o RÅ€gäã@sŠdZddlZddlmZe de¡z ddlZddlZWney.ddlm Z e dƒd‚wGdd„dƒZ dd d „Z d d „Z d d„Z dS)a£Code for doing logistic regressions (DEPRECATED). Classes: - LogisticRegression Holds information for a LogisticRegression classifier. Functions: - train Train a new classifier. - calculate Calculate the probabilities of each class, given an observation. - classify Classify an observation into a class. This module has been deprecated, please consider an alternative like scikit-learn instead. éN)ÚBiopythonDeprecationWarningzŒThe 'Bio.LogisticRegression' module is deprecated and will be removed in a future release of Biopython. Consider using scikit-learn instead.)ÚMissingPythonDependencyErrorzYPlease install NumPy if you want to use Bio.LogisticRegression. See http://www.numpy.org/c@seZdZdZdd„ZdS)ÚLogisticRegressionz’Holds information necessary to do logistic regression classification. Attributes: - beta - List of the weights for each dimension. cCs g|_dS)zInitialize the class.N)Úbeta)Úself©rúJ/var/www/html/myenv/lib/python3.10/site-packages/Bio/LogisticRegression.pyÚ__init__4s zLogisticRegression.__init__N)Ú__name__Ú __module__Ú __qualname__Ú__doc__r rrrrr,s rcCsüt|ƒt|ƒkr tdƒ‚t|ƒ}|ddhkrtdƒ‚|dur d}t|ƒt|dƒd}}|dks5|dkr9tdƒ‚t ||f|¡}||dd…dd…f<t |¡}t ||¡} t ||¡} d} d } d } d}d}}|| krðt t  | |¡¡}|d|}| t  |¡d| t  d|¡}t |ƒ}|durš|t |ƒ|dur²||kr¨| d } |} t  ||¡| kr²nB|| }}|d7}t |¡|}t  || |¡}t  t  ||¡|¡}tj ||¡}t  | d ¡d krè|| 9}| |7} || ksltd ƒ‚tƒ}t| ƒ|_|S)a^Train a logistic regression classifier on a training set. Argument xs is a list of observations and ys is a list of the class assignments, which should be 0 or 1. xs and ys should contain the same number of elements. update_fn is an optional callback function that takes as parameters that iteration number and log likelihood. z$xs and ys should be the same length.rézClasses should be 0's and 1'sNÚdz.No observations or observation of 0 dimension.iôg{®Gáz„?çð?g@gü©ñÒMbP?zDidn't converge.)ÚlenÚ ValueErrorÚsetÚnpÚonesÚ transposeÚasarrayÚzerosÚexpÚdotÚlogÚsumÚiterÚfabsÚidentityÚnumpyÚlinalgÚsolveÚ RuntimeErrorrÚlistr)ÚxsÚysÚ update_fnÚtypecodeÚclassesÚNÚndimsÚXÚXtÚyrÚMAX_ITERATIONSÚCONVERGE_THRESHOLDÚstepsizeÚiÚold_betaÚold_llikÚebetaXÚpÚlogpÚllikÚWÚXtypÚXtWXÚdeltaÚlrrrrÚtrain9s^     $  ä r>cCs<t dg|¡}t t |j|¡¡}|d|}d||gS)zÇCalculate the probability for each class. Arguments: - lr is a LogisticRegression object. - x is the observed data. Returns a list of the probability that it fits each class. rr)rrrrr)r=Úxr5r6rrrÚ calculate„s   r@cCs"t||ƒ}|d|dkrdSdS)z%Classify an observation into a class.rr)r@)r=r?ÚprobsrrrÚclassify•s rB)NN)r ÚwarningsÚBiorÚwarnr rÚ numpy.linalgÚ ImportErrorrrr>r@rBrrrrÚs, ý   ÿýý K