Vision-based Deep Learning Analysis of Unordered Biomedical Tabular Datasets via Optimal Spatial Cartography
Organizations: Department of Radiation Oncology, Stanford University, Stanford, California, USA · Department of Radiology, Stanford University, Stanford, California, USA · Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California, USA · Stanford Cancer Institute, Stanford University, Stanford, California, USA
Abstract
Tabular data are central to biomedical research, from liquid biopsy and bulk and single-cell transcriptomics to electronic health records and phenotypic profiling. Unlike images or sequences, however, tabular datasets lack intrinsic spatial organization: features are treated as unordered dimensions, and their relationships must be inferred implicitly by the model. This limits the ability of vision architectures to exploit local structure and higher-order feature interactions in non-spatial biomedical data. Here we introduce Dynamic Feature Mapping (Dynomap), an end-to-end deep learning framework that learns a task-optimized spatial topology of features directly from data. Dynomap jointly optimizes feature placement and prediction through a fully differentiable rendering mechanism, without relying on heuristics, predefined groupings, or external priors. By transforming high-dimensional tabular vectors into learned feature maps, Dynomap enables vision-based models to operate effectively on unordered biomedical inputs. Across multiple clinical and biological datasets, Dynomap consistently outperformed classical machine learning, modern deep tabular models, and existing vector-to-image approaches. In liquid biopsy data, Dynomap organized clinically relevant gene signatures into coherent spatial patterns and improved multiclass cancer subtype prediction accuracy by up to 18%. In a Parkinson disease voice dataset, it clustered disease-associated acoustic descriptors and improved accuracy by up to 8%. Similar gains and interpretable feature organization were observed in additional biomedical datasets. These results establish Dynomap as a general strategy for bridging tabular and vision-based deep learning and for uncovering structured, clinically relevant patterns in high-dimensional biomedical data.
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Appendix
| Fcer1g | Ubb | Cd79a | Cd79b | Cd3g | Bst2 | Il1b | Vpreb3 |
| Cfh | Cst3 | Fxyd5 | Tmsb10 | Laptm5 | Lsp1 | Gnas | Gng11 |
| S100a4 | Alox5ap | Ly6c1 | Plvap | Ctsl | Irf8 | H2_K1 | Tpm2 |
| Klf2 | Lyz2 | Sepp1 | Ccl3 | Vim | Socs3 | Lyz1 | Igfbp2 |
| Krt14 | Ramp2 | Ckb | Oaz1 | Gm1821 | Marcksl1 | Arpc2 | Arpc3 |
| Hbb_b2 | Car2 | Scgb1a1 | Prss34 | Ccl9 | Defb1 | Tyrobp | Gzma |
| AW112010 | Nkg7 | Ifitm1 | Tg | H2_D1 | Emp3 | Hmgb2 | Lgals1 |
| Park7 | Rpl17 | Sub1 | Ube2i | Erp29 | Mcpt8 | Icam1 | Tsc22d1 |
| Atp5e | Fxyd3 | Rps18 | Ndufb9 | x3110003A17Rik | Dmkn | Uqcrfs1 | Rps19 |
| Rps25 | Ltb | Hnrnpab | Plac9 | Dnaja1 | Itm2b | Id1 | Ier3 |
| Rarres2 | Csrp2 | Mmp3 | Calm1 | Gnai2 | Pfdn5 | Sumo2 | Ctnnb1 |
| Atp5j | Cox4i1 | Rpsa | Slc25a4 | Cct7 | Ddx5 | Atp5h | Rpl23a |
| Snrpd2 | Tagln | Chmp2a | Ndufa4 | Ccl5 | Nbl1 | Rps21 | Uqcrb |
| Rpl10 | Arpc1a | Rpl10a | Akr1a1 | Etfb | Pomp | Srgn | Ubc |
| Acp5 | Rap1b | Hspb8 | Col2a1 | Il6 | Tomm20 | Dsp | Klf4 |
| Malat1 | Epsti1 | Ccl2 | Has1 | Neat1 | Prelid1 | Calr | Hspb1 |
| P4hb | Ppib | Fdps | Mup3 | Cxcl14 | Cxcl2 | x2010107E04Rik | Hrsp12 |
| Miox | Cat | Col8a1 | Cxcl10 | Mgst1 | C1qc | Rpl13a | Mpo |
| Lcn2 | Prtn3 | Eif3e | Gas5 | Impdh2 | Npm1 | Tagln2 | Cox7b |
| Hsp90ab1 | Tcp1 | Procr | Psmb1 | Trf | Emp1 | x1500015O10Rik | Hist1h2ao |
| Myl7 | Tpm1 | Rab11a | Akr1b8 | Rpl36 | Scgb3a2 | Sbpl | Scgb3a1 |
Tabular Prediction
Tabular prediction uses structured rows and columns to forecast labels, values, risks, and outcomes from data.
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