1 Goal

The goal is to predict neurologic status at 6-13 moths after traumatic spinal cord injury based on acute phase assessments one week after injury. We require to prognosticate long-term recovery after SCI by analyzing a subset of the data from the Sygen multicenter clinical trial. The data used to make the prediction of recovery at 6-13 months will be data available in the first month after spinal cord injury. One piece of data that is commonly used to make such predictions are the internacional Standards for Neurological Classification of SCI (INCSCI). This clinical outcome assessment evaluates motor and sensory impairment across the body and helpts localize the neurologic level of the SCI and grade the severity of that injury. Additional data includes demographic information, comorbidities, surgical interventions and medical complications.

1.1 Data

The following files are provided and explained based on the description given at https://asia-spinalinjury.org/.

1.1.1 File 1: metada.csv

Includes time-invariante features (including age, bmi, but also information on previous conditions). PID is the patient ID.

##  [1] "PID"          "bmi_category" "age_category" "sexcd"        "tx1_r"       
##  [6] "srdecc1"      "surgcd1"      "spcsuc1"      "scdecc1"      "hemccd1"     
## [11] "mhpsyccd"     "mhneurcd"     "mhcardcd"     "mhmetacd"

1.1.1.1 Variable Descriptions

Variable Type Description Values
PID Fixed patient id -
age_category Fixed age at time of injury either above or below 65 years <65, >65
sexcd Fixed sex 1, female | 2, male
bmi_category Fixed bmi categorized underweight, healthy, overweight
srdecc1 Fixed first spinal surgery: were spinal roots decompressed during surgery 0, no | 1, yes
surgcd1 Fixed first spinal surgery: was spinal surgery performed 0, no | 1, yes
spcsuc1 Fixed first spinal surgery: Are there more than one area of spinal column surgery 0, no | 1, yes
scdecc1 Fixed first spinal surgery: was the spinal cord decompressed 0, no | 1, yes
hemccd1 Fixed first spinal surgery: did significant changes in the hemodynamic or pulmonary function occur during the operation 0, no | 1, yes
mhpsyccd Fixed has the patient had a past history of psychiatric abnormalities 0, no | 1, yes | 9, unknown
mhneurcd Fixed has the patient had a past history of neurological abnormalities 0, no | 1, yes | 9, unknown
mhcardcd Fixed has the patient had a past history of cardiac abnormalities 0, no | 1, yes | 9, unknown
mhmetacd Fixed has the patient had a past history of metabolic or endocrinologic abnormalities 0, no | 1, yes | 9, unknown
tx1_r Fixed treatment group D1, dose 1 | D2, dose 2 | P, placebo

1.1.2 File 2: train_features.csv

All features, including ISNCSCI and AIS grades, at the time points 1,4,8 and 16 weeks after injury. Each row corresponds a specific patient ID, columns are features at various time points as given in the column names

1.1.2.1 AIS grade and motor scores

Variable Time Points Description Side Values
ais 1,4,8,16 Calculated AIS grade at baseline - A, B, C, D, E
elbfll 1,4,8,16 Motor score C5 Left 0,1,2,3,4,5
wrextl 1,4,8,16 Motor score C6 Left 0,1,2,3,4,5
elbexl 1,4,8,16 Motor score C7 Left 0,1,2,3,4,5
finfll 1,4,8,16 Motor score C8 Left 0,1,2,3,4,5
finabl 1,4,8,16 Motor score T1 Left 0,1,2,3,4,5
hipfll 1,4,8,16 Motor score L2 Left 0,1,2,3,4,5
kneexl 1,4,8,16 Motor score L3 Left 0,1,2,3,4,5
ankdol 1,4,8,16 Motor score L4 Left 0,1,2,3,4,5
gretol 1,4,8,16 Motor score L5 Left 0,1,2,3,4,5
ankpll 1,4,8,16 Motor score S1 Left 0,1,2,3,4,5
elbflr 1,4,8,16 Motor score C5 Right 0,1,2,3,4,5
wrextr 1,4,8,16 Motor score C6 Right 0,1,2,3,4,5
elbexr 1,4,8,16 Motor score C7 Right 0,1,2,3,4,5
finflr 1,4,8,16 Motor score C8 Right 0,1,2,3,4,5
finabr 1,4,8,16 Motor score T1 Right 0,1,2,3,4,5
hipflr 1,4,8,16 Motor score L2 Right 0,1,2,3,4,5
kneetr 1,4,8,16 Motor score L3 Right 0,1,2,3,4,5
ankdor 1,4,8,16 Motor score L4 Right 0,1,2,3,4,5
gretor 1,4,8,16 Motor score L5 Right 0,1,2,3,4,5
ankplr 1,4,8,16 Motor score S1 Right 0,1,2,3,4,5

1.1.2.2 Light touch scores

Variable Time Points Description Side Values
c2ltl 1,4,8,16 Light touch C2 Left 0,1,2
c3ltl 1,4,8,16 Light touch C3 Left 0,1,2
c4ltl 1,4,8,16 Light touch C4 Left 0,1,2
c5ltl 1,4,8,16 Light touch C5 Left 0,1,2
c6ltl 1,4,8,16 Light touch C6 Left 0,1,2
c7ltl 1,4,8,16 Light touch C7 Left 0,1,2
c8ltl 1,4,8,16 Light touch C8 Left 0,1,2
t1ltl 1,4,8,16 Light touch T1 Left 0,1,2
t2ltl 1,4,8,16 Light touch T2 Left 0,1,2
t3ltl 1,4,8,16 Light touch T3 Left 0,1,2
t4ltl 1,4,8,16 Light touch T4 Left 0,1,2
t5ltl 1,4,8,16 Light touch T5 Left 0,1,2
t6ltl 1,4,8,16 Light touch T6 Left 0,1,2
t7ltl 1,4,8,16 Light touch T7 Left 0,1,2
t8ltl 1,4,8,16 Light touch T8 Left 0,1,2
t9ltl 1,4,8,16 Light touch T9 Left 0,1,2
t10ltl 1,4,8,16 Light touch T10 Left 0,1,2
t11ltl 1,4,8,16 Light touch T11 Left 0,1,2
t12ltl 1,4,8,16 Light touch T12 Left 0,1,2
l1ltl 1,4,8,16 Light touch L1 Left 0,1,2
l2ltl 1,4,8,16 Light touch L2 Left 0,1,2
l3ltl 1,4,8,16 Light touch L3 Left 0,1,2
l4ltl 1,4,8,16 Light touch L4 Left 0,1,2
l5ltl 1,4,8,16 Light touch L5 Left 0,1,2
s1ltl 1,4,8,16 Light touch S1 Left 0,1,2
s2ltl 1,4,8,16 Light touch S2 Left 0,1,2
s3ltl 1,4,8,16 Light touch S3 Left 0,1,2
s45ltl 1,4,8,16 Light touch S4/5 Left 0,1,2
c2ltr 1,4,8,16 Light touch C2 Right 0,1,2
c3ltr 1,4,8,16 Light touch C3 Right 0,1,2
c4ltr 1,4,8,16 Light touch C4 Right 0,1,2
c5ltr 1,4,8,16 Light touch C5 Right 0,1,2
c6ltr 1,4,8,16 Light touch C6 Right 0,1,2
c7ltr 1,4,8,16 Light touch C7 Right 0,1,2
c8ltr 1,4,8,16 Light touch C8 Right 0,1,2
t1ltr 1,4,8,16 Light touch T1 Right 0,1,2
t2ltr 1,4,8,16 Light touch T2 Right 0,1,2
t3ltr 1,4,8,16 Light touch T3 Right 0,1,2
t4ltr 1,4,8,16 Light touch T4 Right 0,1,2
t5ltr 1,4,8,16 Light touch T5 Right 0,1,2
t6ltr 1,4,8,16 Light touch T6 Right 0,1,2
t7ltr 1,4,8,16 Light touch T7 Right 0,1,2
t8ltr 1,4,8,16 Light touch T8 Right 0,1,2
t9ltr 1,4,8,16 Light touch T9 Right 0,1,2
t10ltr 1,4,8,16 Light touch T10 Right 0,1,2
t11ltr 1,4,8,16 Light touch T11 Right 0,1,2
t12ltr 1,4,8,16 Light touch T12 Right 0,1,2
l1ltr 1,4,8,16 Light touch L1 Right 0,1,2
l2ltr 1,4,8,16 Light touch L2 Right 0,1,2
l3ltr 1,4,8,16 Light touch L3 Right 0,1,2
l4ltr 1,4,8,16 Light touch L4 Right 0,1,2
l5ltr 1,4,8,16 Light touch L5 Right 0,1,2
s1ltr 1,4,8,16 Light touch S1 Right 0,1,2
s2ltr 1,4,8,16 Light touch S2 Right 0,1,2
s3ltr 1,4,8,16 Light touch S3 Right 0,1,2
s45ltr 1,4,8,16 Light touch S4/5 Right 0,1,2

1.1.2.3 Prin Prick

Variable Time Points Description Side Values
c2ppl 1,4,8,16 Pin prick C2 Left 0,1,2
c3ppl 1,4,8,16 Pin prick C3 Left 0,1,2
c4ppl 1,4,8,16 Pin prick C4 Left 0,1,2
c5ppl 1,4,8,16 Pin prick C5 Left 0,1,2
c6ppl 1,4,8,16 Pin prick C6 Left 0,1,2
c7ppl 1,4,8,16 Pin prick C7 Left 0,1,2
c8ppl 1,4,8,16 Pin prick C8 Left 0,1,2
t1ppl 1,4,8,16 Pin prick T1 Left 0,1,2
t2ppl 1,4,8,16 Pin prick T2 Left 0,1,2
t3ppl 1,4,8,16 Pin prick T3 Left 0,1,2
t4ppl 1,4,8,16 Pin prick T4 Left 0,1,2
t5ppl 1,4,8,16 Pin prick T5 Left 0,1,2
t6ppl 1,4,8,16 Pin prick T6 Left 0,1,2
t7ppl 1,4,8,16 Pin prick T7 Left 0,1,2
t8ppl 1,4,8,16 Pin prick T8 Left 0,1,2
t9ppl 1,4,8,16 Pin prick T9 Left 0,1,2
t10ppl 1,4,8,16 Pin prick T10 Left 0,1,2
t11ppl 1,4,8,16 Pin prick T11 Left 0,1,2
t12ppl 1,4,8,16 Pin prick T12 Left 0,1,2
l1ppl 1,4,8,16 Pin prick L1 Left 0,1,2
l2ppl 1,4,8,16 Pin prick L2 Left 0,1,2
l3ppl 1,4,8,16 Pin prick L3 Left 0,1,2
l4ppl 1,4,8,16 Pin prick L4 Left 0,1,2
l5ppl 1,4,8,16 Pin prick L5 Left 0,1,2
s1ppl 1,4,8,16 Pin prick S1 Left 0,1,2
s2ppl 1,4,8,16 Pin prick S2 Left 0,1,2
s3ppl 1,4,8,16 Pin prick S3 Left 0,1,2
s45ppl 1,4,8,16 Pin prick S4/5 Left 0,1,2
c2ppr 1,4,8,16 Pin prick C2 Right 0,1,2
c3ppr 1,4,8,16 Pin prick C3 Right 0,1,2
c4ppr 1,4,8,16 Pin prick C4 Right 0,1,2
c5ppr 1,4,8,16 Pin prick C5 Right 0,1,2
c6ppr 1,4,8,16 Pin prick C6 Right 0,1,2
c7ppr 1,4,8,16 Pin prick C7 Right 0,1,2
c8ppr 1,4,8,16 Pin prick C8 Right 0,1,2
t1ppr 1,4,8,16 Pin prick T1 Right 0,1,2
t2ppr 1,4,8,16 Pin prick T2 Right 0,1,2
t3ppr 1,4,8,16 Pin prick T3 Right 0,1,2
t4ppr 1,4,8,16 Pin prick T4 Right 0,1,2
t5ppr 1,4,8,16 Pin prick T5 Right 0,1,2
t6ppr 1,4,8,16 Pin prick T6 Right 0,1,2
t7ppr 1,4,8,16 Pin prick T7 Right 0,1,2
t8ppr 1,4,8,16 Pin prick T8 Right 0,1,2
t9ppr 1,4,8,16 Pin prick T9 Right 0,1,2
t10ppr 1,4,8,16 Pin prick T10 Right 0,1,2
t11ppr 1,4,8,16 Pin prick T11 Right 0,1,2
t12ppr 1,4,8,16 Pin prick T12 Right 0,1,2
l1ppr 1,4,8,16 Pin prick L1 Right 0,1,2
l2ppr 1,4,8,16 Pin prick L2 Right 0,1,2
l3ppr 1,4,8,16 Pin prick L3 Right 0,1,2
l4ppr 1,4,8,16 Pin prick L4 Right 0,1,2
l5ppr 1,4,8,16 Pin prick L5 Right 0,1,2
s1ppr 1,4,8,16 Pin prick S1 Right 0,1,2
s2ppr 1,4,8,16 Pin prick S2 Right 0,1,2
s3ppr 1,4,8,16 Pin prick S3 Right 0,1,2
s45ppr 1,4,8,16 Pin prick S4/5 Right 0,1,2

1.1.3 File 3: train_outcomes_MS.csv

ISNCSCI motor scores assessed at either 26 or 52 weeks (as indicated in column “time”). Rows indicate patient IDs.

Variable Time Points Description Side Values
modben 26, 52 Modified Benzel Classification - 1, no motor or sensory function is preserved in the segments S4 to S5
2, sensory but not motor function is preserved in the sacral segments S4 to S5
3, motor function is preserved below the neurological level and the majority of key muscles below the neurological level have a muscle grade less than three and they are unable to walk
4, unable to walk and some functional motor control below the level of injury that is significantly useful (for example assist in transfers) but that is not sufficient for independent walking
5, limited walking and motor function allows walking with assistance or unassisted but significant problems secondary to lack of endurance or fear of falling limit patient mobility
6, unlimited walking and ambulatory without assistance and without significant limitations other than one or both of the following (difficulties with micturition or slightly dyscoordinated gait)
7, neurologically intact with the exception of minimal deficits that cause no functional difficulties
9, not able to assess
elbfll 26, 52 Motor score C5 Left 0,1,2,3,4,5
wrextl 26, 52 Motor score C6 Left 0,1,2,3,4,5
elbexl 26, 52 Motor score C7 Left 0,1,2,3,4,5
finfll 26, 52 Motor score C8 Left 0,1,2,3,4,5
finabl 26, 52 Motor score T1 Left 0,1,2,3,4,5
hipfll 26, 52 Motor score L2 Left 0,1,2,3,4,5
kneexl 26, 52 Motor score L3 Left 0,1,2,3,4,5
ankdol 26, 52 Motor score L4 Left 0,1,2,3,4,5
gretol 26, 52 Motor score L5 Left 0,1,2,3,4,5
ankpll 26, 52 Motor score S1 Left 0,1,2,3,4,5
elbflr 26, 52 Motor score C5 Right 0,1,2,3,4,5
wrextr 26, 52 Motor score C6 Right 0,1,2,3,4,5
elbexr 26, 52 Motor score C7 Right 0,1,2,3,4,5
finflr 26, 52 Motor score C8 Right 0,1,2,3,4,5
finabr 26, 52 Motor score T1 Right 0,1,2,3,4,5
hipflr 26, 52 Motor score L2 Right 0,1,2,3,4,5
kneetr 26, 52 Motor score L3 Right 0,1,2,3,4,5
ankdor 26, 52 Motor score L4 Right 0,1,2,3,4,5
gretor 26, 52 Motor score L5 Right 0,1,2,3,4,5
ankplr 26, 52 Motor score S1 Right 0,1,2,3,4,5

1.1.4 File 3: test_features.csv

All features, including ISNCSCI assessments and AIS grades, at 1 week after injury. Each row corresponds to a specific patient ID, columns are features.

1.1.5 File 4: test_outcomes_MS_template.csv

All features, including ISNCSCI assessments and AIS grades, at 1 week after injury. Each row corresponds to a specific patient ID, columns are features.

1.2 Visualizations