for Inferring Genetic Networks from High-Throughput Sequencing Data
via:cshalizi  arxiv  research-article  graphical-models  regulatory-networks  genomics  machinelearning 
4 weeks ago by arthegall
Bille, Landau, Weimann, "Random Access to Grammar Compressed Strings"
arxiv  strings  algorithms  research-article  computerscience  compression  grammars 
4 weeks ago by arthegall
Cell - Personal Omics Profiling Reveals Dynamic Molecular and Medical Phenotypes
The "Personal Omics" paper.
cell  research-article  genomics  personalized-medicine  personal-genomics 
4 weeks ago by arthegall
[1204.3915] Theory and Inference for a Class of Observation-driven Models with Application to Time Series of Counts
via:cshalizi?  arxiv  counting  time-series  research-article  statistics 
4 weeks ago by arthegall
Kontorovich, Trachtenberg, "Efficiently decoding strings from their shingles" (arXiv)
To read.
arxiv  research-article  string-processing  computerscience  bioinformatics 
4 weeks ago by arthegall
Huang & Gelman, "Sampling for Bayesian computation with large datasets"
Why had I not read this already?
sampling  bayesian-methods  andrew-gelman  pdf  research-article  statistics  machinelearning  multilevel-modeling 
4 weeks ago by arthegall
Schadt, Woo, and Hao, "Bayesian method to predict individual SNP genotypes from gene expression data"
"We show that, not only can genotypic barcodes be derived from individual gene expression data sets that can in turn be used to identify the genotype vector corresponding to the given individual, but such barcodes also have the potential to reliably identify first-degree relatives and even reconstruct nuclear pedigrees directly from gene expression data." -- I think that the logical possibility of doing this is pretty obvious to anyone who's thought this data through (and there are a *lot* more examples of similar kinds of re-identification possible out there), but it's still awesome to see it actually carried out and demonstrated on real data.
genomics  eric-schadt  privacy  genotype  research-article  bioinformatics  data 
6 weeks ago by arthegall
Barretina et al. "The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity" (Nature)
An important new dataset. (Here is the site, from the Broad, where you can browse/download the data: http://www.broadinstitute.org/ccle/home ).
research-article  cancer  cle  nature  genomics  broad  novartis  work  drug-sensitivity  pharma  drug-discovery 
7 weeks ago by arthegall
Ahmed, Xing, "Timeline: A Dynamic Hierarchical Dirichlet Process Model for Recovering Birth/Death and Evolution of Topics in Text Stream"
arxiv  research-article  conversation  topic-models  nlp  eric-xing  dirichlet-process  graphical-models 
7 weeks ago by arthegall
[1203.3464] Gibbs Sampling in Open-Universe Stochastic Languages
Gibbs sampling for BLOG-like models. Stuart Russell is one of the authors.
stuart-russel  machinelearning  blog  probabilistic-methods  graphical-models  arxiv  research-article  gibbs-sampling 
7 weeks ago by arthegall
[1203.2570] Differential Privacy for Functions and Functional Data
"Previous work has focused mainly on methods for which the output is a finite dimensional vector, or an element of some discrete set. We develop methods for releasing functions while preserving differential privacy. Specifically, we show that adding an appropriate Gaussian process to the function of interest yields differential privacy."
larry-wasserman  differential-privacy  databases  arxiv  research-article  gaussian-processes 
7 weeks ago by arthegall
Genome Medicine | Full text | Locus Reference Genomic sequences: an improved basis for describing human DNA variants.
One of the original papers on LRG-- check out boxes 1-3, which provide great canned use-cases for variant naming and coordinate/version handling.
genomics  bioinformatics  locus-reference-genomic  research-article  sequence-variants  data-management 
8 weeks ago by arthegall
Wang, Hellerstein, et al. "BayesStore: managing large, uncertain data repositories with probabilistic graphical models."
Making me think about the old idea of using probabilistic relational models as a way of compressing a database-- shipping the graphical model across the network for distributed (noisy) joins.
database  graphical-models  prms  sql  idea  joe-hellerstein  research-article 
8 weeks ago by arthegall
[1203.0697] Learning High-Dimensional Mixtures of Graphical Models
"We now propose a method for learning the mixture components given n i.i.d. samples y_n
drawn from a graphical mixture model P(y). Our method proceeds in two stages. First, we estimate the graph G_∪ := U_{r}^{h=1} G_h, which is the union of the Markov graphs of the mixture. This is accomplished via a series of rank tests. Note that in the special case when G_h ≡ G_∪, this also gives the graph estimates of the component models. We then use the graph estimate hat{G}_∪ to obtain the pairwise marginals of the respective mixture components via a spectral decomposition method. Finally, we use the Chow-Liu algorithm to obtain tree approximations {T_h}_h of the individual mixture components." -- To do: review how this works in the context of gene expression experiments for transcription factor regulatory relationships, which are (presumably) mixtures of a couple different underlying models or modes.
gene-expression  bioinformatics  research-article  arxiv  via:cshalizi  graphical-models  mixture-models  machinelearning 
11 weeks ago by arthegall
PLoS ONE: Transcriptomic Analysis of Toxoplasma Development Reveals Many Novel Functions and Structures Specific to Sporozoites and Oocysts
"A single felid host is capable of shedding millions of oocysts, which can survive for years in the environment, are resistant to most methods of microbial inactivation during water-treatment and are capable of producing infection in warm-blooded hosts at doses as low as 1–10 ingested oocysts." --- Shudder.
toxoplasma-gondii  feline-behavior  cat-person  plos-one  research-article  biology  genomics  awful 
february 2012 by arthegall
Zhi, Chen "Statistical Guidance for Experimental Design and Data Analysis of Mutation Detection in Rare Monogenic Mendelian Diseases by Exome Sequencing" (PLoS ONE)
"... we present a statistical modeling framework to calculate the power, the probability of identifying truly disease-causing genes, under various inheritance models and experimental conditions, providing guidance for both proper experimental design and data analysis."
sequencing  plos  research-article  genomics  mendelian-disease  statistics  to-read 
february 2012 by arthegall
Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation
bioinformatics  rna-seq  differential-expression  expression-analysis  research-article 
february 2012 by arthegall
[1112.6045] Comparing intermittency and network measurements of words and their dependency on authorship
Other generic text features that can be used to determine authorship. 5th-grade science-fair project on steroids.
clustering  machinelearning  writing  authorship  classification  arxiv  research-article  nlp 
january 2012 by arthegall
PLoS ONE: Improving Transmission Efficiency of Large Sequence Alignment/Map (SAM) Files
compression  file-format  bioinformatics  genomics  sequence-analysis  research-article  plos-one 
january 2012 by arthegall
Yolanda Gil et al. "Expressive Reusable Workflow Templates"
reproducible-research  pdf  research-article  workflow 
december 2011 by arthegall
[1112.3257] Exact Computation of Kullback-Leibler Distance for Hidden Markov Trees and Models
hidden-markov-models  arxiv  research-article  divergence  kullback-leibler-distance 
december 2011 by arthegall
[1104.1605] Efficient Top-K Retrieval in Online Social Tagging Networks
"We first consider a key aspect of the problem, which is accessing the closest or most relevant users for a given seeker. We describe how this can be done on the fly (without any pre-computations) for several possible choices - arguably the most natural ones - of proximity computation in a user network."
social-networks  tagging  folksonomies  research-article  arxiv 
december 2011 by arthegall
[1111.4226] Joint Modeling of Multiple Related Time Series via the Beta Process
Alan Willsky.
time-series  arxiv  research-article  via:?  michael-jordan  learning  machinelearning  beta-process  probabilistic-methods 
december 2011 by arthegall
[1109.3701] Active Ranking using Pairwise Comparisons
arxiv  research-article  machinelearning  ranking  active-learning 
december 2011 by arthegall
[1109.5466] Optimal Sensor Placement for Intruder Detection
arxiv  research-article  sensor-networks  learning  systems  optimization  control 
december 2011 by arthegall
[1109.2938] State-of-the-Art in Sequential Change-Point Detection
change-point  statistics  arxiv  research-article  thesis  signal-processing 
december 2011 by arthegall
[1109.2229] A Learning Theory Approach to Non-Interactive Database Privacy
arxiv  research-article  privacy  database  data  learning  learning-theory 
december 2011 by arthegall
[1109.1880] Fundamentals of Stein's method
via:cshalizi  steins-method  arxiv  research-article  statistics 
december 2011 by arthegall
van Erven, Grunwald, Koolen, & dr Rooij "Adaptive Hedge"
arxiv  research-article  online-optimization  optimization  learning  machinelearning 
december 2011 by arthegall
Staley, "Using Inferential Robustness to Establish the Security of an Evidence Claim"
"I argue that robustness can be understood as a means of establishing the partial security of evidence claims." -- maybe could have some use, in these Watson-style many-paths-to-the-same-fact inference engines, often built on top of triple stores.
inference  epistemology  research-article  philosophy  watson  belief  knowledge 
december 2011 by arthegall
[1112.3062] Using Provenance to support Good Laboratory Practice in Grid Environments
provenance  data  reproducible-research  arxiv  research-article 
december 2011 by arthegall
Zellig Harris, "The structure of science information" (Journal of Biomedical Informatics)
Zellig Harris! Sweet!
via:cshalizi  science  language  grammar  research-article  informatics  linguistics 
december 2011 by arthegall
[1011.5287] Distributed Storage Allocations
"By using an appropriate code, successful recovery can be achieved whenever the total amount of data accessed is at least the size of the original data object. The goal is to find an optimal storage allocation that maximizes the probability of successful recovery."
coding  arxiv  research-article  genomics  idea  storage  data 
december 2011 by arthegall
Chiang et al. "Implementing a genomic data management system using iRODS in Wellcome Trust Sanger Institute"
iRODS paper for "reproducible research" in sequencing, from the Sanger Center.
irods  data  reproducible-research  sanger-center  bioinformatics  science  research-article 
december 2011 by arthegall
[0811.4458v2] Learning Class-Level Bayes Nets for Relational Data
Ah, this is the "Join Bayes Nets" paper, reworked...
via:cshalizi  bayesian-methods  bayesian-networks  arxiv  research-article  probabilistic-relational-models 
december 2011 by arthegall
Mitzenmacher, Vadhan, "Why Simple Hash Functions Work: Exploiting the Entropy in a Data Stream" (PDF)
hashing  michael-mitzenmacher  salil-vadhan  pdf  research-article  universal-hashing 
december 2011 by arthegall
Goodrich, Mitzenmacher, "Invertible Bloom Lookup Tables"
"We present a version of the Bloom filter data structure that supports not only the insertion, deletion, and lookup of key-value pairs, but also allows a complete listing of its contents with high probability, as long the number of key-value pairs is below a designed threshold."
arxiv  research-article  computerscience  bloom-filters  data-structures  invertible-bloom-lookup-tables 
december 2011 by arthegall
Baldi, Barionio, et al. "Countering Gattaca: Efficient and Secure Testing of Fully-Sequenced Human Genomes (Full Version)"
bioinformatics  genomics  privacy  research-article  gattaca  genetic-testing 
november 2011 by arthegall
GrOWL: A tool for visualization and editing of OWL ontologies
Found this in a compilation of Semantic Web papers -- feel like they get about 70% of the idea correct. Their notation for intersections and unions is wrong, and they don't have any notation for Everything, Nothing, or disjoint sets... but it's definitely a step in teh right direction.
owl  ontologies  visualization  semanticweb  research-article 
november 2011 by arthegall
A probability-based approach for the analysis of large-scale RNAi screens - Nature Methods
The "RSA" method for identifying genes form highthroughput siRNA screens. Basically, ranking plus some ad hoc p-value multiplications. <gACK>
bioinformatics  pharma  research-article  hts-screening  nature-publishing  rnai  doing-terrible-things-with-p-values 
september 2011 by arthegall
Romer, "Spurious Volatility in Historical Unemployment Data"
economics  history  christina-roemer  pdf  research-article  unemployment 
september 2011 by arthegall
Food-Miles and the Relative Climate Impacts of Food Choices in the United States - Environmental Science & Technology (ACS Publications)
research-article  energy  food  climate-change  science 
june 2011 by arthegall
[1103.5188] Differential Privacy: on the trade-off between Utility and Information Leakage
privacy  arxiv  research-article  database 
june 2011 by arthegall
Li et al. "The Sequence Alignment/Map format and SAMtools" (Bioinformatics, 2009)
(doi:10.1093/bioinformatics/btp352)
bioinformatics  samtools  bam-file-format  software  research-article 
may 2011 by arthegall
Hopkins, Groom, "The druggable genome" : Article : Nature Reviews Drug Discovery
(doi:10.1038/nrd892) People keep talking about this paper at work -- and Hopkins gave one of the plenaries at IDD this year. I think what this is, is just mapping a lot of the intermediate data that's useful for drug discovery down on to the "genomic coordinate system," and making it available in one location for browsing. Not sure how useful that really is; does it omit something key?
research-article  drug-discovery  genomics  science  annotation  nature  review 
may 2011 by arthegall
[1011.1703] Point process modeling for directed interaction networks
Yes.
delicious  tag-transmission  pet-ideas  arxiv  research-article  social-networks  knowledge-transmission 
may 2011 by arthegall
Wicks et al. "Accelerated clinical discovery using self-reported patient data collected online and a patient-matching algorithm" (Nature Biotechnology, 2011)
PatientsLikeMe in the research context. Self-reported symptoms, matching, and research results.
genetics  medicine  health-care  research-article  clinical-discovery  nature  patients-like-me 
may 2011 by arthegall
Guttman et al. "Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs" (Nature Biotech, 2010)
The research article behind Scripture.
research-article  nature  aviv-regev  broad-institute  transcription  genomics 
may 2011 by arthegall
Assessing the significance of chromosomal aberrations in cancer: Methodology and application to glioma
The paper that develops the GISTIC scoring method for genomic variation in cancer. This is showing up more and more frequently in some of what I'm dealing with at work, so time to read up on it...
gistic  cancer  genomics  research-article  genetic-variation  genetics 
may 2011 by arthegall
Rausch et al. "A consistency-based consensus algorithm for de novo and reference-guided sequence assembly of short reads" (Bioinformatics, 2009)
research-article  bioinformatics  sequencing  assembly 
may 2011 by arthegall
Tumour evolution inferred by single-cell sequencing : Nature : Nature Publishing Group
cancer  oncology  tumor  genomics  sequencing  nature  research-article  via:in-the-pipeline 
april 2011 by arthegall
Lee, Battle, Raina, and Ng, "Efficient sparse coding algorithms"
sparse-coding  machinelearning  least-squares  research-article  andrew-ng 
april 2011 by arthegall
"A General Framework for Representing, Reasoning and Querying with Annotated Semantic Web Data" (arxiv)
Axel Polleres is one of the authors.
axel-polleres  semanticweb  arxiv  research-article  reasoning  annotation 
march 2011 by arthegall
PLoS ONE: Standard Biological Parts Knowledgebase
sbol  igem  partsregistry  synthetic-biology  randy-rettberg  plos  research-article 
march 2011 by arthegall
PLoS ONE: Abundant Human DNA Contamination Identified in Non-Primate Genome Databases
If the contamination is from the researchers who collected or manipulated the samples, does that mean that we should be having them sign medical consent forms before publishing their data in public repositories? I'm only half-joking.
consent  bioinformatics  genomics  dna  contamination  plos  research-article 
february 2011 by arthegall
[1012.3795] Estimating Networks With Jumps
networks  estimation  eric-xing  arxiv  research-article  machinelearning  graphical-models  microarray-analysis  via:cshalizi  from delicious
february 2011 by arthegall
Groth, Gibson, and Velterop, "The Anatomy of a Nanopublication"
This is basically SWAN, but five years after the fact -- but drives home the point of how much fo a missed opportunity SWAN really was.
swan  publishing  rdf  semanticweb  science  nanopublications  research-article 
january 2011 by arthegall
Mortality among Patients Admitted to Hospitals on Weekends as Compared with Weekdays — NEJM
Another "patient mortality by time of year or day of week" paper.
medicine  mortality  research-article  journal-article  staffing  hospitals  timing-effects  from delicious
january 2011 by arthegall
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