Add paper
Browse files- paper/trifuse_ad.md +450 -0
paper/trifuse_ad.md
ADDED
|
@@ -0,0 +1,450 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
# TriFuse-AD: An Honest Multimodal Benchmark for Three-Stage Dementia Staging on OASIS-1 Structural MRI
|
| 2 |
+
|
| 3 |
+
## Abstract
|
| 4 |
+
|
| 5 |
+
We present a controlled, leakage-free benchmark for three-stage cognitive
|
| 6 |
+
classification — cognitively normal (CN), very mild dementia (VMD, CDR=0.5), and
|
| 7 |
+
Alzheimer's dementia (AD, CDR≥1) — on the OASIS-1 cross-sectional cohort, and we
|
| 8 |
+
propose **TriFuse-AD**, a tri-planar CNN + slice-plane Transformer with gated
|
| 9 |
+
demographic fusion. On an age-restricted cohort (≥60 years, 198 subjects) evaluated
|
| 10 |
+
with subject-level repeated stratified 5-fold cross-validation (3 seeds, 15
|
| 11 |
+
evaluations per model), we benchmark eleven models spanning tabular, 2D/2.5D/3D
|
| 12 |
+
CNN, Vision Transformer, hybrid, and multimodal families, and report Macro-F1 with
|
| 13 |
+
bootstrap confidence intervals as the primary metric.
|
| 14 |
+
|
| 15 |
+
Our central finding is a *negative* but informative one: on this small, confounded
|
| 16 |
+
cohort no MRI-only deep network surpasses a plain tabular XGBoost on morphometric
|
| 17 |
+
and demographic features (Macro-F1 0.474), and TriFuse-AD (0.488 ± 0.066) does not
|
| 18 |
+
significantly outperform a trivial DenseNet late-concatenation baseline (0.497 ±
|
| 19 |
+
0.062; paired permutation p = 0.55). A confound analysis shows a structured-feature
|
| 20 |
+
model using whole-brain volume, intracranial volume and demographics alone reaches
|
| 21 |
+
Macro-F1 0.480, confirming that most of the recoverable signal on OASIS-1 is
|
| 22 |
+
morphometric rather than learned from raw voxels. We report these results
|
| 23 |
+
transparently, together with per-class, per-subgroup, ablation, and interpretability
|
| 24 |
+
analyses, as a cautionary and reproducible reference point for small-cohort
|
| 25 |
+
structural-MRI dementia staging. We make no clinical, diagnostic, state-of-the-art,
|
| 26 |
+
or cross-site claims.
|
| 27 |
+
|
| 28 |
+
**Keywords:** Alzheimer's disease, dementia staging, OASIS-1, structural MRI,
|
| 29 |
+
multimodal fusion, confounding, small-sample benchmark, Macro-F1.
|
| 30 |
+
|
| 31 |
+
|
| 32 |
+
## 1. Introduction
|
| 33 |
+
|
| 34 |
+
Automated staging of cognitive decline from structural MRI is an attractive goal:
|
| 35 |
+
T1-weighted scans are cheap, ubiquitous, and carry well-documented atrophy signatures
|
| 36 |
+
of Alzheimer's disease (AD). A large literature reports high accuracy for AD-vs-CN
|
| 37 |
+
classification, and a growing body extends this to intermediate stages. Yet much of
|
| 38 |
+
this literature is difficult to compare or trust, for three recurring reasons.
|
| 39 |
+
|
| 40 |
+
First, **label leakage and target-adjacent inputs.** Clinical staging labels such as
|
| 41 |
+
the Clinical Dementia Rating (CDR) or Mini-Mental State Exam (MMSE) are sometimes
|
| 42 |
+
fed to the model, directly or through hand-picked features, inflating performance in
|
| 43 |
+
a way that would not survive prospective use.
|
| 44 |
+
|
| 45 |
+
Second, **subject-level leakage.** When multiple scans of the same subject, or
|
| 46 |
+
augmented slices from one volume, are split across train and test, the reported
|
| 47 |
+
accuracy measures memorization of subjects rather than generalization.
|
| 48 |
+
|
| 49 |
+
Third, **confounding by age and head size.** Age is strongly correlated with both
|
| 50 |
+
brain atrophy and dementia stage; a model that merely reads off age (or a proxy such
|
| 51 |
+
as whole-brain volume) can appear to "diagnose from MRI" while learning nothing
|
| 52 |
+
disease-specific.
|
| 53 |
+
|
| 54 |
+
This paper takes the opposite stance to the accuracy-maximizing literature. We build
|
| 55 |
+
a deliberately conservative benchmark on the OASIS-1 cross-sectional cohort and ask a
|
| 56 |
+
narrower, more honest question: *under leakage-free, age-restricted, subject-level
|
| 57 |
+
evaluation, how much three-stage signal is actually recoverable from structural MRI,
|
| 58 |
+
and does architectural sophistication help beyond trivial baselines?*
|
| 59 |
+
|
| 60 |
+
Concretely, our contributions are:
|
| 61 |
+
|
| 62 |
+
1. **A reproducible, leakage-free three-stage protocol** on OASIS-1: CN / VMD / AD
|
| 63 |
+
from CDR, with an age≥60 restriction to attenuate the age shortcut, one volume
|
| 64 |
+
per subject, subject-level repeated stratified cross-validation (15 evaluations),
|
| 65 |
+
and CDR/MMSE excluded from all model inputs. Macro-F1 with bootstrap CIs is the
|
| 66 |
+
primary metric, not accuracy, because the classes are imbalanced (98/70/30).
|
| 67 |
+
|
| 68 |
+
2. **A broad, identically-trained model zoo** — eleven models from tabular XGBoost to
|
| 69 |
+
3D Swin Transformers and two recent CNN-Transformer hybrids, all retrained on our
|
| 70 |
+
folds so numbers are mutually comparable and never copied across datasets.
|
| 71 |
+
|
| 72 |
+
3. **TriFuse-AD**, a tri-planar shared-CNN encoder with a slice-plane Transformer and
|
| 73 |
+
a gated demographic-fusion head, presented not as a winner but as a well-specified
|
| 74 |
+
point in the design space that we ablate component-by-component.
|
| 75 |
+
|
| 76 |
+
4. **An explicit confound and subgroup analysis** quantifying how much of the signal
|
| 77 |
+
is available from demographics and morphometry alone, and how performance varies
|
| 78 |
+
across age bands and sex.
|
| 79 |
+
|
| 80 |
+
Our results are sobering. Multimodal fusion helps — the two top models both fuse MRI
|
| 81 |
+
with structured features — but TriFuse-AD's gated tri-planar attention does not beat
|
| 82 |
+
a plain late-concatenation baseline, and no MRI-only network beats tabular XGBoost.
|
| 83 |
+
We argue that reporting this clearly is more useful to the field than another
|
| 84 |
+
incremental accuracy number obtained under looser controls.
|
| 85 |
+
|
| 86 |
+
|
| 87 |
+
## 2. Related Work
|
| 88 |
+
|
| 89 |
+
**Deep learning for AD classification.** Convolutional networks on 2D slices, 2.5D
|
| 90 |
+
slice stacks, and full 3D volumes have all been applied to ADNI and OASIS. 3D CNNs
|
| 91 |
+
(e.g., 3D ResNet, DenseNet variants) model volumetric context directly but are
|
| 92 |
+
data-hungry; 2.5D approaches trade volumetric completeness for ImageNet-pretrained
|
| 93 |
+
2D backbones and lower memory. Vision Transformers and 3D Swin Transformers have more
|
| 94 |
+
recently been applied to brain MRI, and hybrid CNN-Transformer designs (compact HCCT,
|
| 95 |
+
CNN-VSwinFormer) aim to combine local inductive bias with global attention. Reported
|
| 96 |
+
accuracies vary widely and are frequently not comparable because of differing
|
| 97 |
+
cohorts, label definitions, and validation protocols.
|
| 98 |
+
|
| 99 |
+
**Multimodal fusion.** Combining imaging with tabular clinical/demographic data is
|
| 100 |
+
well established, from early concatenation to gated and attention-based fusion. On
|
| 101 |
+
small cohorts, however, the marginal value of sophisticated fusion over simple
|
| 102 |
+
concatenation is rarely tested with matched training and statistics.
|
| 103 |
+
|
| 104 |
+
**Confounding and evaluation critique.** A recurrent methodological thread warns that
|
| 105 |
+
age, sex, and head-size confounds, together with subject-level leakage, can dominate
|
| 106 |
+
apparent MRI-based performance, and that accuracy on imbalanced stages is misleading.
|
| 107 |
+
Our work is squarely in this tradition: rather than proposing a higher number, we
|
| 108 |
+
instrument the benchmark to expose how much signal is confound-driven, and we hold
|
| 109 |
+
every model to the same leakage-free protocol.
|
| 110 |
+
|
| 111 |
+
**OASIS-1.** The OASIS cross-sectional release provides T1-weighted scans with CDR,
|
| 112 |
+
MMSE, and morphometric summaries (eTIV, nWBV, ASF) for a demographically broad adult
|
| 113 |
+
cohort. It is smaller and less standardized than ADNI, which makes it a realistic
|
| 114 |
+
stress test for small-sample generalization — and a setting where honest reporting of
|
| 115 |
+
variance and confounding matters most.
|
| 116 |
+
|
| 117 |
+
|
| 118 |
+
## 3. Data and Cohort
|
| 119 |
+
|
| 120 |
+
**Source.** We use the OASIS-1 cross-sectional release (416 subjects, ages 18–96).
|
| 121 |
+
Each subject has T1-weighted MPRAGE scans and an atlas-registered, brain-masked,
|
| 122 |
+
gain-field-corrected volume (`*_111_t88_masked_gfc`, 176×208×176, 1 mm isotropic),
|
| 123 |
+
along with demographic and morphometric summaries: age, sex, education, socioeconomic
|
| 124 |
+
status (SES), estimated total intracranial volume (eTIV), normalized whole-brain
|
| 125 |
+
volume (nWBV), atlas scaling factor (ASF), MMSE, and CDR. We reconstruct the
|
| 126 |
+
per-subject metadata from the individual OASIS subject records.
|
| 127 |
+
|
| 128 |
+
**Labels.** We map CDR to three cognitive stages:
|
| 129 |
+
|
| 130 |
+
| CDR | Stage | Meaning |
|
| 131 |
+
|-----|-------|---------|
|
| 132 |
+
| 0 | CN | cognitively normal |
|
| 133 |
+
| 0.5 | VMD | very mild dementia |
|
| 134 |
+
| ≥1 | AD | Alzheimer's dementia |
|
| 135 |
+
|
| 136 |
+
We deliberately name CDR=0.5 **very mild dementia (VMD)**, not "MCI": the CDR
|
| 137 |
+
operationalization is not equivalent to a clinical MCI diagnosis, and conflating them
|
| 138 |
+
would overstate clinical relevance. **CDR and MMSE are never used as model inputs** —
|
| 139 |
+
they define or correlate with the label and would constitute leakage. They are
|
| 140 |
+
retained only for cohort description and confound analysis.
|
| 141 |
+
|
| 142 |
+
**Age restriction.** Because age is the dominant confound (young CN subjects are
|
| 143 |
+
trivially separable from older AD subjects on brain size alone), we restrict to
|
| 144 |
+
**age ≥ 60**. This removes the easy young-CN population and forces models to
|
| 145 |
+
discriminate stages within an older cohort where atrophy overlaps across stages.
|
| 146 |
+
|
| 147 |
+
**Final cohort.** The age≥60 filter yields **198 subjects**: CN = 98, VMD = 70,
|
| 148 |
+
AD = 30. Mean age 76.3 ± 8.1; 131 male / 67 female. One volume per subject. The
|
| 149 |
+
class imbalance (roughly 3 : 2 : 1) and the small AD count (≈6 AD subjects per test
|
| 150 |
+
fold) are central to how we evaluate and how we interpret variance.
|
| 151 |
+
|
| 152 |
+
|
| 153 |
+
## 4. Method
|
| 154 |
+
|
| 155 |
+
### 4.1 Preprocessing
|
| 156 |
+
|
| 157 |
+
*3D pipeline.* Each volume is loaded, reoriented to a canonical axis order,
|
| 158 |
+
cropped to the nonzero brain bounding box, intensity-clipped to the 0.5–99.5
|
| 159 |
+
percentile range, z-scored over brain voxels, and resized to 128×128×128 for 3D CNNs
|
| 160 |
+
or 96×112×112 for the more memory-intensive 3D transformers.
|
| 161 |
+
|
| 162 |
+
*2.5D pipeline.* From each volume we extract, per anatomical plane (axial, coronal,
|
| 163 |
+
sagittal), 9 slices spanning 30–70% of the depth range, each resized to 224×224 —
|
| 164 |
+
27 slices per subject. This gives ImageNet-pretrained 2D backbones a multi-view
|
| 165 |
+
summary of the volume without the memory cost of full 3D.
|
| 166 |
+
|
| 167 |
+
All preprocessing statistics that could leak (none beyond per-volume normalization
|
| 168 |
+
here) are computed within each volume; tabular imputation and standardization
|
| 169 |
+
statistics are fit on the training fold only (Section 5).
|
| 170 |
+
|
| 171 |
+
### 4.2 TriFuse-AD architecture
|
| 172 |
+
|
| 173 |
+
TriFuse-AD has three parts:
|
| 174 |
+
|
| 175 |
+
**(1) Shared tri-planar CNN encoder.** All 27 slices (3 planes × 9 slices) pass
|
| 176 |
+
through a single ImageNet-pretrained ConvNeXt-Tiny backbone (num_classes=0, producing
|
| 177 |
+
a pooled feature vector per slice). A linear projection maps each to a common
|
| 178 |
+
embedding dimension. Sharing weights across planes and slices keeps the parameter
|
| 179 |
+
count small — important for a 198-subject cohort.
|
| 180 |
+
|
| 181 |
+
**(2) Slice-plane Transformer.** The 27 slice tokens receive additive slice-position
|
| 182 |
+
and plane embeddings (so the model can distinguish an axial slice at 40% depth from a
|
| 183 |
+
sagittal slice at 40% depth), a learned [CLS] token is prepended, and a 2-layer
|
| 184 |
+
Transformer encoder aggregates them. The [CLS] output is the MRI representation
|
| 185 |
+
`z_mri`, followed by layer normalization.
|
| 186 |
+
|
| 187 |
+
**(3) Gated demographic fusion.** A small MLP encodes the structured features into
|
| 188 |
+
`z_tab`. Fusion is gated:
|
| 189 |
+
|
| 190 |
+
```
|
| 191 |
+
g = σ(W_g · [z_mri ; z_tab])
|
| 192 |
+
z = LayerNorm(z_mri + g ⊙ (W_t · z_tab))
|
| 193 |
+
```
|
| 194 |
+
|
| 195 |
+
The gate `g` lets the model modulate how much demographic information is injected per
|
| 196 |
+
example, rather than blindly concatenating. A final 3-way linear head produces class
|
| 197 |
+
logits. The ablation (Section 7) replaces (2) with mean-pooling, replaces the gate
|
| 198 |
+
with plain concatenation, drops the metadata branch, and restricts to a single plane,
|
| 199 |
+
isolating each component's contribution.
|
| 200 |
+
|
| 201 |
+
### 4.3 Baselines
|
| 202 |
+
|
| 203 |
+
We compare against ten other models, all trained on identical folds:
|
| 204 |
+
|
| 205 |
+
- **Tabular:** XGBoost and an MLP on the structured features (age, sex, education,
|
| 206 |
+
SES, eTIV, nWBV, ASF).
|
| 207 |
+
- **2D / 2.5D CNN:** ResNet50 (center axial slice), DenseNet121 (9-axial 2.5D).
|
| 208 |
+
- **3D CNN:** 3D ResNet18 (MONAI).
|
| 209 |
+
- **Transformers:** ViT-B/16 (2.5D, two-stage finetune), 3D Swin-T (MONAI).
|
| 210 |
+
- **Hybrids:** a compact 3D HCCT and a lightweight CNN-VSwinFormer, both retrained on
|
| 211 |
+
our folds (no cross-dataset numbers copied).
|
| 212 |
+
- **Multimodal baseline:** DenseNet + late concatenation of structured features.
|
| 213 |
+
|
| 214 |
+
|
| 215 |
+
## 5. Experimental Setup
|
| 216 |
+
|
| 217 |
+
**Cross-validation.** We use subject-level repeated stratified 5-fold CV with seeds
|
| 218 |
+
{7, 13, 21} → **15 evaluations per model**. Stratification is by class × age band ×
|
| 219 |
+
sex. Splits are strictly subject-level; we assert zero subject overlap across
|
| 220 |
+
train / validation / test in every fold. All fold-dependent statistics
|
| 221 |
+
(tabular imputation medians, standardization, class-balance weights) are fit on the
|
| 222 |
+
training fold only.
|
| 223 |
+
|
| 224 |
+
**Training.** Torch models use AdamW with cosine schedule, two learning-rate groups
|
| 225 |
+
(a lower rate for pretrained backbones), bf16 automatic mixed precision, and early
|
| 226 |
+
stopping on validation Macro-F1. The default loss is class-balanced focal loss
|
| 227 |
+
(effective-number class weights, γ=2, label smoothing 0.05); a weighted
|
| 228 |
+
cross-entropy variant is used in the ablation. Hyperparameters are frozen per model
|
| 229 |
+
before the run; the test fold is never used for selection.
|
| 230 |
+
|
| 231 |
+
**Metrics.** The **primary metric is Macro-F1**, which weights all three stages
|
| 232 |
+
equally despite imbalance. We also report balanced accuracy, accuracy, macro
|
| 233 |
+
precision/recall, one-vs-rest macro AUC, and per-class F1/recall. We report
|
| 234 |
+
mean ± standard deviation over the 15 runs, and a bootstrap 95% CI on Macro-F1 from
|
| 235 |
+
the pooled out-of-fold (OOF) predictions. Significance between the proposed model and
|
| 236 |
+
the best baseline uses a paired permutation test on per-run Macro-F1.
|
| 237 |
+
|
| 238 |
+
|
| 239 |
+
## 6. Results
|
| 240 |
+
|
| 241 |
+
### 6.1 Main comparison
|
| 242 |
+
|
| 243 |
+
Table 1 reports Macro-F1 (mean ± std over 15 runs) with the bootstrap 95% CI, ordered
|
| 244 |
+
best to worst.
|
| 245 |
+
|
| 246 |
+
**Table 1 — Three-stage (CN/VMD/AD) classification, OASIS-1 age≥60, 198 subjects.**
|
| 247 |
+
|
| 248 |
+
| Rank | Model | Input | Macro-F1 | Bal. Acc. | F1(AD) | Macro-F1 95% CI |
|
| 249 |
+
|------|-------|-------|----------|-----------|--------|-----------------|
|
| 250 |
+
| 1 | DenseNet + concat | MRI+tab | **0.497 ± 0.062** | 0.525 | 0.390 | [0.47, 0.53] |
|
| 251 |
+
| 2 | **TriFuse-AD** | MRI+tab | 0.488 ± 0.066 | 0.508 | 0.367 | [0.46, 0.54] |
|
| 252 |
+
| 3 | XGBoost | tab | 0.474 ± 0.065 | 0.473 | 0.377 | [0.44, 0.52] |
|
| 253 |
+
| 4 | ViT-B/16 | 2.5D | 0.462 ± 0.085 | 0.490 | 0.323 | — |
|
| 254 |
+
| 5 | DenseNet121 | 2.5D | 0.449 ± 0.077 | 0.468 | 0.365 | — |
|
| 255 |
+
| 6 | 3D HCCT | 3D | 0.407 ± 0.078 | 0.450 | 0.279 | — |
|
| 256 |
+
| 7 | 3D Swin-T | 3D | 0.403 ± 0.085 | 0.442 | 0.280 | — |
|
| 257 |
+
| 8 | Tabular MLP | tab | 0.390 ± 0.097 | 0.442 | 0.412 | — |
|
| 258 |
+
| 9 | ResNet50 | 2D | 0.368 ± 0.074 | 0.399 | 0.205 | — |
|
| 259 |
+
| 10 | 3D ResNet18 | 3D | 0.354 ± 0.069 | 0.413 | 0.240 | — |
|
| 260 |
+
| 11 | CNN-VSwinFormer-lite | 3D | 0.354 ± 0.078 | 0.400 | 0.242 | — |
|
| 261 |
+
|
| 262 |
+
Three observations stand out.
|
| 263 |
+
|
| 264 |
+
**Multimodal fusion occupies the top two spots.** Both models that fuse MRI with
|
| 265 |
+
structured features (DenseNet+concat, TriFuse-AD) outrank every single-modality
|
| 266 |
+
model. Fusing morphometry/demographics with imaging is the single most reliable
|
| 267 |
+
lever on this cohort.
|
| 268 |
+
|
| 269 |
+
**But sophistication does not pay off.** TriFuse-AD's gated tri-planar attention
|
| 270 |
+
(0.488) does **not** beat the trivial DenseNet late-concatenation baseline (0.497).
|
| 271 |
+
A paired permutation test on per-run Macro-F1 gives Δ = −0.009, **p = 0.55** — the
|
| 272 |
+
two are statistically indistinguishable, and the point estimate actually favors the
|
| 273 |
+
simpler model. We therefore make no claim that TriFuse-AD is superior.
|
| 274 |
+
|
| 275 |
+
**No MRI-only network beats tabular XGBoost.** The best pure-imaging model (ViT-B/16,
|
| 276 |
+
0.462) sits below XGBoost on seven structured features (0.474), and the pure-3D
|
| 277 |
+
networks (3D ResNet18, CNN-VSwinFormer-lite, 3D Swin-T) are the weakest of all
|
| 278 |
+
(≈0.35–0.40) — below even the tabular MLP on some metrics. On a 198-subject cohort,
|
| 279 |
+
volumetric deep networks overfit and underperform a gradient-boosted table.
|
| 280 |
+
|
| 281 |
+
### 6.2 Variance and the small-AD problem
|
| 282 |
+
|
| 283 |
+
Standard deviations are large relative to the differences between models (±0.06 to
|
| 284 |
+
±0.10). The transformer models show the highest variance (ViT ±0.085, Swin ±0.085),
|
| 285 |
+
consistent with our prior expectation: with ≈6 AD subjects per test fold, a single
|
| 286 |
+
misclassified AD case swings fold-level Macro-F1 substantially. This is why we report
|
| 287 |
+
distributions over 15 runs rather than a single split, and why we treat rank
|
| 288 |
+
differences within a CI-width of each other as ties rather than wins.
|
| 289 |
+
|
| 290 |
+
Per-class F1 (Table 3b in the artifacts) confirms the AD class is the hardest
|
| 291 |
+
everywhere: F1(AD) tops out at 0.41 (tabular MLP, which trades CN/VMD precision for
|
| 292 |
+
AD recall) and is 0.37–0.39 for the fusion models. VMD (CDR=0.5) is the most
|
| 293 |
+
confused stage, frequently absorbed into CN or AD — expected, since it is the
|
| 294 |
+
clinical boundary zone.
|
| 295 |
+
|
| 296 |
+
|
| 297 |
+
## 7. Ablation Study
|
| 298 |
+
|
| 299 |
+
We ablate TriFuse-AD component-by-component, all variants sharing the full training
|
| 300 |
+
recipe and folds.
|
| 301 |
+
|
| 302 |
+
**Table 2 — TriFuse-AD ablation (Macro-F1, balanced accuracy, F1(AD)).**
|
| 303 |
+
|
| 304 |
+
| Variant | Macro-F1 | Bal. Acc. | F1(AD) |
|
| 305 |
+
|---------|----------|-----------|--------|
|
| 306 |
+
| A1: axial-only (single plane) | 0.477 ± 0.071 | 0.497 | 0.338 |
|
| 307 |
+
| A2: mean-pool (no Transformer) | 0.465 ± 0.083 | 0.497 | 0.367 |
|
| 308 |
+
| A3: no metadata (MRI only) | 0.390 ± 0.103 | 0.431 | 0.234 |
|
| 309 |
+
| A4: concat (no gate) | 0.487 ± 0.053 | 0.514 | 0.373 |
|
| 310 |
+
| A5: weighted-CE (vs focal) | **0.500 ± 0.054** | 0.518 | 0.413 |
|
| 311 |
+
| Full TriFuse-AD | 0.488 ± 0.066 | 0.508 | 0.367 |
|
| 312 |
+
|
| 313 |
+
The ablation is more informative than the headline number:
|
| 314 |
+
|
| 315 |
+
- **Metadata is the dominant component (A3).** Removing the demographic/morphometric
|
| 316 |
+
branch collapses Macro-F1 from 0.488 to 0.390 and F1(AD) from 0.367 to 0.234 — a
|
| 317 |
+
larger drop than any imaging-side change. This is the single clearest effect in the
|
| 318 |
+
study and directly mirrors the confound analysis: the structured features carry
|
| 319 |
+
most of the signal.
|
| 320 |
+
|
| 321 |
+
- **The gate does not help (A4).** Replacing gated fusion with plain concatenation
|
| 322 |
+
gives 0.487 — identical to the full model (0.488) within noise, and with *lower*
|
| 323 |
+
variance (±0.053 vs ±0.066). The gating mechanism, the architectural novelty of
|
| 324 |
+
TriFuse-AD, earns nothing here.
|
| 325 |
+
|
| 326 |
+
- **The Transformer barely helps (A2).** Mean-pooling the slice tokens instead of the
|
| 327 |
+
Transformer aggregator gives 0.465 vs 0.488 — a small, within-noise difference.
|
| 328 |
+
|
| 329 |
+
- **Tri-planar vs axial-only is marginal (A1).** Three planes (0.488) over axial-only
|
| 330 |
+
(0.477) is again within noise.
|
| 331 |
+
|
| 332 |
+
- **Loss choice (A5).** Weighted cross-entropy slightly edges out class-balanced focal
|
| 333 |
+
loss (0.500 vs 0.488) and gives the best F1(AD) of any TriFuse variant (0.413),
|
| 334 |
+
though still within the confidence band.
|
| 335 |
+
|
| 336 |
+
**Takeaway:** the only component with a large, unambiguous effect is the metadata
|
| 337 |
+
branch. The imaging-side sophistication (tri-planar views, slice-plane Transformer,
|
| 338 |
+
gated fusion) contributes little beyond what a single-plane CNN with concatenated
|
| 339 |
+
demographics already achieves. This is an honest internal-validity result that we
|
| 340 |
+
report rather than bury.
|
| 341 |
+
|
| 342 |
+
|
| 343 |
+
## 8. Confound and Subgroup Analysis
|
| 344 |
+
|
| 345 |
+
### 8.1 How much signal is in the structured features alone?
|
| 346 |
+
|
| 347 |
+
To quantify confounding, we train shortcut baselines that use **no MRI at all**, on
|
| 348 |
+
the same folds/seeds and evaluated identically.
|
| 349 |
+
|
| 350 |
+
**Table 3 — No-MRI shortcut baselines (Macro-F1, balanced accuracy, AD recall).**
|
| 351 |
+
|
| 352 |
+
| Model | Features | Macro-F1 | Bal. Acc. | AD recall |
|
| 353 |
+
|-------|----------|----------|-----------|-----------|
|
| 354 |
+
| Age-only logistic | age | 0.324 ± 0.014 | 0.390 | 0.589 |
|
| 355 |
+
| Demographic XGBoost | age, sex, educ, SES | 0.417 ± 0.015 | 0.417 | 0.167 |
|
| 356 |
+
| Full-structured XGBoost | + eTIV, nWBV, ASF | 0.480 ± 0.014 | 0.476 | 0.367 |
|
| 357 |
+
|
| 358 |
+
The result is decisive. **A structured-feature model with no imaging reaches
|
| 359 |
+
Macro-F1 0.480** — higher than every MRI-only network in Table 1 and statistically
|
| 360 |
+
level with the best multimodal models (0.488–0.497). Adding the morphometric volumes
|
| 361 |
+
(eTIV, nWBV, ASF) to demographics lifts Macro-F1 from 0.417 to 0.480, i.e. brain
|
| 362 |
+
volume is doing most of the work. Age alone already recovers meaningful signal
|
| 363 |
+
(0.324, with high AD recall because AD subjects skew older even within the ≥60
|
| 364 |
+
cohort).
|
| 365 |
+
|
| 366 |
+
This is the crux of the paper. On OASIS-1 at age≥60, the recoverable three-stage
|
| 367 |
+
signal is largely **morphometric and demographic**, not something the deep networks
|
| 368 |
+
extract from raw voxels beyond what a single normalized-brain-volume number provides.
|
| 369 |
+
Any claim that a deep model "learns AD imaging biomarkers" here has to first clear
|
| 370 |
+
the 0.480 structured-only bar — and none of ours does so convincingly.
|
| 371 |
+
|
| 372 |
+
### 8.2 Subgroup robustness
|
| 373 |
+
|
| 374 |
+
Slicing the pooled OOF predictions by age band and sex (for the strongest models)
|
| 375 |
+
shows performance is **not stable across age**. For XGBoost, Macro-F1 falls from
|
| 376 |
+
0.735 in the 60–69 band to 0.401 in the 80+ band. The youngest band is easiest
|
| 377 |
+
because within age≥60 the 60–69 CN subjects still separate relatively cleanly; by
|
| 378 |
+
80+, atrophy is widespread across all three stages and the task is hardest. Sex
|
| 379 |
+
differences are smaller (male 0.486 vs female 0.440 for XGBoost). This age gradient
|
| 380 |
+
is itself evidence of residual confounding: even after restricting to ≥60, age
|
| 381 |
+
continues to structure the difficulty.
|
| 382 |
+
|
| 383 |
+
|
| 384 |
+
## 9. Interpretability
|
| 385 |
+
|
| 386 |
+
We apply Grad-CAM to TriFuse-AD's shared CNN encoder on a held-out fold (6 correctly
|
| 387 |
+
and 3 incorrectly classified test subjects), reporting the center slice per plane.
|
| 388 |
+
This is **qualitative only**. We do not claim the model localizes specific structures;
|
| 389 |
+
we observe that, for correctly classified AD/VMD cases, activation tends to fall over
|
| 390 |
+
peri-ventricular and medial-temporal regions — anatomy broadly associated with AD
|
| 391 |
+
atrophy — while misclassified cases show diffuse or off-target activation. Given the
|
| 392 |
+
confound analysis, we caution explicitly against over-reading these maps: a model
|
| 393 |
+
whose signal is dominated by whole-brain volume may attend to atrophy-correlated
|
| 394 |
+
regions incidentally rather than through disease-specific feature learning.
|
| 395 |
+
|
| 396 |
+
|
| 397 |
+
## 10. Discussion
|
| 398 |
+
|
| 399 |
+
**What we found.** Under a leakage-free, age-restricted, subject-level protocol on
|
| 400 |
+
OASIS-1: (i) multimodal fusion beats every single modality; (ii) but the proposed
|
| 401 |
+
gated tri-planar Transformer does not beat trivial late concatenation (p = 0.55),
|
| 402 |
+
and its ablation shows the metadata branch — not the imaging architecture — carries
|
| 403 |
+
the effect; (iii) no MRI-only network beats tabular XGBoost; and (iv) a no-MRI
|
| 404 |
+
structured model reaches Macro-F1 0.480, level with the best fusion models.
|
| 405 |
+
|
| 406 |
+
**Why this matters.** The dominant narrative in MRI-based AD staging is one of
|
| 407 |
+
steadily rising accuracy from ever-larger networks. Our controlled reproduction
|
| 408 |
+
suggests that on a small, realistic cohort much of the achievable signal is
|
| 409 |
+
morphometric/demographic and available without deep learning, and that architectural
|
| 410 |
+
novelty can vanish once trivial baselines and proper variance reporting are in place.
|
| 411 |
+
We think the field benefits more from this being stated plainly than from another
|
| 412 |
+
loosely-controlled record.
|
| 413 |
+
|
| 414 |
+
**Is TriFuse-AD useless?** No — but its value here is as a *well-specified, honestly
|
| 415 |
+
ablated* design point, not a winner. The gating and Transformer components are
|
| 416 |
+
defensible ideas that simply do not earn their complexity on 198 subjects; they may
|
| 417 |
+
behave differently on larger cohorts (ADNI-scale), which is the natural next test.
|
| 418 |
+
|
| 419 |
+
## 11. Limitations
|
| 420 |
+
|
| 421 |
+
- **Single cohort, small n.** 198 subjects, 30 AD; results are OASIS-1-specific and
|
| 422 |
+
not validated cross-site. We make no cross-dataset or SOTA claims.
|
| 423 |
+
- **Non-clinical labels.** CDR-derived stages, with CDR=0.5 named VMD not MCI; not a
|
| 424 |
+
clinical diagnosis. No diagnostic or clinical-decision claims.
|
| 425 |
+
- **Residual confounding.** Age≥60 attenuates but does not remove the age/atrophy
|
| 426 |
+
confound, as the subgroup gradient shows.
|
| 427 |
+
- **Cross-sectional only.** No longitudinal progression modeling.
|
| 428 |
+
- **Compute environment.** The instance filesystem is non-persistent; all data and
|
| 429 |
+
results are re-derivable from the released code, but no long-term artifact store is
|
| 430 |
+
assumed.
|
| 431 |
+
|
| 432 |
+
## 12. Conclusion
|
| 433 |
+
|
| 434 |
+
We built a deliberately conservative three-stage dementia-staging benchmark on
|
| 435 |
+
OASIS-1 and evaluated eleven models plus a component ablation, confound analysis,
|
| 436 |
+
subgroup breakdown, and interpretability under one leakage-free protocol. Our
|
| 437 |
+
proposed TriFuse-AD is competitive but does **not** significantly outperform a
|
| 438 |
+
trivial multimodal baseline, and no imaging network beats a no-MRI structured model.
|
| 439 |
+
Rather than a state-of-the-art claim, we offer a reproducible, honestly-reported
|
| 440 |
+
reference point showing how much of the apparent MRI signal on small confounded
|
| 441 |
+
cohorts is actually morphometric — and a reminder that variance, confounding, and
|
| 442 |
+
trivial baselines must be reported before architectural credit is assigned.
|
| 443 |
+
|
| 444 |
+
---
|
| 445 |
+
|
| 446 |
+
*Reproducibility.* All models are trained on identical subject-level folds
|
| 447 |
+
(seeds 7/13/21 × 5-fold). Tables 1–3 and all figures (main comparison, per-model
|
| 448 |
+
confusion matrices, ROC curves, subgroup chart, Grad-CAM montage) are regenerated
|
| 449 |
+
deterministically from saved out-of-fold predictions. CDR and MMSE are excluded from
|
| 450 |
+
all model inputs.
|