Query Results

Number of results 10000
Lowest scoring result 20.40532
Abstracts of results results.html
Complete abstracts of the articles in Medline predicted to be relevant (limited number per page).
Abstracts of all results ZIP file or all_results.html
All result abstracts on a single page. (can take a long time to load - downloading the zip file is recommended)
Abstracts of input examples inputs.html
Complete abstracts of the Medline records given as relevant training examples. They have been ranked by classifier scores.
PubMed IDs of results results.txt
PubMed IDs and scores of classifier predictions, ranked by decreasing score.
PubMed IDs of inputs inputs.txt
PubMed IDs and scores of the relevant training examples.
Started at 2009/08/25 14:25:34 GMT
Time at which query was started
Finished at 2009/08/25 14:33:27 GMT
Time at which this file was written.
Feature score method scores_laplace_split
Name of the method used to calculate feature scores. Docstring for the method: For feature probabilities we use a Laplace prior, of 1 success and 1 failure in total, split between the classes according to size. This avoids problems with class skew.
Min Information Gain 2e-05
We exclude features with less than this value of Information Gain.
Base score -58.6694956223
The log likelihood ratio of an empty article (one in which every feature failed to occur).
Prior score -8.05337364949
The log of the prior probability ratio for an article being relevant versus irrelevant (added to log likelihood ratio to obtain the final score). Equals the logit of the estimated prevalence of relevant articles in Medline (which may be estimated from the input size or specified separately).
Limit 10000
The maximum number of results to include.
Threshold -30.0
Default Naive Bayes classification threshold is zero. This threshold is the minimum log probability ratio for predicting an article to be relevant.
Minimum date 20070101
The minimum date considered when parsing Medline (both when making feature counts, and when querying)

Feature Statistics

Quantity Relevant Docs Irrelevant Docs
Number of documents 430 1355229
Number of selected, occurring features 13590 42456
Total occurrences of selected features 50842 91648131
Selected features per Medline record 118.237 67.626
Of the considered feature types, 42754 features are selected out of 1811480 occurring at least once in training data. The aggressivity of selection is 42.370. The complete database lists 3703762 potential features.

Features with high TF.IDF

Features with TF.IDF above 0.2 or 0.3 could make good keywords. TF.IDF is term frequency times inverse document frequency, where we treat the set of input citations as a single document

TF-IDF Type Term Term ID Score Pos Neg
0.03 w Microarray 1384 5.64 278 8760
0.02 mesh Oligonucleotide Array Sequence Analysis 1436 4.90 218 10266
0.02 w Genes 1395 3.87 298 61121
0.02 mesh Gene Expression Profiling 1435 4.30 175 12479
0.02 w Expression 2275 3.54 335 125234
0.01 w Gene 1420 3.23 291 103707
0.01 qual genetics 799 3.02 347 229715
0.01 w Cells 213 2.38 266 176453
0.01 qual metabolism 199 2.54 340 311111
0.01 w Transcription 6546 2.92 124 28859
0.01 w Analysis 825 2.05 248 203013
0.01 w Cell 384 2.02 217 160864
0.01 mesh Mice 3193 2.20 164 86300
0.01 w Up-regulated 6506 4.03 82 5660
0.01 w Transcriptional 5946 3.25 97 15106
0.01 w Genome-wide 7493 4.33 74 3697
0.01 w Profiling 1389 3.88 78 6194
0.01 mesh Gene Expression Regulation 5970 3.08 97 17937
0.01 w Microarrays 1434 4.30 70 3580
0.01 w Identified 2348 1.97 157 100182