- Sep 2020
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Local file Local file
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0.6
0.6% ??
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the United Kingdom
indigenous population
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- Feb 2020
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people.csail.mit.edu people.csail.mit.edu
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The parametervector for a classcis~θc={θc1,θc2,...,θcn}
needed for CNB formula
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However, the class probabilities tend to beoverpowered by the combination of word probabilities,so we use a uniform prior estimate for simplicity
what is the uniform prior estimate for the class?
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- Dec 2019
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academic.oup.com academic.oup.com
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ages 2–10 y
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average stature
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height velocity
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0.8 cm/mo (10 cm/y)
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1 y
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median height velocity
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1 y of life
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infants
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≈1.7 cm/mo (20 cm/y)
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≈3.7 cm/mo (44 cm/y)
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shortly after birth
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average stature
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median height velocity
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average stature
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puberty
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infancy
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height velocity
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average stature
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height velocity
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average stature
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height
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average stature
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height
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48.5 ± 0.1; n = 595
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47.4 ± 0.2 cm; n = 242
value, sd, n
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birth length
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average stature
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mean birth length
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average stature
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Height
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average-stature
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median weight-for-age
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average stature
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5th
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- Nov 2019
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www.sciencedirect.com www.sciencedirect.com
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Ref. [44], and for BioNLP, in Ref. [45].
useful for me
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Add handling of negation and hedging
key
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(or the entire document)
hopefully
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affects recall
halved
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ActualRelatedNot RelatedPredictedRelated2010Not Related2731Precision = 67%Recall = 43%
i am not sure that this is an improvement if you are losing 57% of your recall! depends of what you value more, novel relationship discover or accuracy
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define a set of selected features for each one.
what features? PO? symantics? entity patterns?
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OMIM MorbidMap
not very surprising due to the size of omim and the inevitable gaps in the data
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The simple NER approach that we applied to medical records, leveraging Uruguayan terminology dictionaries from SNOMED CT, produced the results listed in Table 3 for the domains of disease and finding entities. A physician manually evaluated the expected vs. found entities for each medical record, considering an entity as correctly identified when its recognized name was exactly or nearly exactly as expected. We obtained a precision of 94% when counting entity repetitions (more than one mention), and 87% leaving repetitions apart
not mentioning negation which is important
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Fig. 5. Structure of the mini ontology: A graph with nodes representing entities and edges representing relations between them.
i note there is no connection between pubmed and phenotype which suggests that the genotype-phenotype is omim based. OMIM has quite shallow phenotyping as i am aware
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hipertensión arterial (English arterial hypertension), the dictionary-based approach correctly recognizes hipertensión arterial disease in Spanish, but the CoreNLP node recognized both hipertensión (English hypertension) and arterial only individually.
sounds like a language incompatibility as arterial hypertension is not a term used in english medicine
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Since an actual set of medical records in Spanish was not available for research, we manually transcribed 109 clinical notes with physician observations, from actual patient cases, used for medical education.
this type of case will be succinct and cherry picked for educational purposes - will need real life validation
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The knowledge base can be queried in two ways: 1) starting from the medical record, and leading to related entities (like genes); or 2) starting from genes of interest (previously obtained from patients genome or exome analysis), and leading to related diseases and substances
This all sounds very useful as an approach to a new case clincally
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Mini Ontology, is permanently updated from a corpus that contains novel articles, on a daily basis
contemperaneous
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{relation_type, entitity_1, entity_2}.
must predefine the relations
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Wu et al. [22] compare alternatives based on word embeddings to improve NER results in BioNLP, against existent proposals based on CRF, MaxEnt, and SVM. Chiu et al. [23] devise guidelines for good word2vec based embeddings, both CBOW and skip-gram, working on PubMed and the PMC corpus. For auxiliary tasks, these authors use GeniaSS as a sentence splitter and NLTK [24] for word tokenizing
The challenges of word embedding and text processing in a specialised domain
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GeniaSS as a sentence splitter
Will be useful to add to my pipeline
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Genia Tagger [13] has been frequently used both for part of speech tagging and named entity recognition (NER) in the BioNLP domain. For Spanish medical documents, Genia Tagger has been used in conjunction with Freeling [14] for entity recognition and automatic annotation [15]
NER annotations
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HGVS
genomic variant ontolgy
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OMIM
genotype phenotype ontology
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SNOMED CT,
medical language ontology - very large
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The goal of this work is to provide tools for the medical geneticist that optimize his/her access to the latest research pertaining to a specific patient (or to specific genomic information)
SUggesting the reverse and forward genetics genotype - phenotype (need high prob variants) phenotype - genotype (need good phenotyping) approaches
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This makes attempts to become properly acquainted with the latest findings that could be relevant to a specific patient particularly challenging
Impossible?
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Are there known substance/drug interactions?;
less relevant in clinical genetics
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Is this variant pathogenic?; With which phenotypes/diseases is this variant associated?;
All relevant
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The literature requires reviewing in such a way that will allow the gathering of the latest findings
Case reports sequencing cohorts case series reviews and meta-analysis contemporaneous literature is key for rare conditions
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A patient genome can be sequenced in a few hours or even minutes [1],
Not much use without the analysis that supports any interpretation
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PubMed abstracts
Key advantage we should have with full text analysis
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reader.elsevier.com reader.elsevier.com
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A patient genome can be sequenced in a few hours or evenminutes [1],
I would dispute this. The analysis is the useful part
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- Jun 2019
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europepmc.org europepmc.org
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Nonsyndromic intellectual disability
Tags
Annotators
URL
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science.sciencemag.org science.sciencemag.org
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P = 0.01
doesn't match the figure
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- May 2019
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Local file Local file
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Enlarged ventricles
ventriculomegaly
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ituitarystalk hypoplasi
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Patient 1
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general or cortical atrophy
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neuronal migration defect
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enlarged cisterna magna
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- Apr 2019
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screening, surveillance, and interventional measures,
will need to consider locally available options for all of these
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excess toxicities withparticular cytotoxic therapies
indication for genetic testing
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