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 names of biological pathways 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>Deficient Mismatch Repair and Lymphocytic Response to Tumor as Prognostic Markers in Stage II Colon Cancer Patients. OBJECTIVE: To investigate the relationship between colon cancer subtypes defined by the status of tumor-infiltrating lymphocytes and mismatch repair (MMR) combination with clinicopathological features and survival. STUDY DESIGN: Observational study. PLACE AND DURATION OF STUDY: Department of Medical Oncology, HaydarpaAŸa Numune Research and Training Hospital, Istanbul, Turkey, from July 2010 to March 2020. METHODOLOGY: Eighty-three patients with operated stage II colon cancer were included in the study. Pathology, surgery and oncological treatment and follow-up information were obtained from patient files; And statistical analyses were performed on overall survival . Tumor-infiltrating lymphocytes and mismatch repair status was determined with the help of immunohistochemistry. RESULTS: TIL-high and deficient <b><andsystem-candidate></b> status were detected in 26 patients (31.3%) and 21 patients (25.3%), respectively. Tumors were divided into four subgroups according to tumor-infiltrating lymphocytes and MMR status. TIL-high/deficient mmr tumors had the most favourable prognosis, while TIL-low/proficient MMR tumors exhibited poor overall survival. CONCLUSION: The combination of tumor-infiltrating lymphocytes and MMR could enable us to differentiate patients' survival outcomes in more details. Therefore, considering that the tumor-infiltrating lymphocytes and MMR status, evaluated by IHC, may be a cost-effective and effective option for risk classification in patients with stage II colon cancer. Key Word: Lymphocytic response, Mismatch repair, Prognosis, Tumor-infiltrating lymphocytes, Stage II cancer, Colon cancer.</i> <br> <br>In this example <i>MMR</i> abbreviation, which refers to the mismatch repair, 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 biological pathways.<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 biological pathways.<br> <br>

The optimal threshold value for the short names of biological pathways for the LABEL_1, was calculated using a gold standard (add link). It is<b> >= 0.999702513217926</b>.<br> <br> The Mathew Correlation Coefficient of the model for the long names (>= 15 symbols) is 0.987.<br> The ROC AUC value of the model, calculated for the short names (<= 4 symbols) is 0.877.