Notebook

In [1]:

import keras
from keras.models import Sequential, Model, load_model

from keras.layers import Dense, Dropout, Activation, Flatten, Input, Lambda
from keras.layers import Conv2D, MaxPooling2D, Conv1D, MaxPooling1D, LSTM, ConvLSTM2D, GRU, BatchNormalization, LocallyConnected2D, Permute
from keras.layers import Concatenate, Reshape, Softmax, Conv2DTranspose, Embedding, Multiply
from keras.callbacks import ModelCheckpoint, EarlyStopping, Callback
from keras import regularizers
from keras import backend as K
import keras.losses

import tensorflow as tf
from tensorflow.python.framework import ops

import isolearn.keras as iso

import numpy as np

import tensorflow as tf
import logging
logging.getLogger('tensorflow').setLevel(logging.ERROR)

import pandas as pd

import os
import pickle
import numpy as np

import scipy.sparse as sp
import scipy.io as spio

import matplotlib.pyplot as plt

import isolearn.io as isoio
import isolearn.keras as isol

from genesis.visualization import *
from genesis.generator import *
from genesis.predictor import *
from genesis.optimizer import *
import sklearn
from sklearn.decomposition import PCA
from sklearn.manifold import TSNE

from scipy.stats import pearsonr

import seaborn as sns

from matplotlib import colors

import editdistance

def subselect_list(li, ixs) :
    return [
        li[ixs[k]] for k in range(len(ixs))
    ]

class IdentityEncoder(iso.SequenceEncoder) :
    
    def __init__(self, seq_len, channel_map) :
        super(IdentityEncoder, self).__init__('identity', (seq_len, len(channel_map)))
        
        self.seq_len = seq_len
        self.n_channels = len(channel_map)
        self.encode_map = channel_map
        self.decode_map = {
            nt: ix for ix, nt in self.encode_map.items()
        }
    
    def encode(self, seq) :
        encoding = np.zeros((self.seq_len, self.n_channels))
        
        for i in range(len(seq)) :
            if seq[i] in self.encode_map :
                channel_ix = self.encode_map[seq[i]]
                encoding[i, channel_ix] = 1.

        return encoding
    
    def encode_inplace(self, seq, encoding) :
        for i in range(len(seq)) :
            if seq[i] in self.encode_map :
                channel_ix = self.encode_map[seq[i]]
                encoding[i, channel_ix] = 1.
    
    def encode_inplace_sparse(self, seq, encoding_mat, row_index) :
        raise NotImplementError()
    
    def decode(self, encoding) :
        seq = ''
    
        for pos in range(0, encoding.shape[0]) :
            argmax_nt = np.argmax(encoding[pos, :])
            max_nt = np.max(encoding[pos, :])
            seq += self.decode_map[argmax_nt]

        return seq
    
    def decode_sparse(self, encoding_mat, row_index) :
        raise NotImplementError()

#Plot joint histograms
def plot_joint_histo(measurements, labels, x_label, y_label, colors=None, n_bins=50, figsize=(6, 4), legend_outside=False, save_fig=False, fig_name="default_1", fig_dpi=150, min_val=None, max_val=None, max_y_val=None) :
    
    min_hist_val = np.min(measurements[0])
    max_hist_val = np.max(measurements[0])
    for i in range(1, len(measurements)) :
        min_hist_val = min(min_hist_val, np.min(measurements[i]))
        max_hist_val = max(max_hist_val, np.max(measurements[i]))
    
    if min_val is not None :
        min_hist_val = min_val
    if max_val is not None :
        max_hist_val = max_val

    hists = []
    bin_edges = []
    means = []
    for i in range(len(measurements)) :
        hist, b_edges = np.histogram(measurements[i], range=(min_hist_val, max_hist_val), bins=n_bins, density=True)
        
        hists.append(hist)
        bin_edges.append(b_edges)
        means.append(np.mean(measurements[i]))
    
    bin_width = bin_edges[0][1] - bin_edges[0][0]


    f = plt.figure(figsize=figsize)

    for i in range(len(measurements)) :
        if colors is not None :
            plt.bar(bin_edges[i][1:] - bin_width/2., hists[i], width=bin_width, linewidth=2, edgecolor='black', color=colors[i], label=labels[i])
        else :
            plt.bar(bin_edges[i][1:] - bin_width/2., hists[i], width=bin_width, linewidth=2, edgecolor='black', label=labels[i])
    
    plt.xticks(fontsize=14)
    plt.yticks(fontsize=14)
    
    plt.xlim(min_hist_val, max_hist_val)
    if max_y_val is not None :
        plt.ylim(0, max_y_val)

    plt.xlabel(x_label, fontsize=14)
    plt.ylabel(y_label, fontsize=14)

    if colors is not None :
        for i in range(len(measurements)) :
            plt.axvline(x=means[i], linewidth=2, color=colors[i], linestyle="--")

    if not legend_outside :
        plt.legend(fontsize=14, loc='upper left')
    else :
        plt.legend(fontsize=14, bbox_to_anchor=(1.04,1), loc="upper left")
    
    plt.tight_layout()
    
    if save_fig :
        plt.savefig(fig_name + ".eps")
        plt.savefig(fig_name + ".svg")
        plt.savefig(fig_name + ".png", dpi=fig_dpi, transparent=True)
    
    plt.show()

#Plot join histograms
def plot_joint_cmp(measurements, labels, y_label, plot_type='violin', colors=None, figsize=(6, 4), legend_outside=False, save_fig=False, fig_name="default_1", fig_dpi=150, min_y_val=None, max_y_val=None) :
    
    f = plt.figure(figsize=figsize)

    sns_g = None
    if colors is not None :
        if plot_type == 'violin' :
            sns_g = sns.violinplot(data=measurements, palette=colors, scale='width') #, x=labels
        elif plot_type == 'strip' :
            sns_g = sns.stripplot(data=measurements, palette=colors, alpha=0.1, jitter=0.3, linewidth=2, edgecolor='black') #, x=labels
            for i in range(len(measurements)) :
                plt.plot(x=[i, i+1], y=[np.median(measurements[i]), np.median(measurements[i])], linewidth=2, color=colors[i], linestyle="--")
        elif plot_type == 'bar' :
            for i in range(len(measurements)) :
                plt.bar([i], [np.percentile(measurements[i], 95)], width=0.4, color=colors[i], label=str(i) + ") " + labels[i], linewidth=2, edgecolor='black')
                plt.bar([i+0.2], [np.percentile(measurements[i], 80)], width=0.4, color=colors[i], linewidth=2, edgecolor='black')
                plt.bar([i+0.4], [np.percentile(measurements[i], 50)], width=0.4, color=colors[i], linewidth=2, edgecolor='black')
    else :
        if plot_type == 'violin' :
            sns_g = sns.violinplot(data=measurements, scale='width') #, x=labels
        elif plot_type == 'strip' :
            sns_g = sns.stripplot(data=measurements, alpha=0.1, jitter=0.3, linewidth=2, edgecolor='black') #, x=labels
        elif plot_type == 'bar' :
            for i in range(len(measurements)) :
                plt.bar([i], [np.percentile(measurements[i], 95)], width=0.25, label=str(i) + ") " + labels[i], linewidth=2, edgecolor='black')
                plt.bar([i+0.125], [np.percentile(measurements[i], 80)], width=0.25, linewidth=2, edgecolor='black')
                plt.bar([i+0.25], [np.percentile(measurements[i], 50)], width=0.25, linewidth=2, edgecolor='black')
    
    plt.xticks(np.arange(len(labels)), fontsize=14)
    plt.yticks(fontsize=14)
    
    #plt.xlim(min_hist_val, max_hist_val)
    if min_y_val is not None and max_y_val is not None :
        plt.ylim(min_y_val, max_y_val)

    plt.ylabel(y_label, fontsize=14)
    
    if plot_type not in ['violin', 'strip'] :
        if not legend_outside :
            plt.legend(fontsize=14, loc='upper left')
        else :
            plt.legend(fontsize=14, bbox_to_anchor=(1.04,1), loc="upper left")
    else :
        if not legend_outside :
            f.get_axes()[0].legend(fontsize=14, loc="upper left", labels=[str(label_i) + ") " + label for label_i, label in enumerate(labels)])
        else :
            f.get_axes()[0].legend(fontsize=14, bbox_to_anchor=(1.04,1), loc="upper left", labels=[str(label_i) + ") " + label for label_i, label in enumerate(labels)])
    
    plt.tight_layout()
    
    if save_fig :
        plt.savefig(fig_name + ".eps")
        plt.savefig(fig_name + ".svg")
        plt.savefig(fig_name + ".png", dpi=fig_dpi, transparent=True)
    
    plt.show()

#Load generated data from models to be evaluated

def load_sequences(file_path, split_on_tab=True, seq_template=None, max_n_sequences=1e6, select_best_fitness=False, predictor=None, batch_size=32) :
    seqs = []
    
    with open(file_path, "rt") as f :
        for l in f.readlines() :
            l_strip = l.strip()
            seq = l_strip
            if split_on_tab :
                seq = l_strip.split("\t")[0]
            
            if seq_template is not None :
                seq = ''.join([
                    seq_template[j] if seq_template[j] != 'N' else seq[j]
                    for j in range(len(seq))
                ])

            seqs.append(seq)
        
    if select_best_fitness and predictor is not None :
        onehots = np.expand_dims(np.concatenate([
            np.expand_dims(acgt_encoder.encode(seq), axis=0) for seq in seqs
        ], axis=0), axis=-1)

        #Predict fitness
        score_pred = predictor.predict(x=[onehots[..., 0]], batch_size=batch_size)
        score_pred = np.ravel(score_pred[:, 5])
        
        sort_index = np.argsort(score_pred)[::-1]
        seqs = [
            seqs[sort_index[i]] for i in range(len(seqs))
        ]
    
    return seqs[:max_n_sequences]

#Evaluate metrics for each model

def compute_metrics(seqs, n_seqs_to_test=960, batch_size=64, opt_len=90) :
    
    n_seqs_to_test = min(len(seqs), n_seqs_to_test)
    
    onehots = np.expand_dims(np.concatenate([
        np.expand_dims(acgt_encoder.encode(seq), axis=0) for seq in seqs
    ], axis=0), axis=1)

    #Predict fitness
    score_pred = saved_predictor.predict(x=[onehots[:n_seqs_to_test]], batch_size=batch_size)
    score_pred = np.ravel(score_pred[:, 0])
    
    return score_pred

from keras.backend.tensorflow_backend import set_session

def contain_tf_gpu_mem_usage() :
    config = tf.ConfigProto()
    config.gpu_options.allow_growth = True
    sess = tf.Session(config=config)
    set_session(sess)

contain_tf_gpu_mem_usage()

Using TensorFlow backend.

In [2]:

sequence_template = 'N' * 1000

problem_prefix = "dragonn_genesis_max_spi1"

n_seqs_to_test = 4000

In [3]:

#Specfiy file path to pre-trained predictor network

saved_predictor_model_path = "../../../seqprop/examples/dragonn/SPI1.classification.model.hdf5"

def _dummy_min_pred(y_true, y_pred) :
    return y_pred

saved_predictor = load_model(saved_predictor_model_path, custom_objects={
    'ambig_binary_crossentropy' : _dummy_min_pred,
    'precision' : _dummy_min_pred,
    'recall' : _dummy_min_pred,
    'specificity' : _dummy_min_pred,
    'fpr' : _dummy_min_pred,
    'fnr' : _dummy_min_pred,
    'fdr' : _dummy_min_pred,
    'f1' : _dummy_min_pred
})

saved_predictor = Model(
    inputs=saved_predictor.inputs,
    outputs = [saved_predictor.get_layer('dense_2').output]
)

saved_predictor.compile(
    loss='mse',
    optimizer=keras.optimizers.SGD(lr=0.1)
)


acgt_encoder = IdentityEncoder(1000, {'A':0, 'C':1, 'G':2, 'T':3})

In [13]:

#Trajectory comparison configuration

traj_dirs = [
    "samples/basinhopping_dragonn_max_spi1_10000_iters_dense_score/",
    
    "samples/genesis_dragonn_max_spi1_25000_updates_similarity_margin_02_earthmover_weight_01_target_700_fixed/",
    "samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/"
]

traj_file_funcs = [
    lambda i: "intermediate_iter_" + str((i+1) * 100) + ".txt",
    
    lambda i: "intermediate_epoch_" + str(i) + "_960_sequences.txt" if i < 10 else "intermediate_epoch_" + str((i-9)*10) + "_960_sequences.txt",
    lambda i: "intermediate_epoch_" + str(i) + "_960_sequences.txt" if i < 10 else "intermediate_epoch_" + str((i-9)*10) + "_960_sequences.txt"
]

traj_scale_generator_touch_funcs = [
    lambda i: (i+1) * 100,#4096,
    
    lambda i: (i+1) * 100 * 64 if i < 11 else (i-10)*10 * 100 * 64,
    lambda i: (i+1) * 100 * 64 if i < 11 else (i-10)*10 * 100 * 64
]

traj_names = [
    "Simulated Annealing (10000 iters)",
    
    "DEN (seq margin 0.2)",
    "DEN (seq/lat margin 0.2/0.9)"
]

In [14]:

#Load and predict sequence trajectory data

def load_and_aggregate_score(file_path, agg_mode='mean', perc=50, split_on_tab=True, seq_template=None, predictor=None, batch_size=32, max_n_sequences=960) :
    seqs = []
    
    print("Processing '" + str(file_path) + "'...")
    
    try :
        with open(file_path, "rt") as f :
            for l in f.readlines() :
                l_strip = l.strip()
                seq = l_strip
                if split_on_tab :
                    seq = l_strip.split("\t")[0]

                if seq_template is not None :
                    seq = ''.join([
                        seq_template[j] if seq_template[j] != 'N' else seq[j]
                        for j in range(len(seq))
                    ])

                seqs.append(seq)
        
        if len(seqs) > max_n_sequences :
            seqs = seqs[:max_n_sequences]
    
        score_pred = compute_metrics(
            seqs,
            n_seqs_to_test=len(seqs),
            batch_size=batch_size,
            opt_len=np.sum([1 if seq_template[j] == 'N' else 0 for j in range(len(seq_template))])
        )
        
        if agg_mode == "mean" :
            return np.mean(score_pred), score_pred
        elif agg_mode == "perc" :
            return np.percentile(score_pred, perc), score_pred
        else :
            return np.mean(score_pred), score_pred
        
    except FileNotFoundError :
        return np.nan, np.zeros(max_n_sequences)

max_n_files = 250

traj_ys = [
    [
        load_and_aggregate_score(
            traj_dirs[model_i] + traj_file_funcs[model_i](file_i),
            agg_mode='perc',
            seq_template=sequence_template,
            predictor=saved_predictor,
            batch_size=32,
            max_n_sequences=512
        )
        for file_i in range(max_n_files)
    ]
    for model_i in range(len(traj_dirs))
]

traj_gen_xs = [
    [
        traj_scale_generator_touch_funcs[model_i](file_i)
        for file_i in range(max_n_files)
    ]
    for model_i in range(len(traj_dirs))
]

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Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_margin_02_earthmover_weight_01_target_700_fixed/intermediate_epoch_2300_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_margin_02_earthmover_weight_01_target_700_fixed/intermediate_epoch_2310_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_margin_02_earthmover_weight_01_target_700_fixed/intermediate_epoch_2320_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_margin_02_earthmover_weight_01_target_700_fixed/intermediate_epoch_2330_960_sequences.txt'...
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Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_margin_02_earthmover_weight_01_target_700_fixed/intermediate_epoch_2360_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_margin_02_earthmover_weight_01_target_700_fixed/intermediate_epoch_2370_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_margin_02_earthmover_weight_01_target_700_fixed/intermediate_epoch_2380_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_margin_02_earthmover_weight_01_target_700_fixed/intermediate_epoch_2390_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_margin_02_earthmover_weight_01_target_700_fixed/intermediate_epoch_2400_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_0_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_2_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_3_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_4_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_5_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_6_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_7_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_8_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_9_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_10_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_20_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_30_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_40_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_50_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_60_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_70_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_80_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_90_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_100_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_110_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_120_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_130_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_140_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_150_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_160_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_170_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_180_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_190_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_200_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_210_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_220_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_230_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_240_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_250_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_260_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_270_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_280_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_290_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_300_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_310_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_320_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_330_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_340_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_350_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_360_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_370_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_380_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_390_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_400_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_410_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_420_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_430_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_440_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_450_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_460_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_470_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_480_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_490_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_500_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_510_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_520_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_530_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_540_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_550_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_560_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_570_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_580_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_590_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_600_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_610_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_620_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_630_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_640_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_650_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_660_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_670_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_680_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_690_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_700_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_710_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_720_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_730_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_740_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_750_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_760_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_770_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_780_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_790_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_800_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_810_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_820_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_830_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_840_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_850_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_860_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_870_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_880_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_890_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_900_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_910_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_920_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_930_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_940_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_950_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_960_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_970_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_980_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_990_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1000_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1010_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1020_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1030_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1040_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1050_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1060_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1070_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1080_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1090_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1100_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1110_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1120_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1130_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1140_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1150_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1160_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1170_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1180_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1190_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1200_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1210_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1220_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1230_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1240_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1250_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1260_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1270_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1280_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1290_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1300_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1310_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1320_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1330_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1340_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1350_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1360_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1370_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1380_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1390_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1400_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1410_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1420_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1430_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1440_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1450_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1460_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1470_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1480_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1490_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1500_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1510_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1520_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1530_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1540_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1550_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1560_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1570_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1580_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1590_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1600_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1610_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1620_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1630_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1640_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1650_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1660_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1670_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1680_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1690_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1700_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1710_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1720_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1730_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1740_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1750_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1760_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1770_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1780_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1790_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1800_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1810_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1820_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1830_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1840_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1850_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1860_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1870_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1880_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1890_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1900_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1910_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1920_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1930_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1940_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1950_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1960_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1970_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1980_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_1990_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_2000_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_2010_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_2020_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_2030_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_2040_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_2050_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_2060_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_2070_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_2080_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_2090_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_2100_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_2110_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_2120_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_2130_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_2140_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_2150_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_2160_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_2170_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_2180_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_2190_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_2200_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_2210_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_2220_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_2230_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_2240_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_2250_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_2260_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_2270_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_2280_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_2290_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_2300_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_2310_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_2320_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_2330_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_2340_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_2350_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_2360_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_2370_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_2380_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_2390_960_sequences.txt'...
Processing 'samples/genesis_dragonn_max_spi1_25000_updates_similarity_seq_margin_02_lat_margin_09_earthmover_weight_01_target_700/intermediate_epoch_2400_960_sequences.txt'...

In [15]:

#Clean up trajectories and convert to numpy arrays

traj_raw = []

for model_i in range(len(traj_dirs)) :
    #traj_ys[model_i] = np.array(list(zip(*traj_ys[model_i])))
    traj_ys[model_i] = list(zip(*traj_ys[model_i]))
    traj_raw.append(np.array(traj_ys[model_i][1]))
    traj_ys[model_i] = np.array(traj_ys[model_i][:1])
    
    traj_gen_xs[model_i] = np.array(traj_gen_xs[model_i])
    
    isnan_index = np.nonzero(np.isnan(traj_ys[model_i][0]))[0]
    
    first_isnan_ix = None
    if len(isnan_index) > 0 :
        first_isnan_ix = isnan_index[0]
    
    if first_isnan_ix is not None :
        traj_ys[model_i] = traj_ys[model_i][:, :first_isnan_ix]
        traj_gen_xs[model_i] = traj_gen_xs[model_i][:first_isnan_ix]

In [16]:

#Plot overlapping training trajectories

def plot_trajectories(traj_indices, traj_names, iteration_scales, iteration_constants, add_zeros, iterations, measures, model_names, measure_ix, x_label, y_label, colors=None, figsize=(6, 4), legend_outside=False, save_fig=False, fig_name="default_1", fig_dpi=150, min_x_val=0, max_x_val=None, min_y_val=None, max_y_val=None, log10_scale=False) :
    
    f = plt.figure(figsize=figsize)
    
    max_iter_val = 0
    
    ls = []
    for i, [model_ix, traj_name] in enumerate(zip(traj_indices, traj_names)) :
        #for model_ix, [iters, all_meas] in enumerate(zip(iterations, measures)) :
        
        iters, all_meas = iterations[model_ix], measures[model_ix]
        
        meas = np.zeros(all_meas[measure_ix, :].shape)
        meas[:] = all_meas[measure_ix, :]
        
        iters_copy = np.zeros(iters.shape)
        iters_copy[:] = iters[:]
        
        if add_zeros[i] is not None :
            iters_copy = np.concatenate([np.array([0]), iters_copy], axis=0)
            meas = np.concatenate([np.array([add_zeros[i]]), meas], axis=0)
        
        iters_copy[1:] = iters_copy[1:] * iteration_scales[i] + iteration_constants[i]
        
        if log10_scale :
            iters_copy[1:] = np.log10(iters_copy[1:])
        
        max_iter_val = max(max_iter_val, np.max(iters_copy))
        
        l1 = None
        if colors is not None :
            l1 = plt.plot(iters_copy, meas, color=colors[model_ix], linewidth=2, label=traj_name)
        else :
            l1 = plt.plot(iters_copy, meas, linewidth=2, label=traj_name)
        
        ls.append(l1[0])

    if log10_scale :
        plt.xticks(np.arange(int(max_iter_val) + 1), 10**np.arange(int(max_iter_val) + 1), fontsize=14, rotation=45)
    else :
        plt.xticks(fontsize=14, rotation=45)
    plt.yticks(fontsize=14)
    
    if max_x_val is not None :
        plt.xlim(min_x_val, max_x_val)
    else :
        plt.xlim(min_x_val, max_iter_val)
    
    if min_y_val is not None and max_y_val is not None :
        plt.ylim(min_y_val, max_y_val)

    plt.xlabel(x_label, fontsize=14)
    plt.ylabel(y_label, fontsize=14)
    
    if not legend_outside :
        plt.legend(handles=ls, fontsize=14, loc='upper left')
    else :
        plt.legend(handles=ls, fontsize=14, bbox_to_anchor=(1.04,1), loc="upper left")
    
    plt.tight_layout()
    
    if save_fig :
        plt.savefig(fig_name + ".eps")
        plt.savefig(fig_name + ".svg")
        plt.savefig(fig_name + ".png", dpi=fig_dpi, transparent=True)
    
    plt.show()

In [17]:

#Plot trajectory data

experiment_suffix = "_traj_comparisons_4_target_700_seq_penalty"

model_colors = ['indigo', 'black', 'dimgrey']

figsize = (12, 4)

#Generator time scale

plot_trajectories(
    [0, 0, 0, 1, 1, 1],
    [
        "Simulated Annealing (10000 iters) - 1,000 Seqs",
        "Simulated Annealing (10000 iters) - 100,000 Seqs",
        "Simulated Annealing (10000 iters) - 10,000,000 Seqs",
        "DEN Earthm - 1,000 Seqs",
        "DEN Earthm - 100,000 Seqs",
        "DEN Earthm - 10,000,000 Seqs",
    ],
    [1000.0, 100000.0, 10000000.0, 1.0, 1.0, 1.0],
    [0.0, 0.0, 0.0, 1000.0, 100000.0, 10000000.0],
    [0, 0, 0, 0, 0, 0],
    traj_gen_xs,
    traj_ys,
    traj_names,
    0,
    'Generator calls',
    'Fitness score',
    colors=model_colors,
    min_x_val=3,
    #max_x_val=40000,
    min_y_val=0,
    max_y_val=90,
    figsize=figsize,
    save_fig=True,
    fig_name=problem_prefix + experiment_suffix + "_fitness_log_logscale",
    legend_outside=True,
    log10_scale=True
)

In [19]:

#Plot trajectory data

experiment_suffix = "_traj_comparisons_4_target_700_lat_penalty"

model_colors = ['indigo', 'black', 'dimgrey']

figsize = (12, 4)

#Generator time scale

plot_trajectories(
    [0, 0, 0, 2, 2, 2],
    [
        "Simulated Annealing (10000 iters) - 1,000 Seqs",
        "Simulated Annealing (10000 iters) - 100,000 Seqs",
        "Simulated Annealing (10000 iters) - 10,000,000 Seqs",
        "DEN Earthm - 1,000 Seqs",
        "DEN Earthm - 100,000 Seqs",
        "DEN Earthm - 10,000,000 Seqs",
    ],
    [1000.0, 100000.0, 10000000.0, 1.0, 1.0, 1.0],
    [0.0, 0.0, 0.0, 1000.0, 100000.0, 10000000.0],
    [0, 0, 0, 0, 0, 0],
    traj_gen_xs,
    traj_ys,
    traj_names,
    0,
    'Generator calls',
    'Fitness score',
    colors=model_colors,
    min_x_val=3,
    #max_x_val=40000,
    min_y_val=0,
    max_y_val=90,
    figsize=figsize,
    save_fig=True,
    fig_name=problem_prefix + experiment_suffix + "_fitness_log_logscale_2",
    legend_outside=True,
    log10_scale=True
)

In [21]:

from scipy.interpolate import interp1d

def plot_bars(internal_traj_indices, traj_indices, traj_names, iteration_scales, iteration_constants, add_zeros, iterations, measures, model_names, measure_ix, x_label, y_label, colors=None, figsize=(6, 4), legend_outside=False, save_fig=False, fig_name="default_1", fig_dpi=150, min_x_val=0, max_x_val=None, min_y_val=None, max_y_val=None, log10_scale=False) :
    

    max_iter_val = 0
    max_meas_val = -np.inf
    
    iter_interps = []
    meas_interps = []

    for i, [model_ix, traj_name] in enumerate(zip(traj_indices, traj_names)) :
        #for model_ix, [iters, all_meas] in enumerate(zip(iterations, measures)) :

        iters, all_meas = iterations[model_ix], measures[model_ix]

        meas = np.zeros(all_meas[measure_ix, :].shape)
        meas[:] = all_meas[measure_ix, :]

        iters_copy = np.zeros(iters.shape)
        iters_copy[:] = iters[:]

        if add_zeros[i] is not None :
            iters_copy = np.concatenate([np.array([0]), iters_copy], axis=0)
            meas = np.concatenate([np.array([add_zeros[i]]), meas], axis=0)

        iters_copy[1:] = iters_copy[1:] * iteration_scales[i] + iteration_constants[i]

        max_iter_val = max(max_iter_val, np.max(iters_copy))
        max_meas_val = max(max_meas_val, np.max(meas))
        
        f_interp = interp1d(iters_copy, meas)
        
        iter_interp = np.linspace(iters_copy[0], iters_copy[-1], 1000)
        meas_interp = f_interp(iter_interp)
        
        if log10_scale :
            iter_interp[1:] = np.log10(iter_interp[1:])
        
        iter_interps.append(iter_interp)
        meas_interps.append(meas_interp)
    
    
    if log10_scale :
        max_iter_val = np.log10(max_iter_val)
    
    meas_perc_50 = 0.5 * max_meas_val
    meas_perc_80 = 0.8 * max_meas_val
    meas_perc_95 = 0.95 * max_meas_val
    meas_perc_99 = 0.99 * max_meas_val
    
    f = plt.figure(figsize=figsize)
    
    for i, [model_ix, traj_name] in enumerate(zip(internal_traj_indices, traj_names)) :
    
        iter_interp = iter_interps[i]
        meas_interp = meas_interps[i]
        
        first_iter_perc_50_ind = np.nonzero(meas_interp >= meas_perc_50)[0]
        first_iter_perc_50_ix = iter_interp[first_iter_perc_50_ind[0]] if len(first_iter_perc_50_ind) > 0 else max_iter_val
        
        first_iter_perc_80_ind = np.nonzero(meas_interp >= meas_perc_80)[0]
        first_iter_perc_80_ix = iter_interp[first_iter_perc_80_ind[0]] if len(first_iter_perc_80_ind) > 0 else max_iter_val
        
        first_iter_perc_95_ind = np.nonzero(meas_interp >= meas_perc_95)[0]
        first_iter_perc_95_ix = iter_interp[first_iter_perc_95_ind[0]] if len(first_iter_perc_95_ind) > 0 else max_iter_val
        
        first_iter_perc_99_ind = np.nonzero(meas_interp >= meas_perc_99)[0]
        first_iter_perc_99_ix = iter_interp[first_iter_perc_99_ind[0]] if len(first_iter_perc_99_ind) > 0 else max_iter_val
        
        if colors is not None :
            plt.bar([model_ix + 0.25 * int(i % 3)], [first_iter_perc_99_ix], width=0.25, color=colors[model_ix][3], edgecolor='black', linewidth=1, label=model_names[model_ix])
            plt.bar([model_ix + 0.25 * int(i % 3)], [first_iter_perc_95_ix], width=0.25, color=colors[model_ix][2], edgecolor='black', linewidth=1, label=model_names[model_ix])
            plt.bar([model_ix + 0.25 * int(i % 3)], [first_iter_perc_80_ix], width=0.25, color=colors[model_ix][1], edgecolor='black', linewidth=1, label=model_names[model_ix])
            plt.bar([model_ix + 0.25 * int(i % 3)], [first_iter_perc_50_ix], width=0.25, color=colors[model_ix][0], edgecolor='black', linewidth=1, label=model_names[model_ix])

    plt.xticks([], [])
    
    if log10_scale :
        plt.yticks(np.arange(int(max_iter_val) + 1), 10**np.arange(int(max_iter_val) + 1), fontsize=14, rotation=45)
    else :
        plt.yticks(fontsize=14, rotation=45)
    plt.yticks(fontsize=14)
    
    if min_x_val is not None and max_x_val :
        plt.xlim(min_x_val, max_x_val)
    
    if min_y_val is not None and max_y_val is not None :
        plt.ylim(min_y_val, max_y_val)

    plt.xlabel(x_label, fontsize=14)
    plt.ylabel(y_label, fontsize=14)
    
    if not legend_outside :
        plt.legend(fontsize=14, loc='upper left')
    else :
        plt.legend(fontsize=14, bbox_to_anchor=(1.04,1), loc="upper left")
    
    plt.tight_layout()
    
    if save_fig :
        plt.savefig(fig_name + ".eps")
        plt.savefig(fig_name + ".svg")
        plt.savefig(fig_name + ".png", dpi=fig_dpi, transparent=True)
    
    plt.show()


experiment_suffix = "_traj_comparisons_bars_4_target_700_seq_penalty"

model_colors = [
    [
        'violet',
        'mediumorchid',
        'darkviolet',
        'indigo'
    ],
    [
        'yellow',
        'gold',
        'orange',
        'darkorange'
    ],
    [
        'yellow',
        'gold',
        'orange',
        'darkorange'
    ]
]

figsize = (12, 6)

#Generator time scale

plot_bars(
    [0, 0, 0, 1, 1, 1],
    [0, 0, 0, 1, 1, 1],
    [
        "Simulated Annealing (10000 iters) - 1,000 Seqs",
        "Simulated Annealing (10000 iters) - 100,000 Seqs",
        "Simulated Annealing (10000 iters) - 10,000,000 Seqs",
        "DEN Earthm - 1,000 Seqs",
        "DEN Earthm - 100,000 Seqs",
        "DEN Earthm - 10,000,000 Seqs",
    ],
    [1000.0, 100000.0, 10000000.0, 1.0, 1.0, 1.0],
    [0.0, 0.0, 0.0, 1000.0, 100000.0, 10000000.0],
    [0, 0, 0, 0, 0, 0],
    traj_gen_xs,
    traj_ys,
    traj_names,
    0,
    'Generative Algorithm',
    'Generator Calls',
    colors=model_colors,
    #min_x_val=3,
    #max_x_val=40000,
    min_y_val=3,
    max_y_val=11.5,
    figsize=figsize,
    save_fig=True,
    fig_name=problem_prefix + experiment_suffix + "_fitness_log_logscale_2",
    legend_outside=True,
    log10_scale=True
)


experiment_suffix = "_traj_comparisons_bars_4_target_700_lat_penalty"

model_colors = [
    [
        'violet',
        'mediumorchid',
        'darkviolet',
        'indigo'
    ],
    [
        'yellow',
        'gold',
        'orange',
        'darkorange'
    ],
    [
        'yellow',
        'gold',
        'orange',
        'darkorange'
    ]
]

figsize = (12, 6)

#Generator time scale

plot_bars(
    [0, 0, 0, 1, 1, 1],
    [0, 0, 0, 2, 2, 2],
    [
        "Simulated Annealing (10000 iters) - 1,000 Seqs",
        "Simulated Annealing (10000 iters) - 100,000 Seqs",
        "Simulated Annealing (10000 iters) - 10,000,000 Seqs",
        "DEN Earthm - 1,000 Seqs",
        "DEN Earthm - 100,000 Seqs",
        "DEN Earthm - 10,000,000 Seqs",
    ],
    [1000.0, 100000.0, 10000000.0, 1.0, 1.0, 1.0],
    [0.0, 0.0, 0.0, 1000.0, 100000.0, 10000000.0],
    [0, 0, 0, 0, 0, 0],
    traj_gen_xs,
    traj_ys,
    traj_names,
    0,
    'Generative Algorithm',
    'Generator Calls',
    colors=model_colors,
    #min_x_val=3,
    #max_x_val=40000,
    min_y_val=3,
    max_y_val=11.5,
    figsize=figsize,
    save_fig=True,
    fig_name=problem_prefix + experiment_suffix + "_fitness_log_logscale_2",
    legend_outside=True,
    log10_scale=True
)

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