notebooks/01_numerical_representation.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import sys\n",
    "sys.path.insert(0, '../rudeus')\n",
    "import pandas as pd"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Import data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>id</th>\n",
       "      <th>sequence</th>\n",
       "      <th>target</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>1</td>\n",
       "      <td>GSDPQVLRGSGHCKWFNVRMGFGFISMTSREGSPLENPVDVFVHQS...</td>\n",
       "      <td>single</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>2</td>\n",
       "      <td>QRIYSSIEEIIQQAQASEIGQKKEFYVYGNLVSIQMKNKLYYYRCT...</td>\n",
       "      <td>single</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>3</td>\n",
       "      <td>MGEELREEERGEVRSELITKGEKKLVLIRWNTGKTSAGRLFGRYGP...</td>\n",
       "      <td>single</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>4</td>\n",
       "      <td>MEGWQRAFVLHSRPWSETSLMLDVFTEESGRVRLVAKGARSKRSTL...</td>\n",
       "      <td>single</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>5</td>\n",
       "      <td>MARGMNHVYLIGALARDPELRYTGNGMAVFEATVAGEDRVIGNDGR...</td>\n",
       "      <td>single</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1228</th>\n",
       "      <td>1229</td>\n",
       "      <td>MNEIVVKGARVHNLKNITVRIPKNRLVVITGVSGSGKSSLAMDTIY...</td>\n",
       "      <td>double</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1229</th>\n",
       "      <td>1230</td>\n",
       "      <td>MADRLIVRGAREHNLKNVSLDLPRDSLIVFTGLSGSGKSSLAFDTI...</td>\n",
       "      <td>double</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1230</th>\n",
       "      <td>1231</td>\n",
       "      <td>MQHKTIMDKIIIQGARENNLKNIFLEIPKNQFVVFTGLSGSGKSTL...</td>\n",
       "      <td>double</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1231</th>\n",
       "      <td>1232</td>\n",
       "      <td>MTMESGAENQQSGDAAVTEAENQQMTVQAQPQIATLAQVSMPAAHA...</td>\n",
       "      <td>double</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1232</th>\n",
       "      <td>1233</td>\n",
       "      <td>MAAKKTVTKADLVDQVAQATGLKKKDVKAMVDALLAKVEEALANGS...</td>\n",
       "      <td>double</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>1233 rows × 3 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "        id                                           sequence  target\n",
       "0        1  GSDPQVLRGSGHCKWFNVRMGFGFISMTSREGSPLENPVDVFVHQS...  single\n",
       "1        2  QRIYSSIEEIIQQAQASEIGQKKEFYVYGNLVSIQMKNKLYYYRCT...  single\n",
       "2        3  MGEELREEERGEVRSELITKGEKKLVLIRWNTGKTSAGRLFGRYGP...  single\n",
       "3        4  MEGWQRAFVLHSRPWSETSLMLDVFTEESGRVRLVAKGARSKRSTL...  single\n",
       "4        5  MARGMNHVYLIGALARDPELRYTGNGMAVFEATVAGEDRVIGNDGR...  single\n",
       "...    ...                                                ...     ...\n",
       "1228  1229  MNEIVVKGARVHNLKNITVRIPKNRLVVITGVSGSGKSSLAMDTIY...  double\n",
       "1229  1230  MADRLIVRGAREHNLKNVSLDLPRDSLIVFTGLSGSGKSSLAFDTI...  double\n",
       "1230  1231  MQHKTIMDKIIIQGARENNLKNIFLEIPKNQFVVFTGLSGSGKSTL...  double\n",
       "1231  1232  MTMESGAENQQSGDAAVTEAENQQMTVQAQPQIATLAQVSMPAAHA...  double\n",
       "1232  1233  MAAKKTVTKADLVDQVAQATGLKKKDVKAMVDALLAKVEEALANGS...  double\n",
       "\n",
       "[1233 rows x 3 columns]"
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df = pd.read_csv(\"../rudeus_data/raw_data/single_double_dna.csv\")\n",
    "df"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Protein Language Models"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "from machine_learning.numerical_representation import BioEmbeddings"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "using_bioembedding_instance = BioEmbeddings(df, 'id', 'sequence')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Reducing embeddings: 1233it [00:01, 732.65it/s]\n"
     ]
    },
    {
     "data": {
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       "      <td>-0.032394</td>\n",
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       "      <td>0.012536</td>\n",
       "      <td>0.043216</td>\n",
       "      <td>0.084375</td>\n",
       "      <td>0.007837</td>\n",
       "      <td>0.069794</td>\n",
       "      <td>-0.044134</td>\n",
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       "      <td>-0.032315</td>\n",
       "      <td>-0.122054</td>\n",
       "      <td>-0.010417</td>\n",
       "      <td>-0.071897</td>\n",
       "      <td>0.109930</td>\n",
       "      <td>0.055475</td>\n",
       "      <td>0.002491</td>\n",
       "      <td>-0.050859</td>\n",
       "      <td>-0.043207</td>\n",
       "      <td>-0.031467</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.012507</td>\n",
       "      <td>0.089238</td>\n",
       "      <td>-0.022887</td>\n",
       "      <td>-0.037875</td>\n",
       "      <td>0.013370</td>\n",
       "      <td>0.073821</td>\n",
       "      <td>0.096903</td>\n",
       "      <td>0.017133</td>\n",
       "      <td>0.064631</td>\n",
       "      <td>-0.039452</td>\n",
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       "      <td>-0.041239</td>\n",
       "      <td>-0.128768</td>\n",
       "      <td>0.013445</td>\n",
       "      <td>-0.089572</td>\n",
       "      <td>0.113357</td>\n",
       "      <td>0.028909</td>\n",
       "      <td>-0.003931</td>\n",
       "      <td>-0.059228</td>\n",
       "      <td>-0.044582</td>\n",
       "      <td>-0.015745</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.019659</td>\n",
       "      <td>0.057286</td>\n",
       "      <td>-0.021680</td>\n",
       "      <td>-0.040389</td>\n",
       "      <td>0.014894</td>\n",
       "      <td>0.037244</td>\n",
       "      <td>0.083684</td>\n",
       "      <td>0.005021</td>\n",
       "      <td>0.065194</td>\n",
       "      <td>-0.036202</td>\n",
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       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>-0.053598</td>\n",
       "      <td>-0.126727</td>\n",
       "      <td>0.013942</td>\n",
       "      <td>-0.089992</td>\n",
       "      <td>0.106270</td>\n",
       "      <td>0.019663</td>\n",
       "      <td>-0.009753</td>\n",
       "      <td>-0.045075</td>\n",
       "      <td>-0.045403</td>\n",
       "      <td>-0.019771</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.026003</td>\n",
       "      <td>0.064901</td>\n",
       "      <td>-0.031808</td>\n",
       "      <td>-0.035478</td>\n",
       "      <td>0.020381</td>\n",
       "      <td>0.035428</td>\n",
       "      <td>0.084140</td>\n",
       "      <td>0.008325</td>\n",
       "      <td>0.061186</td>\n",
       "      <td>-0.041064</td>\n",
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       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>-0.055171</td>\n",
       "      <td>-0.123368</td>\n",
       "      <td>0.010215</td>\n",
       "      <td>-0.087683</td>\n",
       "      <td>0.107859</td>\n",
       "      <td>0.021741</td>\n",
       "      <td>-0.003519</td>\n",
       "      <td>-0.051125</td>\n",
       "      <td>-0.038727</td>\n",
       "      <td>-0.013142</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.014707</td>\n",
       "      <td>0.067381</td>\n",
       "      <td>-0.025004</td>\n",
       "      <td>-0.037318</td>\n",
       "      <td>0.013757</td>\n",
       "      <td>0.041707</td>\n",
       "      <td>0.090888</td>\n",
       "      <td>0.021773</td>\n",
       "      <td>0.070574</td>\n",
       "      <td>-0.041105</td>\n",
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       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
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       "      <td>-0.047186</td>\n",
       "      <td>-0.126568</td>\n",
       "      <td>0.016551</td>\n",
       "      <td>-0.091217</td>\n",
       "      <td>0.114245</td>\n",
       "      <td>0.028997</td>\n",
       "      <td>-0.011451</td>\n",
       "      <td>-0.054338</td>\n",
       "      <td>-0.046695</td>\n",
       "      <td>-0.021423</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.015729</td>\n",
       "      <td>0.071683</td>\n",
       "      <td>-0.026062</td>\n",
       "      <td>-0.039263</td>\n",
       "      <td>0.015930</td>\n",
       "      <td>0.054902</td>\n",
       "      <td>0.090228</td>\n",
       "      <td>0.004987</td>\n",
       "      <td>0.065474</td>\n",
       "      <td>-0.042609</td>\n",
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       "    <tr>\n",
       "      <th>1229</th>\n",
       "      <td>-0.051686</td>\n",
       "      <td>-0.128937</td>\n",
       "      <td>0.017885</td>\n",
       "      <td>-0.089340</td>\n",
       "      <td>0.111332</td>\n",
       "      <td>0.024499</td>\n",
       "      <td>-0.011107</td>\n",
       "      <td>-0.054856</td>\n",
       "      <td>-0.046236</td>\n",
       "      <td>-0.017079</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.022589</td>\n",
       "      <td>0.071391</td>\n",
       "      <td>-0.027886</td>\n",
       "      <td>-0.037365</td>\n",
       "      <td>0.019784</td>\n",
       "      <td>0.049307</td>\n",
       "      <td>0.091884</td>\n",
       "      <td>0.014374</td>\n",
       "      <td>0.066112</td>\n",
       "      <td>-0.041239</td>\n",
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       "      <th>1230</th>\n",
       "      <td>-0.041520</td>\n",
       "      <td>-0.126039</td>\n",
       "      <td>0.007327</td>\n",
       "      <td>-0.090880</td>\n",
       "      <td>0.113951</td>\n",
       "      <td>0.031531</td>\n",
       "      <td>-0.010603</td>\n",
       "      <td>-0.054147</td>\n",
       "      <td>-0.047652</td>\n",
       "      <td>-0.024619</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.011880</td>\n",
       "      <td>0.071534</td>\n",
       "      <td>-0.028025</td>\n",
       "      <td>-0.037676</td>\n",
       "      <td>0.016719</td>\n",
       "      <td>0.061040</td>\n",
       "      <td>0.093330</td>\n",
       "      <td>0.009919</td>\n",
       "      <td>0.064024</td>\n",
       "      <td>-0.042506</td>\n",
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       "    <tr>\n",
       "      <th>1231</th>\n",
       "      <td>-0.046474</td>\n",
       "      <td>-0.127358</td>\n",
       "      <td>-0.004217</td>\n",
       "      <td>-0.073223</td>\n",
       "      <td>0.108792</td>\n",
       "      <td>0.039449</td>\n",
       "      <td>-0.004596</td>\n",
       "      <td>-0.049178</td>\n",
       "      <td>-0.044158</td>\n",
       "      <td>-0.014196</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.006698</td>\n",
       "      <td>0.086611</td>\n",
       "      <td>-0.018506</td>\n",
       "      <td>-0.027007</td>\n",
       "      <td>0.024811</td>\n",
       "      <td>0.059834</td>\n",
       "      <td>0.097593</td>\n",
       "      <td>0.028478</td>\n",
       "      <td>0.077590</td>\n",
       "      <td>-0.045125</td>\n",
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       "    <tr>\n",
       "      <th>1232</th>\n",
       "      <td>-0.043099</td>\n",
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       "      <td>0.023720</td>\n",
       "      <td>-0.088778</td>\n",
       "      <td>0.103328</td>\n",
       "      <td>0.024288</td>\n",
       "      <td>-0.011344</td>\n",
       "      <td>-0.062268</td>\n",
       "      <td>-0.041151</td>\n",
       "      <td>-0.007892</td>\n",
       "      <td>...</td>\n",
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       "      <td>0.073401</td>\n",
       "      <td>-0.014165</td>\n",
       "      <td>-0.040095</td>\n",
       "      <td>0.023925</td>\n",
       "      <td>0.065251</td>\n",
       "      <td>0.095360</td>\n",
       "      <td>0.009302</td>\n",
       "      <td>0.068400</td>\n",
       "      <td>-0.043873</td>\n",
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       "  </tbody>\n",
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       "<p>1233 rows × 512 columns</p>\n",
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      ],
      "text/plain": [
       "           p_0       p_1       p_2       p_3       p_4       p_5       p_6  \\\n",
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       "1    -0.032315 -0.122054 -0.010417 -0.071897  0.109930  0.055475  0.002491   \n",
       "2    -0.041239 -0.128768  0.013445 -0.089572  0.113357  0.028909 -0.003931   \n",
       "3    -0.053598 -0.126727  0.013942 -0.089992  0.106270  0.019663 -0.009753   \n",
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       "...        ...       ...       ...       ...       ...       ...       ...   \n",
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       "1230 -0.041520 -0.126039  0.007327 -0.090880  0.113951  0.031531 -0.010603   \n",
       "1231 -0.046474 -0.127358 -0.004217 -0.073223  0.108792  0.039449 -0.004596   \n",
       "1232 -0.043099 -0.142669  0.023720 -0.088778  0.103328  0.024288 -0.011344   \n",
       "\n",
       "           p_7       p_8       p_9  ...     p_502     p_503     p_504  \\\n",
       "0    -0.060004 -0.036764 -0.033473  ... -0.020152  0.082769 -0.032394   \n",
       "1    -0.050859 -0.043207 -0.031467  ... -0.012507  0.089238 -0.022887   \n",
       "2    -0.059228 -0.044582 -0.015745  ... -0.019659  0.057286 -0.021680   \n",
       "3    -0.045075 -0.045403 -0.019771  ... -0.026003  0.064901 -0.031808   \n",
       "4    -0.051125 -0.038727 -0.013142  ... -0.014707  0.067381 -0.025004   \n",
       "...        ...       ...       ...  ...       ...       ...       ...   \n",
       "1228 -0.054338 -0.046695 -0.021423  ... -0.015729  0.071683 -0.026062   \n",
       "1229 -0.054856 -0.046236 -0.017079  ... -0.022589  0.071391 -0.027886   \n",
       "1230 -0.054147 -0.047652 -0.024619  ... -0.011880  0.071534 -0.028025   \n",
       "1231 -0.049178 -0.044158 -0.014196  ... -0.006698  0.086611 -0.018506   \n",
       "1232 -0.062268 -0.041151 -0.007892  ... -0.002684  0.073401 -0.014165   \n",
       "\n",
       "         p_505     p_506     p_507     p_508     p_509     p_510     p_511  \n",
       "0    -0.036015  0.012536  0.043216  0.084375  0.007837  0.069794 -0.044134  \n",
       "1    -0.037875  0.013370  0.073821  0.096903  0.017133  0.064631 -0.039452  \n",
       "2    -0.040389  0.014894  0.037244  0.083684  0.005021  0.065194 -0.036202  \n",
       "3    -0.035478  0.020381  0.035428  0.084140  0.008325  0.061186 -0.041064  \n",
       "4    -0.037318  0.013757  0.041707  0.090888  0.021773  0.070574 -0.041105  \n",
       "...        ...       ...       ...       ...       ...       ...       ...  \n",
       "1228 -0.039263  0.015930  0.054902  0.090228  0.004987  0.065474 -0.042609  \n",
       "1229 -0.037365  0.019784  0.049307  0.091884  0.014374  0.066112 -0.041239  \n",
       "1230 -0.037676  0.016719  0.061040  0.093330  0.009919  0.064024 -0.042506  \n",
       "1231 -0.027007  0.024811  0.059834  0.097593  0.028478  0.077590 -0.045125  \n",
       "1232 -0.040095  0.023925  0.065251  0.095360  0.009302  0.068400 -0.043873  \n",
       "\n",
       "[1233 rows x 512 columns]"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df_fasttext = using_bioembedding_instance.apply_prottrans_t5_xlu50()\n",
    "df_fasttext"
   ]
  }
 ],
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