Difference between revisions of "WormBase-Caltech Weekly Calls"

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* What do we mean exactly by "defective" and how, specifically, is this distinct from "abnormal"?
 
* What do we mean exactly by "defective" and how, specifically, is this distinct from "abnormal"?
 
* Definitions include meanings or words:
 
* Definitions include meanings or words:
 +
** "Variations in the ability"
 
** "aberrant"
 
** "aberrant"
 +
** "defect"
 
** "defective"
 
** "defective"
** "defect"
 
 
** "defects"
 
** "defects"
 
** "deficiency"
 
** "deficiency"
 +
** "deficient"
 
** "disrupted"
 
** "disrupted"
 +
** "impaired"
 +
** "incompetent"
 
** "ineffective"
 
** "ineffective"
 
** "perturbation that disrupts"
 
** "perturbation that disrupts"
** "variations in the ability"
+
** ???
** failure to execute the characteristic response = abnormal?
+
** Failure to execute the characteristic response = abnormal?
 
** abnormal
 
** abnormal
 
** abnormality leading to specific outcomes
 
** abnormality leading to specific outcomes
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** failure
 
** failure
 
** failure OR delayed
 
** failure OR delayed
 +
** failure, slower OR late
 
** failure/abnormal
 
** failure/abnormal
 +
** reduced
 +
** slower

Revision as of 18:15, 12 September 2019

Previous Years

2009 Meetings

2011 Meetings

2012 Meetings

2013 Meetings

2014 Meetings

2015 Meetings

2016 Meetings

2017 Meetings

2018 Meetings


GoToMeeting link: https://www.gotomeet.me/wormbase1


2019 Meetings

January

February

March

April

May

June

July

August


September 12, 2019

Update on SVM pipeline

  • New SVM pipeline: more analysis and more parameter tuning
  • avoiding precision (and F-value) as a measure (dependent on ratio of positives and negatives in test set)
  • "dumb" machine starts out with precision above 0.6
  • G-value (Michael's invention); does not depend on distribution of sets
  • Applied to various data types
  • Analysis: 10-fold cross validation
    • Randomly select 10% pos and neg (without replacement) and repeat until all papers sampled
  • F-value changes over different p/n values; G-value does not (essentially flat)
  • Area Under the Curve (AUC): probability that a random positive scores higher than random negative
  • AUC values for many WB data types upper 80%'s into 90%'s
  • Ranjana: How many papers for a good training set? Michael: we don't know yet
  • Can't reproduce old training sets (for old SVM); provide Michael better training sets if you want improved SVM
  • If SVM still not good enough, Michael will work on deep neural networks (Tensor Flow)
  • Michael can provide training sets he has used recently

Clarifying definitions of "defective" and "deficient" for phenotypes

  • WB phenotype ontology has many "variant/abnormal" terms and distinct subclass terms for "defective/deficient"
  • Have tried to create a logical definition pattern for these terms, but the vagueness of the meaning of "defective" and how it is distinct from "abnormal" has stalled the process
  • What do we mean exactly by "defective" and how, specifically, is this distinct from "abnormal"?
  • Definitions include meanings or words:
    • "Variations in the ability"
    • "aberrant"
    • "defect"
    • "defective"
    • "defects"
    • "deficiency"
    • "deficient"
    • "disrupted"
    • "impaired"
    • "incompetent"
    • "ineffective"
    • "perturbation that disrupts"
    •  ???
    • Failure to execute the characteristic response = abnormal?
    • abnormal
    • abnormality leading to specific outcomes
    • fail to exhibit the same taxis behavior = abnormal?
    • failure
    • failure OR delayed
    • failure, slower OR late
    • failure/abnormal
    • reduced
    • slower