This model is a fine-tuned model of [BiomedNLP-PubMedBERT-base-uncased-abstract-fulltext](https://arxiv.org/abs/2007.15779) ([hugging-face card](https://huggingface.co/microsoft/BiomedNLP-PubMedBERT-base-uncased-abstract-fulltext)). The current model was developed for the web-based [ANDDigest](https://anddigest.sysbio.ru/) system for the classification of the short names of genes and proteins in texts on the basis of their context. The analyzed name should be replaced in text with <andsystem-candidate> tag.<br>
<br>
<b>Input:</b><br>
Any biomedical text where a name of classified object is replaced with <andsystem-candidate> tag, for example, [this](https://pubmed.ncbi.nlm.nih.gov/35107961/) pubmed abstract:<br>
<i>Plastic – (not) fantastic? Impact of bisphenol A on functioning of mammalian oocytes and embryos Bisphenol A is a monomeric organic compound belonging to phenols. It is widely used in the production of resins, polycarbonates and plastics. Mass production of this compound contributed to its widespread presence in the environment, and thus - in the organisms of animals and humans. <b>\<andsystem-candidate\></b> belongs to xenoestrogens, synthetic compounds exerting an estrogen-like effect on cells. BPA can therefore disrupt the functioning of animal (including human) organisms. This article focuses on the impact of BPA on selected aspects of mammalian fertility. Recent literature data indicate that BPA disturbs several processes in oocytes and embryos, including epigenetic modifications, energy metabolism and spindle assembly, and as a result, decreases their developmental competence. We discuss the latest data on the influence of BPA on cellular processes taking place in oocytes and early embryos and describe molecular mechanisms responsible for this effect. We also discuss the significance of the results obtained from experiments conducted in vitro and/or on animal models in the context of BPA impact on fertility of women.</i>
<br>
<br>In this example <i>BPA</i>, which is a chemical compound bisphenol A, was replaced with <i>\<andsystem-candidate\></i>. Please keep in mind that maximum length of input sequence for BERT is limited to 512 tokens.
<br>
<b>Output:</b><br>
<i>LABEL_0</i> refers to the probability of the <i>FALSE</i> recognition, i.e. if the context of \<andsystem-candidate\> doesn't corresponds to the context specific for genes or proteins.<br>
<i>LABEL_1</i> refers to the probability of the <i>TRUE</i> recognition, i.e. when the context of \<andsystem-candidate\> corresponds to the context specific for genes or proteins.<br>
<br>

The optimal threshold value for the short names of genes or proteins for the LABEL_1, was calculated using a gold standard (add link). It is<b> \>\= 0.9999139308929443</b>.<br>
<br>
The Mathew Correlation Coefficient of the model for the long names (\>\= 15 symbols) is 0.982.<br>
The ROC AUC value of the model, calculated for the short names (\<\= 4 symbols) is 0.939.
{"tags": ["ANDDigest", "ANDSystem"], "extra_gated_fields": {"I agree to share my contact information": "checkbox"}, "widget": [{"text": "Plastic \u2013 (not) fantastic? Impact of bisphenol A on functioning of mammalian oocytes and embryos Bisphenol A is a monomeric organic compound belonging to phenols. It is widely used in the production of resins, polycarbonates and plastics. Mass production of this compound contributed to its widespread presence in the environment, and thus - in the organisms of animals and humans. <andsystem-candidate> belongs to xenoestrogens, synthetic compounds exerting an estrogen-like effect on cells. BPA can therefore disrupt the functioning of animal (including human) organisms. This article focuses on the impact of BPA on selected aspects of mammalian fertility. Recent literature data indicate that BPA disturbs several processes in oocytes and embryos, including epigenetic modifications, energy metabolism and spindle assembly, and as a result, decreases their developmental competence. We discuss the latest data on the influence of BPA on cellular processes taking place in oocytes and early embryos and describe molecular mechanisms responsible for this effect. We also discuss the significance of the results obtained from experiments conducted in vitro and/or on animal models in the context of BPA impact on fertility of women.", "example_title": "BPA"}, {"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. Key Words: Neurobrucellosis, Demyelination, White matter.", "example_title": "fever"}, {"text": "A unique human immunodeficiency virus culture secreting soluble gp160. A clone of the HUT78 cell line, chronically infected with the HIV-1 isolate HTLV-III451, has been demonstrated to secrete unprocessed HIV-1 envelope precursor protein gp160 as well as mature gp120. Further, when grown in serum-free defined medium these cells released approximately five times the amount of virus compared with cultures in normal medium. These proteins corresponded in their immunologic reactivities with the respective envelope proteins of the HTLV-IIIB isolate. They formed high-affinity soluble complexes with the <andsystem-candidate> and inhibited the syncytium formation induced by HTLV-IIIB on CD4-positive cells. This is the first description of an HIV-1 culture system capable of shedding into the medium native gp160 that is soluble in the absence of detergents.", "example_title": "CD4 antigen"}]}
transformers pytorch bert text-classification ANDDigest ANDSystem arxiv:2007.15779 autotrain_compatible endpoints_compatible region:us
TAGS
#transformers #pytorch #bert #text-classification #ANDDigest #ANDSystem #arxiv-2007.15779 #autotrain_compatible #endpoints_compatible #region-us 

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 genes and proteins in texts on the basis of their context. The analyzed name should be replaced in text with <andsystem-candidate> tag.<br>
<br>
<b>Input:</b><br>
Any biomedical text where a name of classified object is replaced with <andsystem-candidate> tag, for example, this pubmed abstract:<br>
<i>Plastic – (not) fantastic? Impact of bisphenol A on functioning of mammalian oocytes and embryos Bisphenol A is a monomeric organic compound belonging to phenols. It is widely used in the production of resins, polycarbonates and plastics. Mass production of this compound contributed to its widespread presence in the environment, and thus - in the organisms of animals and humans. <b>\<andsystem-candidate\></b> belongs to xenoestrogens, synthetic compounds exerting an estrogen-like effect on cells. BPA can therefore disrupt the functioning of animal (including human) organisms. This article focuses on the impact of BPA on selected aspects of mammalian fertility. Recent literature data indicate that BPA disturbs several processes in oocytes and embryos, including epigenetic modifications, energy metabolism and spindle assembly, and as a result, decreases their developmental competence. We discuss the latest data on the influence of BPA on cellular processes taking place in oocytes and early embryos and describe molecular mechanisms responsible for this effect. We also discuss the significance of the results obtained from experiments conducted in vitro and/or on animal models in the context of BPA impact on fertility of women.</i>
<br>
<br>In this example <i>BPA</i>, which is a chemical compound bisphenol A, was replaced with <i>\<andsystem-candidate\></i>. Please keep in mind that maximum length of input sequence for BERT is limited to 512 tokens.
<br>
<b>Output:</b><br>
<i>LABEL_0</i> refers to the probability of the <i>FALSE</i> recognition, i.e. if the context of \<andsystem-candidate\> doesn't corresponds to the context specific for genes or proteins.<br>
<i>LABEL_1</i> refers to the probability of the <i>TRUE</i> recognition, i.e. when the context of \<andsystem-candidate\> corresponds to the context specific for genes or proteins.<br>
<br>

The optimal threshold value for the short names of genes or proteins for the LABEL_1, was calculated using a gold standard (add link). It is<b> \>\= 0.9999139308929443</b>.<br>
<br>
The Mathew Correlation Coefficient of the model for the long names (\>\= 15 symbols) is 0.982.<br>
The ROC AUC value of the model, calculated for the short names (\<\= 4 symbols) is 0.939.
TAGS
#transformers #pytorch #bert #text-classification #ANDDigest #ANDSystem #arxiv-2007.15779 #autotrain_compatible #endpoints_compatible #region-us 

passage: TAGS
#transformers #pytorch #bert #text-classification #ANDDigest #ANDSystem #arxiv-2007.15779 #autotrain_compatible #endpoints_compatible #region-us 
