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How to use transition_counts method in hypothesis

Best Python code snippet using hypothesis

functions.py

Source:functions.py

1#!/usr/bin/python2import numpy as np3import pdb4def initialize_mdp_data(num_states):5    """6    Return a variable that contains all the parameters/state you need for your MDP.7    Assume that no transitions or rewards have been observed.8    Initialize the value function array to small random values (0 to 0.10, say).9    Initialize the transition probabilities uniformly (ie, probability of10        transitioning for state x to state y using action a is exactly11        1/num_states).12    Initialize all state rewards and counts to zero.13    Args:14        num_states: The number of states.  This value is constant.15    Returns: The initial MDP parameters.  It should be a Python dict with the16        following key/value structure.  You may add more key/value pairs to this17        to make things simpler, but the autograders will only consider the18        following:19        {20        'transition_probs': np.ndarray, dtype=np.float64,21            shape=(num_states, num_actions, num_states). The MDP transition22            probability for each transition.23        'transition_counts': np.ndarray, dtype=np.float64,24            shape=(num_states, num_actions, num_states). The count of the number25            of times each transition was taken (Used for tracking transitions to26            later calculate avg_reward and transition_probs)27        'avg_reward': np.ndarray, dtype=np.float64, shape=(num_states,). The28            average reward for entering each MDP state.29        'sum_reward': np.ndarray, dtype=np.float64, shape=(num_states,). The30            summed reward earned when entering each MDP state (used to track rewards for later calculating avg_reward).31        'value': np.ndarray, dtype=np.float64, shape=(num_states,). The32            state-value calculated for each MDP state (after value/policy33            iteration).34        'num_states': Int.  Convenience value.  This will not change throughout35            the MDP and can be calculated from the shapes of other variables.36        }37    """38    num_actions = 2 # RIGHT AND LEFT ACTIONS39    mdp_data = {40        'transition_probs': None,41        'transition_counts': None,42        'avg_reward': None,43        'sum_reward': None,44        'value': None,45        'num_states': None46    }47    mdp_data['transition_probs'] = (1.0/num_states)*np.ones((num_states, num_actions, num_states))48    mdp_data['transition_counts'] = np.zeros((num_states, num_actions, num_states))49    mdp_data['avg_reward'] = np.zeros(num_states)50    mdp_data['sum_reward'] = np.zeros(num_states)51    mdp_data['value'] = np.random.uniform(low=0.0, high=0.1, size=(num_states,))52    mdp_data['num_states'] = num_states53    return mdp_data54def choose_action(state, mdp_data):55    """56    Choose the next action (0 or 1) that is optimal according to your current57    mdp_data. When there is no optimal action, return a random action.58    Args:59        state: The current state in the MDP60        mdp_data: The parameters for your MDP. See initialize_mdp_data.61    Returns:62        int, 0 or 1.  The index of the optimal action according to your current MDP.63    """64    right = mdp_data['transition_probs'][state, 0, :].dot(mdp_data['value'])65    left = mdp_data['transition_probs'][state, 1, :].dot(mdp_data['value'])66    action = 167    if right > left:68        action = 069    return action70def update_mdp_transition_counts_sum_reward(mdp_data, state, action, new_state, reward):71    """72    Update the transition count and reward sum information in your mdp_data. 73    Do not change the other MDP parameters (those get changed later).74    Record the number of times `state, action, new_state` occurs.75    Record the rewards for every `new_state`.76    Args:77        mdp_data: The parameters of your MDP. See initialize_mdp_data.78        state: The state that was observed at the start.79        action: The action you performed.80        new_state: The state after your action.81        reward: The reward after your action (i.e. reward corresponding to new_state).82    Returns:83        Nothing84    """85    mdp_data['transition_counts'][state, action, new_state] = mdp_data['transition_counts'][state, action, new_state] + 186    mdp_data['sum_reward'][new_state] = mdp_data['sum_reward'][new_state] + reward87    return88def update_mdp_transition_probs_avg_reward(mdp_data):89    """90    Update the estimated transition probabilities and average reward values in your MDP.91    Make sure you account for the case when a state-action pair has never92    been tried before, or the state has never been visited before. In that93    case, you must not change that component (and thus keep it at the94    initialized uniform distribution).95    96    Args:97        mdp_data: The data for your MDP. See initialize_mdp_data.98    Returns:99        Nothing100    """101    for i in range(len(mdp_data['transition_counts'])):102        for j in range(len(mdp_data['transition_counts'][i])):103            suma = mdp_data['transition_counts'][i, j].sum()104            if suma > 0.0:105                for k in range(len(mdp_data['transition_counts'][i][j])):106                    mdp_data['transition_probs'][i, j, k] = mdp_data['transition_counts'][i, j, k]/suma107    108    for i in range(len(mdp_data['avg_reward'])):109        if mdp_data['transition_counts'][i].sum() > 0.0:110            mdp_data['avg_reward'][i] = mdp_data['sum_reward'][i]/mdp_data['transition_counts'][:,:,i].sum() 111    return112def update_mdp_value(mdp_data, tolerance, gamma):113    """114    Update the estimated values in your MDP.115    Perform value iteration using the new estimated model for the MDP.116    The convergence criterion should be based on `TOLERANCE` as described117    at the top of the file.118    119    Args:120        mdp_data: The data for your MDP. See initialize_mdp_data.121        tolerance: The tolerance to use for the convergence criterion.122        gamma: Your discount factor.123    Returns:124        Nothing125    """126    current_diff = 9e10127    while current_diff > tolerance:128        right = mdp_data['transition_probs'][:, 0, :].dot(mdp_data['value'])129        left = mdp_data['transition_probs'][:, 1, :].dot(mdp_data['value'])130        #Bellman update131        value = mdp_data['avg_reward'] + gamma*np.maximum(right, left)132        current_diff = np.max(np.abs(value - mdp_data['value']))133        mdp_data['value'] = value    ...

deciphering_utils.py

Source:deciphering_utils.py

...39        i0 = i140        i += 141        42    return p43def compute_transition_counts(text, char_to_ix):44    """45    Computes transition counts for a given text, useful to compute if you want to compute 46    the probabilities again and again, using compute_log_probability_by_counts.47    48    Arguments:49    text: Text as a list of characters50    51    char_to_ix: character to index mapping52    53    Returns:54    transition_counts: transition_counts[i, j] gives number of times character j follows i55    """56    N = len(char_to_ix)57    transition_counts = np.zeros((N, N))58    c1 = text[0]59    i = 060    while i < len(text)-1:61        c2 = text[i+1]62        transition_counts[char_to_ix[c1],char_to_ix[c2]] += 163        c1 = c264        i += 165    66    return transition_counts67def compute_log_probability_by_counts(transition_counts, text, permutation_map, char_to_ix, frequency_statistics, transition_matrix):68    """69    Computes the log probability of a text under a given permutation map (switching the 70    charcter c from permutation_map[c]), given the transition counts and the text71    72    Arguments:73    74    transition_counts: a matrix such that transition_counts[i, j] gives the counts of times j follows i,75                       see compute_transition_counts76    77    text: text to compute probability of, should be list of characters78    79    permutation_map[c]: gives the character to replace 'c' by80    81    char_to_ix: characters to index mapping82    83    frequency_statistics: frequency of character i is stored in frequency_statistics[i]84    85    transition_matrix: probability of j following i stored at [i, j] in this matrix86    87    Returns:88    89    p: log likelihood of the given text90    """91    c0 = char_to_ix[permutation_map[text[0]]]92    p = np.log(frequency_statistics[c0])93    94    p_map_indices = {}95    for c1, c2 in permutation_map.items():96        p_map_indices[char_to_ix[c1]] = char_to_ix[c2]97    98    indices = [value for (key, value) in sorted(p_map_indices.items())]99    100    p += np.sum(transition_counts*np.log(transition_matrix[indices,:][:, indices]))101    102    return p103def compute_difference(text_1, text_2):104    """105    Compute the number of times to text differ in character at same positions106    107    Arguments:108    109    text_1: first text list of characters110    text_2: second text, should have same length as text_1111    112    Returns113    cnt: number of times the texts differ in character at same positions114    """115    116    cnt = 0117    for x, y in zip(text_1, text_2):118        if y != x:119            cnt += 1120            121    return cnt122def get_state(text, transition_matrix, frequency_statistics, char_to_ix):123    """124    Generates a default state of given text statistics125    126    Arguments:127    pretty obvious128    129    Returns:130    state: A state that can be used along with,131           compute_probability_of_state, propose_a_move,132           and pretty_state for metropolis_hastings133    134    """135    transition_counts = compute_transition_counts(text, char_to_ix)136    p_map = generate_identity_p_map(char_to_ix.keys())137    138    state = {"text" : text, "transition_matrix" : transition_matrix, 139             "frequency_statistics" : frequency_statistics, "char_to_ix" : char_to_ix,140            "permutation_map" : p_map, "transition_counts" : transition_counts}141    142    return state143def compute_probability_of_state(state):144    """145    Computes the probability of given state using compute_log_probability_by_counts146    """147    148    p = compute_log_probability_by_counts(state["transition_counts"], state["text"], state["permutation_map"], 149                                          state["char_to_ix"], state["frequency_statistics"], state["transition_matrix"])...

hmmlearn.py

Source:hmmlearn.py

1import sys2import os3import string4def get_data(inputfile):5    sentences = []6    with open(inputfile, 'r') as f:7        txt = f.readline()8        while txt:9            sentences.append(txt.split())10            txt = f.readline()11    return sentences12def get_probabilities(sentences):13    transitions, emissions = {}, {}14    transition_counts, emission_counts = {}, {}15    start = "Initial"16    end = "Finish"17    prev_tag = "None"18    transition_counts[start] = len(sentences) 19    transitions[start] = {}20    for sentence in sentences:21        for i in range(len(sentence)):22            index = sentence[i].rfind('/')23            word = sentence[i][:index].lower()24            tag = sentence[i][index + 1:]25            # Keep track of total tag emissions26            if tag in emission_counts:27                emission_counts[tag] += 128            else:29                emission_counts[tag] = 130            # Keep track of word - tag emissions31            if word in emissions:32                if tag in emissions[word]:33                    emissions[word][tag] += 134                else:35                    emissions[word][tag] = 136            else:37                emissions[word] = {}38                emissions[word][tag] = 139            # Keep track of transitions40            if i == 0:41                if tag in transitions[start]:42                    transitions[start][tag] += 143                else:44                    transitions[start][tag] = 145                prev_tag = tag46            else:47                if prev_tag in transitions:48                    if tag in transitions[prev_tag]:49                        transitions[prev_tag][tag] += 150                    else:51                        transitions[prev_tag][tag] = 152                    transition_counts[prev_tag] += 153                else:54                    transitions[prev_tag] = {}55                    transitions[prev_tag][tag] = 156                    transition_counts[prev_tag] = 157                prev_tag = tag 58            if i == (len(sentence) - 1):59                if tag in transitions:60                    if end in transitions[tag]:61                        transitions[tag][end] += 162                    else:63                        transitions[tag][end] = 164                    transition_counts[tag] += 165                else:66                    transitions[tag] = {}67                    transitions[tag][end] = 1  68                    transition_counts[tag] = 1   69    ecount = 070    for word in emissions:71        for tag in emissions[word]:72            emissions[word][tag] = float(emissions[word][tag] / emission_counts[tag])73            ecount += 174    tcount = 075    t_types = []76    for tag_from in transitions:77        temp = 078        for tag_to in transitions[tag_from]:79            if tag_to not in t_types:80                t_types.append(tag_to)81            temp += transitions[tag_from][tag_to]82            tcount += 183        transitions[tag_from]["Total"] = temp84        tcount += 185    return transitions, emissions, ecount, tcount, t_types86def create_model(transitions, emissions, ecount, tcount, num_types):87    with open('hmmmodel.txt', 'w') as f:88        f.write("Emission probabilities - word, TAG, float - #{0}\n".format(ecount))89        for word in emissions:90            for tag in emissions[word]:91                f.write("{0} {1} {2}\n".format(word, tag, emissions[word][tag]))92        f.write("Transition probabilities - TAG1, TAG2, float - #{0}\n".format(tcount))93        f.write("Transition types - #{0}\n".format(num_types))94        for tag_from in transitions:95            for tag_to in transitions[tag_from]:96                f.write("{0} {1} {2}\n".format(tag_from, tag_to, transitions[tag_from][tag_to]))97def main(argv):98    sentences = get_data(argv[0])99    transitions, emissions, ecount, tcount, transition_types = get_probabilities(sentences)100    create_model(transitions, emissions, ecount, tcount, len(transition_types))101if __name__ == "__main__":...

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