adaptation_specialization_material/plots/pacs.py

import pandas as pd 

import pandas as pd
import pickle
import numpy as np
from scipy.stats import entropy

from os.path import join as opj, exists

import argparse

import textwrap

from sklearn.preprocessing import MultiLabelBinarizer

parser = argparse.ArgumentParser()
parser.add_argument("--input")
args = parser.parse_args()

ngrams = pd.read_csv(opj(args.input, "ngrams.csv"))


articles = pd.read_parquet("../semantics/inspire-harvest/database/articles.parquet")[["article_id", "date_created", "pacs_codes", "curated"]]
articles = articles[articles["date_created"].str.len() >= 4]
articles["year"] = articles["date_created"].str[:4].astype(int)-2000
articles["article_id"] = articles.article_id.astype(int)
_articles = pd.read_csv(opj(args.input, "articles.csv"))
articles = _articles.merge(articles, how="inner")
years = articles["year"].values

topics = pd.read_csv(opj(args.input, "topics.csv"))
is_junk_topic = np.array(topics["label"].str.contains("Junk"))

pacs_description = pd.read_csv("inspire-harvest/database/pacs_codes.csv").set_index("code")["description"].to_dict()
codes = set(pacs_description.keys())
has_pacs_code = articles["pacs_codes"].map(lambda l: set(l)&codes).map(len) > 0
articles = articles[has_pacs_code]

binarizer = MultiLabelBinarizer()
pacs = binarizer.fit_transform(articles["pacs_codes"])
n_categories = pacs.shape[1]

print((pacs-pacs.mean(axis=0)).shape)

cat_classes = np.array([np.identity(n_categories)[cl] for cl in range(n_categories)])
cat_labels = binarizer.inverse_transform(cat_classes)

with open(opj(args.input, "etm_instance.pickle"), "rb") as handle:
    etm_instance = pickle.load(handle)
if not exists(opj(args.input, "theta.npy")):
    theta = etm_instance.get_document_topic_dist()
    np.save(opj(args.input, "theta.npy"), theta)
else:
    theta = np.load(opj(args.input, "theta.npy"))

print(theta[:,~is_junk_topic].mean(axis=0).sum())

topic_matrix = np.load(opj(args.input, "topics_counts.npy"))
print("Theta average entropy:", np.exp(entropy(theta[:,~is_junk_topic], axis=1)).mean())
print("Topic matrix average entropy:", np.nanmean(np.exp(np.nan_to_num(entropy(topic_matrix, axis=1)))))

theta = theta[has_pacs_code,:]


n_articles = theta.shape[0]

R = (theta-theta.mean(axis=0)).T@(pacs-pacs.mean(axis=0))/n_articles
R /= np.outer(theta.std(axis=0), pacs.std(axis=0))

print(R.shape)
print(R)

topics["top_pacs"] = ""
topics["relevant"] = 1
topics.loc[is_junk_topic, "label"] = "Uninterpretable"
topics.loc[is_junk_topic, "relevant"] = 0

for i in range(R.shape[0]):
    ind = np.argsort(R[i,:])
    top = ind[-5:][::-1]
    topics.loc[i, "top_pacs"] = "\\\\ ".join([f"{textwrap.shorten(pacs_description[cat_labels[j][0]], width=40)} ({R[i,j]:.2f})" for j in top if cat_labels[j][0] in pacs_description])

topics["top_words"] = topics["top_words"].str.replace(",", ", ")
topics["top_words"] = topics["top_words"].str.replace("_", "\\_")
# topics["top_words"] = topics["top_words"].str.replace(r"(^(.*)-ray)|((.*)-ray)", "$\\gamma$-ray", regex=True)
# topics["top_words"] = topics["top_words"].apply(lambda s: "\\\\ ".join(textwrap.wrap(s, width=45, break_long_words=False)))
# topics["top_words"] = topics["top_words"].apply(lambda s: '\\begin{tabular}{l}' + s +'\\end{tabular}')

topics["top_pacs"] = topics["top_pacs"].apply(lambda s: '\\shortstack[l]{' + s +'}')

topics.sort_values(["relevant", "label"], ascending=[False, True], inplace=True)

pd.set_option('display.max_colwidth', None)

latex = topics.to_latex(
    columns=["label", "top_words", "top_pacs"],
    header = ["Research area", "Top words", "Most correlated PACS categories"],
    index=False,    
    multirow=True,
    multicolumn=True,
    longtable=True,
    column_format='p{0.15\\textwidth}|b{0.425\\textwidth}|b{0.425\\textwidth}',
    escape=False,
    caption="Research areas, their top-words, and their correlation with a standard classification (PACS).",
    label="table:research_areas"
)

latex = latex.replace(')} \\\\\n', ')}\\\\ \\hline\n')

with open(opj(args.input, "topics.tex"), "w+") as fp:
    fp.write(latex)


keep_pacs = pacs.sum(axis=0)>=100
R = R[:,keep_pacs]
R = R[~is_junk_topic]

labels = [cat_labels[i][0] for i in range(len(keep_pacs)) if keep_pacs[i]]
breaks_1 = np.array([True if (i==0 or labels[i-1][:5]!=labels[i][:5]) else False for i in range(len(labels))])
breaks_2 = np.array([True if (i==0 or labels[i-1][:2]!=labels[i][:2]) else False for i in range(len(labels))])


order = np.load(opj(args.input, "topics_order.npy"))
print(order)
R = R[order,:]

import seaborn as sns
import matplotlib
from matplotlib import pyplot as plt 
matplotlib.use("pgf")
matplotlib.rcParams.update(
    {
        "pgf.texsystem": "xelatex",
        "font.family": "serif",
        "font.serif": "Times New Roman",
        "text.usetex": True,
        "pgf.rcfonts": False,
    }
)
plt.rcParams["text.latex.preamble"].join([
        r"\usepackage{amsmath}",              
        r"\setmainfont{amssymb}",
])
from matplotlib.gridspec import GridSpec


plt.clf()
fig = plt.figure(figsize=(6.4*2, 6.4*2.5))
gs = GridSpec(9,8,hspace=0,wspace=0)

ax_heatmap = fig.add_subplot(gs[0:8,2:8])
sns.heatmap(
    R.T,
    cmap="RdBu",
    vmin=-0.5, vmax=+0.5,
    square=False,
    ax=ax_heatmap,
    cbar_kws={"shrink": 0.25}
)
ax_heatmap.invert_yaxis()
ax_heatmap.yaxis.set_visible(False)

topics = pd.read_csv(opj(args.input, "topics.csv"))
topics = topics[~topics["label"].str.contains("Junk")]["label"].tolist()
ordered_topics = [topics[i] for i in order]
ax_heatmap.set_xticklabels(ordered_topics, rotation = 90)
xmin, xmax = ax_heatmap.get_xlim()
ymin, ymax = ax_heatmap.get_ylim()

ax_breaks = fig.add_subplot(gs[0:8,0:2])
ax_breaks.set_xlim(0,8)
ax_breaks.set_ylim(ymin,ymax)
ax_breaks.axis("off")

import re
html = open("../semantics/inspire-harvest/database/pacs.html", "r").read()
# Regex pattern to extract the code and label
pattern = r'<span class="pacs_num">(\d{2}\.\d{2}\.\d{2})</span>\s*(.*?)</h2>'
matches = re.findall(pattern, html)
matches = {
    matches[i][0][:2]: matches[i][1]
    for i in range(len(matches))
}

import textwrap

prev_break = 0
for i in range(len(breaks_1)):
    if breaks_1[i] == True:
        ax_heatmap.hlines(y=i-0.5, xmin=xmin, xmax=xmax, color="lightgray", lw=0.125/2)

    if breaks_2[i] == True or i == len(breaks_1)-1:
        ax_breaks.hlines(y=i-0.5, xmin=2, xmax=10, color="lightgray", lw=0.125)
        ax_heatmap.hlines(y=i-0.5, xmin=xmin, xmax=xmax, color="lightgray", lw=0.125)

        print(prev_break, i, labels[i], prev_break+(i-prev_break)/2.0)
        if prev_break != i:
            text = textwrap.shorten(matches[labels[i-1][:2]], width=35*3)
            lines = textwrap.wrap(text, width=35)
            too_small = len(lines) >= 0.35*(i-prev_break-2)

            if too_small:
                text = textwrap.shorten(matches[labels[i-1][:2]], width=35*2)
                lines = textwrap.wrap(text, width=35)
                too_small = len(lines) >= 0.35*(i-prev_break-2)

            if too_small:
                text = textwrap.shorten(matches[labels[i-1][:2]], width=35)
                lines = textwrap.wrap(text, width=35)
                too_small = len(lines) >= 0.5*(i-prev_break-2)

            if (not too_small) or i == len(breaks_1)-1:
                ax_breaks.text(
                    7.5,
                    prev_break+(i-prev_break)/2.0,
                    "\n".join(lines),
                    ha="right",
                    va="center",
                    fontsize=8
                )

            prev_break = i


plt.savefig(opj(args.input, "pacs_clustermap.eps"), bbox_inches="tight")