hectic.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 41,
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd\n",
    "# data manipulation, gathering\n",
    "import numpy as np # for array manipulation# for dataframe manipulation/reading in data\n",
    "import json # for reading in Data\n",
    "from itertools import islice # for slicing and dicing JSON records\n",
    "import os # for getting the filepath information\n",
    "import re # to identify characters that are to be removed\n",
    "import nltk # for preprocessing of textual data\n",
    "from nltk.corpus import stopwords # for removing stopwords\n",
    "from nltk.tokenize import word_tokenize # for tokenizing text\n",
    "from nltk.stem import WordNetLemmatizer # for lemmatizing text\n",
    "from sklearn.feature_extraction.text import TfidfVectorizer # for featurizing text\n",
    "from sklearn.metrics.pairwise import cosine_similarity # for getting similarity score\n",
    "from sklearn.decomposition import PCA #for dimensionality reduction\n",
    "from sklearn.cluster import KMeans #for clustering\n",
    "from sklearn.manifold import TSNE #For reducing to 2 dimensions for plotting\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 42,
   "metadata": {},
   "outputs": [],
   "source": [
    "df = pd.read_csv('initial_df.csv',dtype={'id': \"str\"})"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 43,
   "metadata": {},
   "outputs": [],
   "source": [
    "final_df = pd.read_csv('final_df.csv')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 44,
   "metadata": {},
   "outputs": [],
   "source": [
    "idf = df.reset_index()\n",
    "\n",
    "dataorg = idf[idf['id']==\"0704.0002\"]\n",
    "hula = pd.DataFrame()\n",
    "hula = hula.append(dataorg,ignore_index=True)\n",
    "orgtitle = hula['title'][0]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 67,
   "metadata": {},
   "outputs": [],
   "source": [
    "tfidf_vectorizer = TfidfVectorizer()\n",
    "\n",
    "# Generate the tf-idf vectors for the data\n",
    "tfidf_matrix = tfidf_vectorizer.fit_transform(final_df['final_text'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 68,
   "metadata": {},
   "outputs": [],
   "source": [
    "def get_recommendations(paper_id:str,tfidf_matrix,num_rec):\n",
    "    idx = final_df.index[final_df['id'] == paper_id][0]\n",
    "    sim = cosine_similarity(tfidf_matrix, tfidf_matrix[idx])\n",
    "    sim = sim.reshape(sim.shape[0])\n",
    "    top_n_idx = np.argsort(-sim)[1:num_rec+1]\n",
    "    top_n_id = [final_df['id'][x] for x in top_n_idx]\n",
    "    return top_n_id"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 69,
   "metadata": {},
   "outputs": [],
   "source": [
    "tfidf_vectorizer2 = TfidfVectorizer(max_features=10000)\n",
    "\n",
    "# Generate the tf-idf vectors for the data\n",
    "tfidf_matrix2 = tfidf_vectorizer2.fit_transform(final_df['final_text'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 70,
   "metadata": {},
   "outputs": [],
   "source": [
    "rec = get_recommendations(704.0001,tfidf_matrix,1000)\n",
    "idxs = list(final_df[final_df['id'].isin(rec)].index)\n",
    "rec_matrix = tfidf_matrix2[idxs]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 71,
   "metadata": {},
   "outputs": [],
   "source": [
    "pca = PCA(n_components=0.95, random_state=42) #Keep 95% of the variance\n",
    "reduced_matrix = pca.fit_transform(rec_matrix.toarray())"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 72,
   "metadata": {},
   "outputs": [],
   "source": [
    "k = 10 # selectable\n",
    "kmeans = KMeans(n_clusters=k, random_state=42)\n",
    "y_pred = kmeans.fit_predict(reduced_matrix)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 73,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "c:\\python 310\\lib\\site-packages\\sklearn\\manifold\\_t_sne.py:800: FutureWarning:\n",
      "\n",
      "The default initialization in TSNE will change from 'random' to 'pca' in 1.2.\n",
      "\n",
      "c:\\python 310\\lib\\site-packages\\sklearn\\manifold\\_t_sne.py:810: FutureWarning:\n",
      "\n",
      "The default learning rate in TSNE will change from 200.0 to 'auto' in 1.2.\n",
      "\n"
     ]
    }
   ],
   "source": [
    "tsne = TSNE(perplexity=100, random_state=42)\n",
    "two_dim_matrix = tsne.fit_transform(reduced_matrix)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 74,
   "metadata": {},
   "outputs": [],
   "source": [
    "import seaborn as sns\n",
    "import matplotlib.pyplot as plt\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 75,
   "metadata": {},
   "outputs": [],
   "source": [
    "import plotly.express as px\n"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Topic Modelling"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 76,
   "metadata": {},
   "outputs": [],
   "source": [
    "from sklearn.decomposition import LatentDirichletAllocation\n",
    "from sklearn.feature_extraction.text import CountVectorizer"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 77,
   "metadata": {},
   "outputs": [],
   "source": [
    "vectorizers = []\n",
    "    \n",
    "for x in range(0, k):\n",
    "    # Creating a vectorizer\n",
    "    vectorizers.append(CountVectorizer(min_df=5, max_df=0.9, stop_words='english', lowercase=True, token_pattern='[a-zA-Z\\-][a-zA-Z\\-]{2,}'))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 78,
   "metadata": {},
   "outputs": [],
   "source": [
    "topic_df = pd.DataFrame()\n",
    "topic_df['id'] =df[final_df['id'].isin(rec)]['id']\n",
    "topic_df['title'] = df[final_df['id'].isin(rec)]['title']\n",
    "topic_df['text'] = df[final_df['id'].isin(rec)]['title']+\" \"+df[final_df['id'].isin(rec)]['abstract']\n",
    "topic_df['cluster'] = y_pred"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 79,
   "metadata": {},
   "outputs": [],
   "source": [
    "vectorized_data = []\n",
    "\n",
    "for current_cluster, cvec in enumerate(vectorizers):\n",
    "    try:\n",
    "        vectorized_data.append(cvec.fit_transform(topic_df.loc[topic_df['cluster'] == current_cluster, 'text']))\n",
    "    except Exception as e:\n",
    "        print(\"Not enough instances in cluster: \" + str(current_cluster))\n",
    "        vectorized_data.append(None)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 80,
   "metadata": {},
   "outputs": [],
   "source": [
    "NUM_TOPICS_PER_CLUSTER = 5 #choose\n",
    "\n",
    "lda_models = []\n",
    "for x in range(0, k):\n",
    "    # Latent Dirichlet Allocation Model\n",
    "    lda = LatentDirichletAllocation(n_components=NUM_TOPICS_PER_CLUSTER, max_iter=10, learning_method='online',verbose=False, random_state=42)\n",
    "    lda_models.append(lda)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 81,
   "metadata": {},
   "outputs": [],
   "source": [
    "clusters_lda_data = []\n",
    "\n",
    "for current_cluster, lda in enumerate(lda_models):\n",
    "    #print(\"Current Cluster: \" + str(current_cluster))\n",
    "    \n",
    "    if vectorized_data[current_cluster] != None:\n",
    "        clusters_lda_data.append((lda.fit_transform(vectorized_data[current_cluster])))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 82,
   "metadata": {},
   "outputs": [],
   "source": [
    "def selected_topics(model, vectorizer, top_n=3):\n",
    "    current_words = []\n",
    "    keywords = []\n",
    "    \n",
    "    for idx, topic in enumerate(model.components_):\n",
    "        words = [(vectorizer.get_feature_names_out()[i], topic[i]) for i in topic.argsort()[:-top_n - 1:-1]]\n",
    "        for word in words:\n",
    "            if word[0] not in current_words:\n",
    "                keywords.append(word)\n",
    "                current_words.append(word[0])\n",
    "                \n",
    "    keywords.sort(key = lambda x: x[1])  \n",
    "    keywords.reverse()\n",
    "    return_values = []\n",
    "    for x in keywords:\n",
    "        return_values.append(x[0])\n",
    "    return \" \".join(return_values)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 83,
   "metadata": {},
   "outputs": [],
   "source": [
    "all_keywords = []\n",
    "for current_vectorizer, lda in enumerate(lda_models):\n",
    "    #print(\"Current Cluster: \" + str(current_vectorizer))\n",
    "\n",
    "    if vectorized_data[current_vectorizer] != None:\n",
    "        all_keywords.append(selected_topics(lda, vectorizers[current_vectorizer]))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 84,
   "metadata": {},
   "outputs": [],
   "source": [
    "cluster_keyword = {x:all_keywords[x] for x in range(k)}\n",
    "word_pred = list(map(cluster_keyword.get, y_pred))\n",
    "topic_df['keywords'] = word_pred"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 85,
   "metadata": {},
   "outputs": [
    {
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         "customdata": [
          [
           "0704.0106",
           "Multiple Parton Scattering in Nuclei: Quark-quark Scattering"
          ],
          [
           "0704.1745",
           "I. The mass gap and solution of the quark confinement problem in QCD"
          ],
          [
           "0705.0953",
           "Search for color charge dependence of energy loss at RHIC"
          ],
          [
           "0706.0456",
           "Parton Distributions for the LHC"
          ],
          [
           "0706.4456",
           "Heavy-Quark Kinetics in the QGP at LHC"
          ],
          [
           "0707.0923",
           "Quark-gluon plasma paradox"
          ],
          [
           "0707.2263",
           "The Role of Surface Tension for the Equation of State of Quark-Gluon\n  Bags"
          ],
          [
           "0707.3033",
           "Dynamical quasiparticles properties and effective interactions in the\n  sQGP"
          ],
          [
           "0707.3800",
           "Higgs production at the LHC in warped extra-dimensional models"
          ],
          [
           "0709.0065",
           "Renormalized Wick expansion for a modified PQCD"
          ],
          [
           "0709.1684",
           "Thermal Charm Production in Quark-Gluon Plasma at LHC"
          ],
          [
           "0709.3174",
           "Midrapidity Production of Secondaries in pp Collisions at RHIC and LHC\n  Energies in the Quark-Gluon String Model"
          ],
          [
           "0710.1051",
           "Charm Production at RHIC"
          ],
          [
           "0710.3930",
           "Interactions of Heavy Hadrons using Regge Phenomenology and the Quark\n  Gluon String Model"
          ],
          [
           "0711.2196",
           "Baryon scattering at high energies: wave function, impact factor, and\n  gluon radiation"
          ],
          [
           "0711.2280",
           "Properties of quark gluon plasma from lattice calculations"
          ],
          [
           "0711.3943",
           "Energetic di-leptons from the Quark Gluon Plasma"
          ],
          [
           "0802.3282",
           "QCD Evolution of Jets in the Quark-Gluon Plasma"
          ],
          [
           "0803.1527",
           "Dilepton from Quark-Gluon Plasma and Quark-Hadron Phase Transition"
          ],
          [
           "0803.1611",
           "The Thermodynamics of Quarks and Gluons"
          ],
          [
           "0803.2124",
           "Relativistic description of the double charmonium production in $e^+e^-$\n  annihilation"
          ],
          [
           "0804.0275",
           "Unstable Quark-Gluon Plasma at LHC"
          ],
          [
           "0804.0455",
           "Deep-Elastic pp Scattering at LHC from Low-x Gluons"
          ],
          [
           "0804.3359",
           "QCD Splitting/Joining Functions at Finite Temperature in the Deep LPM\n  Regime"
          ],
          [
           "0805.0587",
           "Pressure isotropization of an equilibrating quark-gluon plasma"
          ],
          [
           "0805.1093",
           "Heavy Quark Production from Jet Conversions in a Quark-Gluon Plasma"
          ],
          [
           "0805.2650",
           "Associated production of prompt photons and heavy quarks in off-shell\n  gluon-gluon fusion"
          ],
          [
           "0805.4058",
           "Refraction of Gluon jet in QGP"
          ],
          [
           "0805.4821",
           "Production of electroweak gauge bosons in off-shell gluon-gluon fusion"
          ],
          [
           "0806.0644",
           "Di-Quarks and Tri-Quarks on the Lattice"
          ],
          [
           "0806.1535",
           "Maximum Wavelength of Confined Quarks and Gluons and Properties of\n  Quantum Chromodynamics"
          ],
          [
           "0806.1932",
           "Single Spin Asymmetries in Heavy Quark and Antiquark Productions"
          ],
          [
           "0807.0321",
           "NNLO Time-like Splitting Functions in QCD"
          ],
          [
           "0807.1610",
           "Relativistic Nucleus-Nucleus Collisions and the QCD Matter Phase Diagram"
          ],
          [
           "0807.2403",
           "Valence quarks and $k_T$ factorisation"
          ],
          [
           "0807.4939",
           "Coalescence Models For Hadron Formation From Quark Gluon Plasma"
          ],
          [
           "0808.0201",
           "Analytic treatment of leading-order parton evolution equations: theory\n  and tests"
          ],
          [
           "0809.1390",
           "Flavour Changing Neutral Current Constraints from Kaluza-Klein Gluons\n  and Quark Mass Matrices in RS1"
          ],
          [
           "0809.2296",
           "Recent developments in the constituent quark model including\n  quark-antiquark pairs"
          ],
          [
           "0810.1727",
           "The QCD Phase Boundary from Quark-Gluon Dynamics"
          ],
          [
           "0811.2575",
           "On the quark component in prompt photon and electroweak gauge boson\n  production at high energies"
          ],
          [
           "0812.0946",
           "Prompt photon photoproduction at HERA within the framework of the quark\n  Reggeization hypothesis"
          ],
          [
           "0812.1619",
           "Heavy Ions at LHC: A Quest for Quark-Gluon Plasma"
          ],
          [
           "0812.2465",
           "Multiplicity Distribution of Secondary Hadrons at LHC Energy and Total\n  Cross Sections of Hadron-Hadron Interactions"
          ],
          [
           "0812.2536",
           "Strange and charm quark-pair production in strong non-Abelian field"
          ],
          [
           "0812.2896",
           "Confinement and Green functions in Landau-gauge QCD"
          ],
          [
           "0812.4484",
           "QCD Evolution of the Transverse Momentum Dependent Correlations"
          ],
          [
           "0901.0946",
           "Tomography of a quark gluon plasma at RHIC and LHC energies"
          ],
          [
           "0901.4088",
           "Black holes and the quark-gluon plasma"
          ],
          [
           "0902.0741",
           "Transport properties and Langevin dynamics of heavy quarks and quarkonia\n  in the Quark Gluon Plasma"
          ],
          [
           "0902.3519",
           "Quark and gluon form factors to three loops"
          ],
          [
           "0903.2778",
           "The States of Matter in QCD"
          ],
          [
           "0904.3428",
           "Search and study of Quark Gluon Plasma at the CERN-LHC"
          ],
          [
           "0904.3558",
           "Nonzero Mean Squared Momentum of Quarks in the Non-Perturbative QCD\n  Vacuum"
          ],
          [
           "0905.3922",
           "Altarelli-Parisi Equation in Non-Equilibrium QCD"
          ],
          [
           "0906.1742",
           "Hadron mass generation and the strong interaction"
          ],
          [
           "0906.2618",
           "Fourier analysis of the flux-tube distribution in SU(3) lattice QCD"
          ],
          [
           "0906.5234",
           "Electron-Positron to Nucleon-Antinucleon Pair at Threshold and Proton\n  Form Factor"
          ],
          [
           "0907.1918",
           "Anomalous mass dependence of radiative quark energy loss in a\n  finite-size quark-gluon plasma"
          ],
          [
           "0909.2323",
           "Enhanced heavy quark-pair production in strong SU(2) color field"
          ],
          [
           "0910.0134",
           "Beauty baryon production in pp collisions at LHC and b quark\n  distribution in proton"
          ],
          [
           "0910.0394",
           "Relativistic effects in the double S- and P-wave charmonium production\n  in e^+e^- annihilation"
          ],
          [
           "0910.0958",
           "Comparison of gluon flux-tube distributions for quark-diquark and\n  quark-antiquark hadrons"
          ],
          [
           "0910.2050",
           "Predictions of Quark-Gluon String Model for pp at LHC"
          ],
          [
           "0911.3112",
           "Search for New Color-Octet Vector Particle Decaying to ttbar in ppbar\n  Collisions at $\\sqrt{s}=1.96$ TeV"
          ],
          [
           "0911.3621",
           "Factorization of Short- and Long-range Interactions in Charged Meson\n  Production"
          ],
          [
           "0911.4850",
           "Are multiple parton interactions important at high energies? New types\n  of hadrons production processes"
          ],
          [
           "0911.5517",
           "Diphoton production at Tevatron in the quasi-multi-Regge-kinematics\n  approach"
          ],
          [
           "0912.1041",
           "Possible difference between multiplicity distributions and inclusive\n  spectra of secondary hadrons in proton-proton and proton-antiproton\n  collisions at energy sqrt(s)=900 GeV"
          ],
          [
           "0912.1437",
           "Quantum Phase Transitions in Dense QCD"
          ],
          [
           "1002.1779",
           "Low $Q^2$ proton structure function, using gluon and pseudoscalar meson\n  clouds in the constituent quark framework"
          ],
          [
           "1003.0346",
           "Inclusive b and b anti-b production with quasi-multi-Regge kinematics at\n  the Tevatron"
          ],
          [
           "1003.2018",
           "The internal color degrees of freedom for the weakly interacting quarks\n  and gluons"
          ],
          [
           "1003.3531",
           "Viscosity coefficients for hadron and quark-gluon phases"
          ],
          [
           "1003.4200",
           "Heavy quark production at RHIC and LHC within a partonic transport model"
          ],
          [
           "1003.4319",
           "QCD corrections to J/psi polarisation in pp collisions at RHIC"
          ],
          [
           "1003.5508",
           "Dragging Heavy Quarks in Quark Gluon Plasma at the Large Hadron Collider"
          ],
          [
           "1004.2591",
           "Dilepton production by dynamical quasiparticles in the strongly\n  interacting quark gluon plasma"
          ],
          [
           "1004.3069",
           "Dileptons from the nonequilibrium Quark-Gluon Plasma"
          ],
          [
           "1004.4091",
           "Production and elliptic flow of heavy quarks at RHIC and LHC within a\n  partonic transport model"
          ],
          [
           "1006.4603",
           "The quark-gluon medium"
          ],
          [
           "1008.1120",
           "Heavy Quark Production from Relativistic Heavy Ion Collisions"
          ],
          [
           "1008.2306",
           "Shear Viscosity in a Perturbative Quark-Gluon-Plasma"
          ],
          [
           "1008.2730",
           "$J/\\psi$ production and elliptic flow in relativistic heavy-ion\n  collisions"
          ],
          [
           "1008.4432",
           "Initial and Final State Interaction Effects in Small-x Quark\n  Distributions"
          ],
          [
           "1008.4528",
           "Thermal axion production in the primordial quark-gluon plasma"
          ],
          [
           "1009.6137",
           "Quarkonium in a weakly-coupled quark-gluon plasma"
          ],
          [
           "1010.0203",
           "Search for Dijet Resonances in 7 TeV pp Collisions at CMS"
          ],
          [
           "1010.1503",
           "Novel QCD Phenomenology"
          ],
          [
           "1010.3991",
           "All tree-level amplitudes in massless QCD"
          ],
          [
           "1011.0808",
           "Quasi-diffraction production of white quark--gluon clusters at\n  superhigh-energy hadron collisions"
          ],
          [
           "1011.3131",
           "Inclusive jet production at Tevatron in the Regge limit of QCD"
          ],
          [
           "1012.0234",
           "The errant life of a heavy quark in the quark-gluon plasma"
          ],
          [
           "1012.0890",
           "Binding Energies and Melting Temperatures of Heavy Hadrons in\n  Quark-Gluon Plasma"
          ],
          [
           "1012.1178",
           "Probing gluon and heavy-quark nuclear PDFs with photon + heavy quark\n  production in pA collisions"
          ],
          [
           "1012.1544",
           "Direct Photon and Heavy Quark Jet Production at the LHC"
          ],
          [
           "1012.2288",
           "Jets and QCD: A Historical Review of the Discovery of the Quark and\n  Gluon Jets and its Impact on QCD"
          ],
          [
           "1101.4568",
           "Production of four-quark states with double heavy quarks at LHC"
          ],
          [
           "1101.5970",
           "The quark-gluon medium (micro- and macro-QCD)"
          ],
          [
           "1102.1134",
           "Testing for kt-factorization with inclusive prompt photon production at\n  LHC"
          ],
          [
           "1103.0073",
           "Quark-hadron phase transition in Brans-Dicke brane gravity"
          ],
          [
           "1103.0916",
           "Transport Model Studies of the Baryon-Rich Quark-Gluon Plasma formed in\n  Heavy Ion Collisions"
          ]
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           "Combination of electroweak and QCD corrections to single W production at\n  the Fermilab Tevatron and the CERN LHC"
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          },
          "hovermode": "closest",
          "mapbox": {
           "style": "light"
          },
          "paper_bgcolor": "white",
          "plot_bgcolor": "#E5ECF6",
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          },
          "scene": {
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            "gridwidth": 2,
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           "bgcolor": "#E5ECF6",
           "caxis": {
            "gridcolor": "white",
            "linecolor": "white",
            "ticks": ""
           }
          },
          "title": {
           "x": 0.05
          },
          "xaxis": {
           "automargin": true,
           "gridcolor": "white",
           "linecolor": "white",
           "ticks": "",
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           },
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           "zerolinewidth": 2
          },
          "yaxis": {
           "automargin": true,
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           "ticks": "",
           "title": {
            "standoff": 15
           },
           "zerolinecolor": "white",
           "zerolinewidth": 2
          }
         }
        },
        "title": {
         "text": "Clustered Papers"
        },
        "width": 1200,
        "xaxis": {
         "anchor": "y",
         "domain": [
          0,
          1
         ],
         "title": {
          "text": "x"
         }
        },
        "yaxis": {
         "anchor": "x",
         "domain": [
          0,
          1
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         "title": {
          "text": "y"
         }
        }
       }
      }
     },
     "metadata": {},
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   ],
   "source": [
    "fig = px.scatter(topic_df, x=two_dim_matrix[:,0], y=two_dim_matrix[:,1], color='keywords',\n",
    "                 hover_data=['id','title'],\n",
    "                 height= 700, width=1200,\n",
    "                title = \"Clustered Papers\",)\n",
    "\n",
    "fig.update_layout(\n",
    "    coloraxis_colorbar=dict(\n",
    "        title_font=dict(size=20), # Set the font size of the color legend title to 20\n",
    "        tickfont=dict(size=16) # Set the font size of the color legend tick labels to 16\n",
    "    ),\n",
    "    legend=dict(\n",
    "        font=dict(size=11) # Set the font size of the marker legend to 16\n",
    "    )\n",
    ")\n",
    "fig.update_layout(\n",
    "    legend=dict(orientation=\"h\", yanchor=\"bottom\", y=-0.3, xanchor=\"right\", x=1)\n",
    ")\n",
    "fig.show()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 87,
   "metadata": {},
   "outputs": [],
   "source": [
    "from bokeh.plotting import figure, show\n",
    "from bokeh.models import ColumnDataSource, HoverTool\n",
    "from bokeh.palettes import Category10\n",
    "\n",
    "# Load data\n",
    "\n",
    "\n",
    "# Define colors\n",
    "colors = Category10[len(topic_df['keywords'].unique())]\n",
    "\n",
    "# Create Bokeh figure\n",
    "p = figure(title='Clustered Papers', width=1600, height=1200)\n",
    "\n",
    "# Create ColumnDataSource\n",
    "source = ColumnDataSource(data={\n",
    "    'x': two_dim_matrix[:,0],\n",
    "    'y': two_dim_matrix[:,1],\n",
    "    'id': topic_df['id'],\n",
    "    'title': topic_df['title'],\n",
    "    'keywords': topic_df['keywords'],\n",
    "})\n",
    "\n",
    "# Add scatter plot\n",
    "p.scatter('x', 'y', source=source, color='keywords', legend_group='keywords', size=10, fill_alpha=0.8, line_alpha=0.8)\n",
    "\n",
    "# Add hover tool\n",
    "hover = HoverTool(tooltips=[('ID', '@id'), ('Title', '@title')])\n",
    "p.add_tools(hover)\n",
    "\n",
    "# Show the plot\n",
    "show(p)\n"
   ]
  }
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