Background
Methods
Clinical scenario
Ecog status | Mobile prosthesis | Body mass index (BMI) | Grade of differentiation |
---|---|---|---|
Weight | Dental Cusps | Substance Exposition | Surgical Margins |
Height | Galvanic Current | Precancerous Lesions | Martinez-Gimeno Score |
Diabetes | Oral Hygiene |
Duration
| Anneroths Mod Score |
Allergies | Infection | Immunosuppressor Treatments Presence | D2_40Stain |
Cholesterol |
Type Of Infection
|
Immuno Duration
| P53_STAIN |
Hypertension | Physical Agents |
Immuno Type
| P16Ink4aStain |
Family History Of Malignance |
Type Of Physical Agent
| Tumor Maximum Diameter | EGFR Stain |
Smoker | Diet Deficit | Tumor Thickness | CyclinD1Stain |
Smoking Habits |
Fe Haematic Concentration
| Depth Of Invasion | Ki67Stain |
Quantity Per Day | Plummer Vinson | Basaloid Features | HPV_DNA |
Smoking For |
Hb Haematic Concentration
| Lympho Plasmacytic Rection | T Staging |
Ex Smoker |
B12 Vitamins Haematic Concentration
| Lympho Plasmacytic Invasion | N Staging |
Quitted Smoking
|
A Vitamins Haematic Concentration
| Perineural Invasion | M Staging |
Alcohol |
E Vitamins Haematic Concentration
| Degree Of Cells Keratinisation | |
Drinking Habits |
Folati
| Nuclear Pleomorphism | |
Mechanical Trauma | Eating Habits | Number of Mitoses per 10HPF |
Contrast take-up rate | Necrosis | Side of lymph nodes |
---|---|---|
Minor Axis Bigger than 10mm | Central Necrosis | Side Relative to Tumor |
Extra Nodal Spreading | Bone Infiltration | Cluster |
Shape Deviation | Carotid Infiltration | Number of Lymph Nodes |
Texture | Cuteneous Invasion | Number of Lymph Nodes Bigger than 3 |
Water Content | Site of lymph nodes |
Baseline data analysis
Preprocessing
Feature selection
Classification
Disease evolution monitoring
Identification of the most significant genes
Personalized Genetic Signature
Dynamic Bayesian Networks
Results
Baseline data analysis
Clinical-based classification
Classification algorithm | Acc. (%) | Se. (%) | Sp. (%) | Kappa | AUC | |
---|---|---|---|---|---|---|
No feature selection
|
BN
| 73.7(±8.86) | 61.4(±16.04) | 86(±10.86) | 0.47(±0.18) | 0.775(±0.13) |
NB
| 74.6(±15.54) | 68.4(±14.72) | 80.7(±18.31) | 0.49(±0.31) | 0.721(±0.15) | |
ANN
| 74.6(±15.65) | 73.7(±19.78) | 75.4(±19.25) | 0.49(±0.31) | 0.781(±0.12) | |
SVM
| 74.6(±11.84) | 71.9(±17.93) | 77.2(±20.73) | 0.49(±0.24) | 0.746(±0.12) | |
DT
| 81.6(±11.21) | 73.7(±14.35) | 89.5(±11.91) | 0.63(±0.22) | 0.826(±0.10) | |
RF
| 74.6(±13.98) | 68.4(±18.19) | 80.7(±16.56) | 0.49(±0.28) | 0.807(±0.09) | |
CFS
|
BN
| 73.7(±10.20) | 64.9(±15.56) | 82.5(±12.18) | 0.47(±0.20) | 0.776(±0.08) |
NB
| 77.2(±9.73) | 68.4(±14.42) | 86(±12.15) | 0.54(±0.19) | 0.783(±0.10) | |
ANN
| 71.9(±10.03) | 68.4(±14.35) | 75.4(±15.07) | 0.44(±0.20) | 0.736(±0.10) | |
SVM
| 78.1(±10.26) | 66.7(±17.43) | 89.5(±9.09) | 0.56(±0.21) | 0.781(±0.10) | |
DT
| 77.2(±11.88) | 66.7(±12.09) | 87.7(±15.96) | 0.54(±0.24) | 0.788(±0.07) | |
RF
| 72(±14.12) | 64.9(±16.94) | 78.9(±16.39) | 0.44(±0.28) | 0.75(±0.09) | |
Wrapper
|
BN
| 74.6(±10.62) | 66.7(±18.21) | 82.5(±8.05) | 0.49(±0.22) | 0.758(±0.15) |
NB
| 78.1(±10.59) | 73.7(±14.56) | 82.5(±9.19) | 0.56(±0.21) | 0.791(±0.09) | |
ANN
| 77.2(±14.39) | 73.3(±11.09) | 80.7(±19.95) | 0.54(±0.29) | 0.791(±0.13) | |
SVM
| 78.1(±11.62) | 66.7(±17.43) | 89.5(±11.65) | 0.56(±0.23) | 0.781(±0.12) | |
DT
| 83.3(±10.06) | 73.7(±14.35) | 93(±8.05) | 0.67(±0.20) | 0.842(±0.09) | |
RF
| 75.4(±8.60) | 71.9(±12.01) | 78.9(±8.05) | 0.51(±0.17) | 0.826(±0.11) |
Imaging-based classification
Classification algorithm | Acc. (%) | Se. (%) | Sp. (%) | Kappa | AUC | |
---|---|---|---|---|---|---|
No feature selection
|
BN
| 86.4(±10.48) | 77.3(±17.98) | 95.5(±9.56) | 0.73(±0.21) | 0.936(±0.07) |
NB
| 87.5(±11.96) | 75(±23.21) | 100(±0) | 0.75(±0.24) | 0.901(±0.12) | |
ANN
| 83(±10.65) | 81.8(±13.58) | 84.1(±18.83) | 0.69(±0.21) | 0.914(±0.07) | |
SVM
| 84.1(±12.15) | 81.8(±17.98) | 86.4(±19.16) | 0.68(±0.24) | 0.841(±0.12) | |
DT
| 77.3(±17.71) | 72.7(±25.41) | 81.8(±27.29) | 0.55(±0.35) | 0.738(±0.19) | |
RF
| 83(±8.02) | 72.7(±16.70) | 93.2(±16.36) | 0.66(±0.16) | 0.915(±0.11) | |
CFS
|
BN
| 85.23(±11.05) | 81.8(±16.91) | 88.6(±15.06) | 0.7(±0.22) | 0.917(±0.05) |
NB
| 77.3(±6.82) | 65.9(±13.12) | 88.6(±15.06) | 0.55(±0.13) | 0.881(±0.07) | |
ANN
| 83(±11.72) | 84.1(±14.14) | 81.8(±11.35) | 0.66(±0.23) | 0.89(±0.10) | |
SVM
| 87.5(±12.25) | 84.1(±14.76) | 90.9(±14.15) | 0.75(±0.24) | 0.875(±0.12) | |
DT
| 84.1(±11.72) | 77.3(±14.42) | 90.9(±14.15) | 0.68(±0.23) | 0.831(±0.13) | |
RF
| 83(±11.72) | 79.5(±13.58) | 86.4(±14.54) | 0.66(±0.23) | 0.887(±0.11) | |
Wrapper
|
BN
| 85.2(±12.25) | 84.1(±14.76) | 86.4(±14.15) | 0.7(±0.24) | 0.866(±0.11) |
NB
| 90.9(±12.25) | 88.6(±14.76) | 93.2(±14.15) | 0.82(±0.24) | 0.89(±0.12) | |
ANN
| 89.8(±12.25) | 86.4(±14.76) | 93.2(±14.15) | 0.8(±0.24) | 0.854(±0.13) | |
SVM
| 86.4(±12.25) | 86.4(±14.76) | 86.4(±14.15) | 0.73(±0.24) | 0.864(±0.12) | |
DT
| 85.2(±13.64) | 86.4(±14.76) | 84.1(±25.58) | 0.7(±0.28) | 0.835(±0.24) | |
RF
| 88.6(±12.25) | 84.1(±14.76) | 93.2(±14.15) | 0.77(±0.24) | 0.906(±0.13) |
Tissue genomic-based classification
TCAM1 | AMDHD1 | SLC5A12 |
---|---|---|
SOD2 | AY358224 | AK026836 |
FCAR | PHACTR1 | RPRM |
Classification algorithm | Acc. (%) | Se. (%) | Sp. (%) | Kappa | AUC | |
---|---|---|---|---|---|---|
No feature selection
|
BN
| 75.8(±15.44) | 75(±21.15) | 76.7(±19.56) | 0.52(±0.31) | 0.843(±0.09) |
NB
| 74.2(±10.72) | 70(±20.49) | 78.3(±13.72) | 0.48(±0.21) | 0.834(±0.12) | |
ANN
| 74.2(±12.70) | 83.3(±13.61) | 65(±21.44) | 0.48(±0.25) | 0.834(±0.13) | |
SVM
| 74.2(±12.08) | 75(±18.00) | 73.3(±16.10) | 0.48(±0.24) | 0.742(±0.12) | |
DT
| 69.2(±11.82) | 68.3(±21.44) | 67(±25.82) | 0.38(±0.24) | 0.706(±0.14) | |
RF
| 80(±8.96) | 85(±14.59) | 75(±23.90) | 0.6(±0.18) | 0.856(±0.10) | |
CFS
|
BN
| 75.8(±14.83) | 75(±20.86) | 76.7(±17.21) | 0.52(±0.30) | 0.838(±0.09) |
NB
| 75(±12.91) | 75(±17.66) | 75(±19.64) | 0.5(±0.26) | 0.837(±0.10) | |
ANN
| 78.3(±10.54) | 83.3(±13.15) | 73.3(±14.05) | 0.57(±0.21) | 0.854(±0.13) | |
SVM
| 70.1(±9.46) | 73.3(±18.00) | 68.3(±13.72) | 0.42(±0.19) | 0.708(±0.09) | |
DT
| 72.5(±13.72) | 73.3(±16.20) | 71.7(±26.59) | 0.45(±0.27) | 0.724(±0.15) | |
RF
| 76.7(±11.92) | 80(±17.57) | 73.3(±22.50) | 0.53(±0.24) | 0.845(±0.09) | |
Wrapper
|
BN
| 74.2(±12.08) | 70(±18.92) | 78.3(±14.59) | 0.48(±0.24) | 0.782(±0.10) |
NB
| 73.3(±11.15) | 73.3(±18.34) | 73.3(±10.54) | 0.47(±0.22) | 0.833(±0.10) | |
ANN
| 73.3(±15.32) | 81.7(±16.57) | 65(±19.33) | 0.47(±0.31) | 0.772(±0.12) | |
SVM
| 77.5(±9.00) | 76.7(±16.57) | 78.3(±14.05) | 0.55(±0.18) | 0.775(±0.09) | |
DT
| 62.5(±14.83) | 70(±15.32) | 55(±17.66) | 0.25(±0.20) | 0.665(±0.15) | |
RF
| 77.5(±13.49) | 78.3(±17.21) | 76.7(±23.57) | 0.55(±0.27) | 0.842(±0.13) |
Source of gene set | Classifier | Acc (%) | Se (%) | Sp (%) | Kappa statistic | AUC | # of genes |
---|---|---|---|---|---|---|---|
Literature
| RF | 78.94(±8.93) | 82.5(±11.20) | 75.4(±16.56) | 0.58(±0.18) | 0.841(±0.07) | 28 |
Current work
| RF | 80(±8.96) | 85(±14.59) | 75(±23.90) | 0.6(±0.18) | 0.856(±0.10) | 9 |
Union of literature and current work
| ANN | 91.23(±7.23) | 94.7(±11.25) | 87.7(±13.72) | 0.82(±0.14) | 0.957(±0.04) | 37 |
Blood genomic-based classification
THC2410448 | BM683433 | A_24_P942151 |
---|---|---|
A_24_P221960 | OXCT2 | X58809 |
THC2399272 | A_24_P230388 | AL566369 |
CN391963 | A_32_P57247 |
Classification algorithm | Acc. (%) | Se. (%) | Sp. (%) | Kappa | AUC | |
---|---|---|---|---|---|---|
No feature selection
|
BN
| 87.5(±21.94) | 83.3(±42.16) | 91.7(±31.62) | 0.75(±0.48) | 0.965(±0) |
NB
| 91.7(±21.08) | 91.7(±31.62) | 91.7(±31.62) | 0.83(±0.42) | 0.986(±0) | |
ANN
| 95.8(±15.81) | 100(±0) | 91.7(±31.62) | 0.92(±0.32) | 1(±0) | |
SVM
| 95.8(±15.81) | 100(±0) | 91.7(±31.62) | 0.92(±0.32) | 0.958(±0.16) | |
DT
| 87.5(±21.94) | 100(±0) | 75(±48.30) | 0.75(±0.48) | 0.84(±0.24) | |
RF
| 87.5(±19.33) | 91.7(±31.62) | 83.3(±42.16) | 0.75(±0.48) | 0.941(±0) | |
CFS
|
BN
| 83.3(±0) | 91.7(±0) | 75(±0) | 0.67(±0) | 0.972(±0) |
NB
| 83.3(±15.81) | 83.3(±0) | 83.3(±31.62) | 0.67(±0.32) | 0.958(±0) | |
ANN
| 87.5(±15.81) | 91.7(±0) | 83.3(±31.62) | 0.75(±0.32) | 0.972(±0) | |
SVM
| 87.5(±15.81) | 83.3(±0) | 91.7(±31.62) | 0.75(±0.32) | 0.875(±0.16) | |
DT
| 87.5(±18.00) | 100(±0) | 75(±42.16) | 0.75(±0.42) | 0.84(±0.21) | |
RF
| 87.5(±21.94) | 91.7(±31.62) | 83.3(±42.16) | 0.75(±0.48) | 0.92(±0) | |
Wrapper
|
BN
| 70.8(±15.81) | 66.7(±31.62) | 75(±0) | 0.42(±0.32) | 0.859(±0) |
NB
| 83.3(±0) | 83.3(±0) | 83.3(±0) | 0.67(±0) | 0.955(±0) | |
ANN
| 87.5(±10.54) | 91.7(±0) | 83.3(±31.62) | 0.75(±0.32) | 0.924(±0) | |
SVM
| 95.8(±0) | 91.7(±0) | 100(±0) | 0.92(±0) | 0.958(±0) | |
DT
| 79.2(±18.00) | 83.3(±0) | 75(±42.16) | 0.58(±0.42) | 0.799(±0.21) | |
RF
| 66.7(±18.00) | 58.3(±31.62) | 75(±31.62) | 0.33(±0.42) | 0.729(±0.16) |
Multi-type classifier
Source of data | Feature selection | Classifier | Acc (%) | Se (%) | Sp (%) | Kappa | AUC |
---|---|---|---|---|---|---|---|
Clinical
| Wrapper | DT | 83.3 (±10.06) | 73.7 (±14.35) | 93 (±8.05) | 0.67 (±0.20) | 0.842 (±0.09) |
Imaging
| Wrapper | NB | 90.9 (±12.25) | 88.6 (±14.76) | 93.2 (±14.15) | 0.82 (±0.24) | 0.89 (±0.12) |
Tissue genomic
| Union of genes from literature and current work | ANN | 91.23 (±7.23) | 94.7 (±11.25) | 87.7 (±13.72) | 0.82 (±0.14) | 0.957 (±0.04) |
Blood genomic
| No feature selection | ANN | 95.8 (±15.81) | 100 (±0) | 91.7 (±31.62) | 0.92 (±0.32) | 1 (±0) |
Disease evolution monitoring
GeneID | Fold change |
---|---|
HMCN1 | 2.5 |
RGMA | 1.8 |
TSC1 | 2.2 |
AK023526 | 4.7 |
NOTCH2 | 2.8 |
STX6 | 4.8 |
THC2447689 | 2.9 |
THC2344152 | 1.9 |
LEPRE1 | 2.3 |
Evidence | Sensitivity (%) | Specificity (%) | Accuracy (%) |
---|---|---|---|
Baseline
| 63.6 | 100 | 86 |
Baseline & follow-up #1
| 100 | 100 | 100 |