tags:
- ANDDigest
- ANDSystem
extra_gated_fields:
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widget:
- text: >-
Intermittent obstruction of jejunostomy tube due to Ascaris lumbricoides
infection. A 45-year-old Costa Rican woman was seen for a jejunostomy tube
malfunction. There was no evidence of tube malposition or intestinal
obstruction. During endoscopy, a long worm was retrieved from the distal
duodenum; it was later confirmed to be Ascaris lumbricoides. After
treatment with <andsystem-candidate>, no further episodes of tube
occlusion were observed. This case reminds us of the importance of
considering helminthic infections and their atypical manifestations in
patients from endemic regions.
example_title: mebendazole
- text: >-
Neurobrucellosis Presenting with Features of Demyelinating Disorder in a
Pediatric Patient. Brucellosis is an endemic disease in Saudi Arabia,
which can present with variable clinical manifestations. It is a zoonotic
disease transmitted from animals to humans. Brucellosis is a multisystemic
disease that can present with any system involvement; And neurobrucellosis
is a serious complication, sometimes leading to permanent neurological
deficit, if treatment is not started promptly. Herein, we present a 6-year
boy with neurobrucellosis, who developed demyelination of cerebral white
matter and presented with <andsystem-candidate> and seizures.
example_title: fever
This model is a fine-tuned model of BiomedNLP-PubMedBERT-base-uncased-abstract-fulltext (hugging-face card). The current model was developed for the web-based ANDDigest system for the classification of the short names of drugs and metabolites in texts on the basis of their context (the name considered to be short if it's length is 4 symbols or less). The analyzed name should be replaced in text with tag.
Input:
Any biomedical text where a name of classified object is replaced with tag, for example, this pubmed abstract:
Intermittent obstruction of jejunostomy tube due to Ascaris lumbricoides infection. A 45-year-old Costa Rican woman was seen for a jejunostomy tube malfunction. There was no evidence of tube malposition or intestinal obstruction. During endoscopy, a long worm was retrieved from the distal duodenum; it was later confirmed to be Ascaris lumbricoides. After treatment with <andsystem-candidate>, no further episodes of tube occlusion were observed. This case reminds us of the importance of considering helminthic infections and their atypical manifestations in patients from endemic regions.
In this example mebendazole was replaced with <andsystem-candidate>. Please keep in mind that maximum length of input sequence for BERT is limited to 512 tokens.
Output:
LABEL_0 refers to the probability of the FALSE recognition, i.e. if the context of <andsystem-candidate> doesn't corresponds to the context specific for drugs or metabolites.
LABEL_1 refers to the probability of the TRUE recognition, i.e. when the context of <andsystem-candidate> corresponds to the context specific for drugs or metabolites.
The optimal threshold value for the short names of drugs or metabolites for the LABEL_1, was calculated using a gold standard (add link). It is >= 0.999992847442627.
The Mathew Correlation Coefficient of the model for the long names (>= 15 symbols) is 0.983.
The ROC AUC value of the model, calculated for the short names (<= 4 symbols) is 0.907.