A method may reach AUC below 0.5, meaning that the hit score performs worse than random. Different from binary classification, we must not invert ‘predictions’ to reach a better AUC. Logic dictates that the directionality of the hit score (such as, ‘high scores are good’) is fixed by...
However, no systematic annotation pipeline has been developed to interpret biological meaning based on the accumulation of copy number change across the genome associated with a phenotype of interest. In this study, we develop a comprehensive and systematic pipeline for annotating copy number variants ...
Whereas 16 genes modulated by HIV-1 gp120 have previously been associated with HIV replication and/or envelope signaling, the remaining genes are of unknown function or have never been associated with HIV-1 or gp120. Converting this list of genes into biological meaning requires the gathering of...
ALFA can be installed from pip or conda, in this case, an executable is provided meaning that the user can call the program with "alfa" directly. Otherwise, if ALFA is installed from a GitHub clone, the user has to type "python alfa.py". ...
Their meaning is explained in the following table: Position Criteria 1 Bit score of the blast result is >50 and e-value is <e-10 2 Overlap of the blast result is >60% 3 Top token score of assigned HRD is >0.5 2.4.2 Fasta-Format To set AHRD to write its output in FASTA-...
Each biological concept has a number of possible names associated (i.e. all the text forms that annotators have recognised in the documents), but has unambiguous meaning and can be associated with a unique database identifier. Namely, we have used the EcoCyc knowledge base, a key resource ...
In this way, words that have the same meaning share a similar representation, and using simple operations like the cosine distance between two vectors can help to group similar concepts together. This can significantly improve the generalization ability of models learned on limited amounts of data,...
has the same meaning as the formal concept used to annotate it. In many other corpora, text is marked up even if the concept denoted is more specific than the concept used to annotate it; this approach is sometimes referred to as marking up all mentions “within the domain of” the given...
Specifically, the annotations should be accurate by providing information that reflects the reality within the input, and be complete, meaning that they provide all the information required for the given task, e.g., all pixels from an image have an associated label in a segmentation task. For ...
Blast2GO does not only generate functional annotations. You can interrogate the biological meaning of your data with different graphical and statistical functions. Vocabularies. Gene Ontology Terms, InterPro Domains, RFAM IDs and Enzyme Codes are supported by Blast2GO. ...