Doctor5benchmark/DocToR-5
DocToR 5 documents Tracing of Robustness Dataset Summary We introduce the DOCTOR 5 benchmark to systematically test the visual and logical robustness of multimodal models. The dataset features approximately 13k+ document images and over 65000 visual question answering pairs. It covers 12 diverse domains including scientific papers financial reports and business presentations. This resource provides a standardized testbed for evaluating models against generation… See the full description on the dataset page: https://huggingface.co/datasets/Doctor5benchmark/DocToR-5.
0104
1{2 "layout_dets": [3 {4 "category_type": "table_caption",5 "poly": [6 317.1985963213058,7 184.7395583718088,8 1307.0689755819874,9 184.7395583718088,10 1307.0689755819874,11 217.10873744045932,12 317.1985963213058,13 217.1087374404593214 ],15 "ignore": false,16 "order": 1,17 "anno_id": 9,18 "text": "TABLE 3. Mapping of transposon insertions sites that result in white phenotype in C.sakazakii ES5",19 "line_with_spans": [20 {21 "category_type": "text_span",22 "poly": [23 322.66666666666663,24 192,25 1300,26 192,27 1300,28 216,29 322.66666666666663,30 21631 ],32 "text": "TABLE 3. Mapping of transposon insertions sites that result in white phenotype in C.sakazakii ES5"33 }34 ],35 "attribute": {36 "text_language": "text_english",37 "text_background": "white",38 "text_rotate": "normal"39 }40 },41 {42 "category_type": "table",43 "poly": [44 122.74817725245522,45 219.50787020739313,46 1522.135306576751,47 219.50787020739313,48 1522.135306576751,49 1631.6524635451324,50 122.74817725245522,51 1631.652463545132452 ],53 "ignore": false,54 "order": 2,55 "anno_id": 2,56 "html": "<table border=\"1\"><tr><td>$COG functional categorya^a$</td><td>COG functional class</td><td colspan=\"2\">$Annotation^{b,c}$</td></tr><tr><td></td><td></td><td>Homologue</td><td>Gene product</td></tr><tr><td colspan=\"4\">Mutation outside pigment operon</td></tr><tr><td>H: coenzyme transport and metabolism</td><td>Geranylgeranyl pyrophosphate synthase</td><td>crtE</td><td>Geranylgeranyl pyrophosphate synthase</td></tr><tr><td>GC: carbohydrate transport and metabolism/signal transduction mechanisms</td><td>Glucosyl transferases, related to UDP-glucosyltransferase</td><td>crtX</td><td>Zeaxanthin glucosyl transferase</td></tr><tr><td>R/E: general function prediction only/amino acid transport and metabolism</td><td>Acetyltransferase/choline dehydrogenase and related flavoproteins</td><td>crtY</td><td>Lycopene cyclase</td></tr><tr><td>O: secondary metabolites biosynthesis, transport and catabolism</td><td>Phytoene dehydrogenase and related proteins</td><td>crtl</td><td>Phytoene dehydrogenase</td></tr><tr><td>I: lipid transport and metabolism</td><td>Phytoene/squalene synthase</td><td>crtB</td><td>Phytoene synthase</td></tr><tr><td colspan=\"4\">Mutation outside pigment operon</td></tr><tr><td rowspan=\"10\">C: energy production and conversion </td><td>$F_{0}F_{1}$-type ATP synthase, subunit alpha</td><td>ESA_04012</td><td>$F_{0}F_{1}$ ATP synthase subunit alpha </td></tr><tr><td>$F_{0}F_{1}$-type ATP synthase, subunit alpha</td><td>ESA_04006</td><td>$F_{0}F_{1}$ ATP synthase subunit beta</td></tr><tr><td>$F_{0}F_{1}$-type ATP synthase, subunit gamma</td><td>ESA_04007</td><td>$F_{0}F_{1}$ ATP synthase subunit gamma</td></tr><tr><td>$F_{0}F_{1}$-type ATP synthase, subunit epsilon (mitochondrial delta subunit)</td><td>ESA_04005</td><td>$F_{0}F_{1}$ ATP synthase subunit splsion</td></tr><tr><td>Pyruvate/2-oxoglutarate dehydrogenase complex, dihydrolipoamide acetyltransferase (E1) component, and related enzymes</td><td>ESA_02622</td><td>sucA 2-oxoglutarate dehydrogenase</td></tr><tr><td>Pyruvate/2-oxoglutarate dehydrogenase complex, dihydrolipoamide acetyltransferase (E2) component, and related enzymes</td><td>FSA_02621</td><td>Dihydrolipoamide acetyltransferase</td></tr><tr><td>Pyruvate/2-oxoglutarate dehydrogenase complex, dihydrolipoamide acetyltransferase (E2) component, and related enzymes</td><td>ESA_03222</td><td>aceF dihydrolipoamide acetyltransferase</td></tr><tr><td>Malatl/lactate dehydrogenases Succinate dehydrogenase/fumarate reductase, flavoprotein subunit</td><td>ESA_03622 </td><td>Malate dehydrogenase </td></tr><tr><td>Succinate dehydrogenase/fumarate reductase, flavoprotein subunit</td><td>ESA_02624</td><td>Succinate dehydrogenase flavoprotein subunit</td></tr><tr><td>$Na^{+}/H^{+}$antiporter</td><td>ESA_03316</td><td>pH-dependent sodium/proton antiporter</td></tr><tr><td>P: inorganic ion transport and metabolism</td><td>cAMP-binding proteins, catabolite gene activator, and regulatory subunit of cAMP-dependent protein kinases</td><td>FSA_04376</td><td>cAMP regulatory protein</td></tr><tr><td>T: signal transduction mechanisms</td><td>DnaK suppressor protein</td><td>ESA_03194</td><td>DnaK transcriptional regulator DksA</td></tr><tr><td rowspan=\"3\">S: function unknown</td><td rowspan=\"3\">Uncharacterized conserved protein</td><td>$ESA_04343(Ent638_3811)\n^d$</td><td>Hypothetical protein $(intracellular growth attenuator IgA, Enterobacter sp. 638)^d$\n</td></tr><tr><td>$ESA_03563(ETA_03450)\n^d$</td><td>Hypothetical protein $(YhbC-like protein, Enterobacter tasmaniensis Et1-99)^d$</td></tr><tr><td>$ESA_00549(AAG53883)\n^d$</td><td>Hypothetical protein $(sigma factor RpoS, Escherichia coli)^d$</td></tr></table>",57 "attribute": {58 "table_layout": "horizontal",59 "with_span": true,60 "line": "fewer_line",61 "language": "table_en",62 "include_equation": true,63 "include_photo": false,64 "include_background": false,65 "with_structured_text": false66 },67 "table_edit_status": "good"68 },69 {70 "category_type": "table_footnote",71 "poly": [72 138.19340970256346,73 1628.5129213045227,74 1265.0805796595528,75 1628.5129213045227,76 1265.0805796595528,77 1725.5684429923851,78 138.19340970256346,79 1725.568442992385180 ],81 "ignore": false,82 "order": 3,83 "anno_id": 7,84 "text": "$ ^{a} $ NCBI clusters of orthologous groups (COG) of proteins. $ ^{b} $ Cronobacter sakazakii ES5 BAC 9E10 for mutations within the pigment operon (accession no. AM384990.1）. $ ^{c} $ NCBI assembly ATCC BAA-894 C. sakazakii complete genome for mutations outside pigment operon (accession no. 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AM384990.1）."141 },142 {143 "category_type": "footnote_mark",144 "poly": [145 134.46457874201124,146 1678.260665026788,147 148.029114638832,148 1678.260665026788,149 148.029114638832,150 1696.9577280197032,151 134.46457874201124,152 1696.9577280197032153 ],154 "latex": "$ ^{c} $"155 },156 {157 "category_type": "text_span",158 "poly": [159 149.4956933223706,160 1678.967244728048,161 1262.2986126385738,162 1678.967244728048,163 1262.2986126385738,164 1699.6638413508854,165 149.4956933223706,166 1699.6638413508854167 ],168 "text": "NCBI assembly ATCC BAA-894 C. sakazakii complete genome for mutations outside pigment operon (accession no. CP000783.1)."169 },170 {171 "category_type": "footnote_mark",172 "poly": [173 135.931015055181,174 1698.7907734111652,175 150.2287691085867,176 1698.7907734111652,177 150.2287691085867,178 1720.0540999521277,179 135.931015055181,180 1720.0540999521277181 ],182 "latex": "$ ^{d} $"183 },184 {185 "category_type": "text_span",186 "poly": [187 149.3338807445372,188 1699.3157608176932,189 392.2558723641656,190 1699.3157608176932,191 392.2558723641656,192 1724.960116938767,193 149.3338807445372,194 1724.960116938767195 ],196 "text": "Closest annotated homolog."197 }198 ],199 "attribute": {200 "text_language": "text_english",201 "text_background": "white",202 "text_rotate": "normal"203 }204 },205 {206 "category_type": "text_block",207 "poly": [208 115.59128806152968,209 1801.5321991703095,210 790.6654231521392,211 1801.5321991703095,212 790.6654231521392,213 1927.6606999940327,214 115.59128806152968,215 1927.6606999940327216 ],217 "ignore": false,218 "order": 4,219 "anno_id": 0,220 "text": "(data not shown), consistently with the results for LB, all mutant strains showed significantly increased maximum rates of growth ( $ \\mu\\mathrm{m a x}_{\\mathrm{w t}} $ ,0.14; $ \\mu\\mathrm{m a x}_{\\Delta c r t X} $ , 0.22; $ \\mu\\mathrm{m a x}_{\\Delta c r t E} $ , 0.24; and $ \\mu\\mathrm{m a x}_{\\Delta c r t Y} $ , 0.19; P = 0.000).",221 "line_with_spans": [222 {223 "category_type": "text_span",224 "poly": [225 122.66666666666666,226 1812,227 785.3333333333333,228 1812,229 785.3333333333333,230 1834.6666666666665,231 122.66666666666666,232 1834.6666666666665233 ],234 "text": "(data not shown), consistently with the results for LB, all mu-"235 },236 {237 "category_type": "text_span",238 "poly": [239 120,240 1842.6666666666665,241 788,242 1842.6666666666665,243 788,244 1865.3333333333333,245 120,246 1865.3333333333333247 ],248 "text": "tant strains showed significantly increased maximum rates of"249 },250 {251 "category_type": "text_span",252 "poly": [253 119.34318621059637,254 1872.3341843259907,255 215.44112853834812,256 1872.3341843259907,257 215.44112853834812,258 1897.6675176593242,259 119.34318621059637,260 1897.6675176593242261 ],262 "text": "growth ("263 },264 {265 "category_type": "equation_inline",266 "poly": [267 213.31001603334786,268 1870.6666666666667,269 295.445226642847,270 1870.6666666666667,271 295.445226642847,272 1898.6666666666667,273 213.31001603334786,274 1898.6666666666667275 ],276 "latex": "$ \\mu\\mathrm{m a x}_{\\mathrm{w t}} $"277 },278 {279 "category_type": "text_span",280 "poly": [281 293.527100502496,282 1872.763550251248,283 365.527100502496,284 1872.763550251248,285 365.527100502496,286 1898.0968835845813,287 293.527100502496,288 1898.0968835845813289 ],290 "text": "，0.14;"291 },292 {293 "category_type": "equation_inline",294 "poly": [295 370.6666666666668,296 1870.1306444329578,297 481.8424665632862,298 1870.1306444329578,299 481.8424665632862,300 1898.1306444329578,301 370.6666666666668,302 1898.1306444329578303 ],304 "latex": "$ \\mu\\mathrm{m a x}_{\\Delta c r t X} $"305 },306 {307 "category_type": "text_span",308 "poly": [309 480.6751211896624,310 1870.7888235616613,311 554.8920448271418,312 1870.7888235616613,313 554.8920448271418,314 1896.1221568949948,315 480.6751211896624,316 1896.1221568949948317 ],318 "text": ", 0.22;"319 },320 {321 "category_type": "equation_inline",322 "poly": [323 557.3333333333335,324 1870.6666666666665,325 667.5990650323391,326 1870.6666666666665,327 667.5990650323391,328 1898.6666666666665,329 557.3333333333335,330 1898.6666666666665331 ],332 "latex": "$ \\mu\\mathrm{m a x}_{\\Delta c r t E} $"333 },334 {335 "category_type": "text_span",336 "poly": [337 667.3835717337635,338 1870.741247966539,339 739.561642265134,340 1870.741247966539,341 739.561642265134,342 1896.0745812998725,343 667.3835717337635,344 1896.0745812998725345 ],346 "text": ", 0.24;"347 },348 {349 "category_type": "text_span",350 "poly": [351 744.3726138143347,352 1870.475237515008,353 788.2064559657613,354 1870.475237515008,355 788.2064559657613,356 1896.30601202704,357 744.3726138143347,358 1896.30601202704359 ],360 "text": "and"361 },362 {363 "category_type": "equation_inline",364 "poly": [365 116,366 1901.3333333333333,367 232,368 1901.3333333333333,369 232,370 1929.3333333333333,371 116,372 1929.3333333333333373 ],374 "latex": "$ \\mu\\mathrm{m a x}_{\\Delta c r t Y} $"375 },376 {377 "category_type": "text_span",378 "poly": [379 225.35428436165395,380 1902.1578615598844,381 292.6577657871861,382 1902.1578615598844,383 292.6577657871861,384 1927.438820872643,385 225.35428436165395,386 1927.438820872643387 ],388 "text": ", 0.19;"389 },390 {391 "category_type": "equation_ignore",392 "poly": [393 296.6504079351266,394 1900.5074343050203,395 426.03299827406704,396 1900.5074343050203,397 426.03299827406704,398 1929.2831609188645,399 296.6504079351266,400 1929.2831609188645401 ],402 "text": "P = 0.000)."403 }404 ],405 "attribute": {406 "text_language": "text_english",407 "text_background": "white",408 "text_rotate": "normal"409 }410 },411 {412 "category_type": "text_block",413 "poly": [414 114.15800964307827,415 1926.2274215755813,416 796.3985368259448,417 1926.2274215755813,418 796.3985368259448,419 2016.5239619380195,420 114.15800964307827,421 2016.5239619380195422 ],423 "ignore": false,424 "order": 5,425 "anno_id": 4,426 "text": "Cold stress experiments were performed by growing $ \\Delta c r t E, $ $ \\Delta c r t X $ and $ \\Delta c r t Y $ in LB and M9 medium at $ 1 0^{\\circ} \\mathrm{C} $ (for results in M9, see Fig. 1B). Under these conditions, no significant dif-",427 "line_with_spans": [428 {429 "category_type": "text_span",430 "poly": [431 146.66666666666683,432 1934.6666666666667,433 717.81757859247,434 1934.6666666666667,435 717.81757859247,436 1957.3333333333333,437 146.66666666666683,438 1957.3333333333333439 ],440 "text": "Cold stress experiments were performed by growing"441 },442 {443 "category_type": "equation_inline",444 "poly": [445 716.5924233406782,446 1931.4828822436803,447 786.6047764988258,448 1931.4828822436803,449 786.6047764988258,450 1957.5986012788621,451 716.5924233406782,452 1957.5986012788621453 ],454 "latex": "$ \\Delta c r t E， $"455 },456 {457 "category_type": "equation_inline",458 "poly": [459 115.53088556638362,460 1959.6011639379176,461 182.4320277003501,462 1959.6011639379176,463 182.4320277003501,464 1986.6680382363925,465 115.53088556638362,466 1986.6680382363925467 ],468 "latex": "$ \\Delta c r t X $"469 },470 {471 "category_type": "text_span",472 "poly": [473 191.01534943574654,474 1962.4594572354413,475 234.4505709213879,476 1962.4594572354413,477 234.4505709213879,478 1985.9244619460753,479 191.01534943574654,480 1985.9244619460753481 ],482 "text": "and"483 },484 {485 "category_type": "equation_inline",486 "poly": [487 234.5229933313774,488 1964.1974256112435,489 302.4455269483052,490 1964.1974256112435,491 302.4455269483052,492 1987.1787339778732,493 234.5229933313774,494 1987.1787339778732495 ],496 "latex": "$ \\Delta c r t Y $"497 },498 {499 "category_type": "text_span",500 "poly": [501 302.47641924183404,502 1964.0000000000005,503 580.0000000000005,504 1964.0000000000005,505 580.0000000000005,506 1985.3333333333333,507 302.47641924183404,508 1985.3333333333333509 ],510 "text": "in LB and M9 medium at"511 },512 {513 "category_type": "equation_inline",514 "poly": [515 580,516 1960,517 636,518 1960,519 636,520 1988,521 580,522 1988523 ],524 "latex": "$ 1 0^{\\circ} \\mathrm{C} $"525 },526 {527 "category_type": "text_span",528 "poly": [529 637.3333333333335,530 1964,531 788.7634288404207,532 1964,533 788.7634288404207,534 1987.1264986785548,535 637.3333333333335,536 1987.1264986785548537 ],538 "text": "(for results in"539 },540 {541 "category_type": "text_span",542 "poly": [543 121.3333333333336,544 1994.6666666666667,545 789.9748360052404,546 1994.6666666666667,547 789.9748360052404,548 2018.6666666666665,549 121.3333333333336,550 2018.6666666666665551 ],552 "text": "M9, see Fig. 1B). 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