High-resolution T1/T2-weighted MRI, diffusion MRI (where available), and PET scans with amyloid analog
tracers from Alzheimer's disease transgenic mouse models are among the preclinical datasets used in the data
acquisition phase. These scans are co-registered with in- vivo histology images (Aβ/tau immunostaining) and
nanoparticle biodistribution maps produced by fluorescence or autoradiography [1-3]. Histology Aβ area
percentages, behavioral test scores, and pharmacokinetic time-activity curves from ROIs are among the
measured outcomes. Clinical datasets include human MRI and PET scans (amyloid/tau imaging), structural
connectomes, CSF/serum biomarkers, and cognitive performance scores, along with metadata such as scanner
specs, sequence parameters, and demographic information. All data are organized according to the Brain
Imaging Data Structure (BIDS) standard so as to ensure consistency between modalities and participants, [9].
For each domain, preprocessing steps includes skull stripping, bias-field correction (N4), and motion
correction. Human images are aligned in MNI space whereas rodent images are spatially normalized to the
Paxinos map using ANTs. Z-score standardization or histogram matching accomplishes intensity
normalization. Crossdomain harmonization is performed by resampling all pictures to a common voxel grid
(about 1 mm isotropic for humans and 0.5-1 mm scaled equivalent for rodents), and then utilizing ComBat or
histogram matching for intensity Correction [6]. Modality-specific channels are created (e.g., channel 0 = T1
MRI and channel 1 = PET SUVR). ROIs are created in rodents using histology and nanoparticle maps [2,3],
whereas standard FreeSurfer ROIs are used in humans to assure cross-domain concordance. Ground-truth
labeling involves using voxel-wise pathological segmentation masks obtained from registered histology and
nanoparticle biodistribution data, with continuous or categorical outcome labels (e.g. Aβ load, behavioral
scores). In the therapeutic sector, CSF Aβ/tau and cognitive scores are used as target measurements for
downstream correlation rather than direct supervision [5]. The model design includes a 3D ResNet-based
encoder that converts multi-channel volumetric inputs into feature embeddings. Two specialized heads are
used during the preclinical training phase: a U-Net-style segmentation decoder for pathology mapping and a
multilayer perceptron (MLP) outcome head for histological or behavioral prediction. In order to remove
domain-specific biases and enforce feature alignment across rat and human representations, a domain
discriminator network linked by a Gradient Reversal Layer (GRL) allows adversarial training [7,8]. Although
the initial implementation focuses on feature-level adaptation for increased stability, a 3D image-to-image
generator (CycleGAN/pix2pix) can be added for direct picture domain translation.
Training occurs in three stages. The encoder and task-specific heads are optimized using Dice and cross-
entropy losses for segmentation, as well as mean squared error (MSE) or cross-entropy for prediction of
outcomes. Regularization is done using weight decay and dropout, with the AdamW optimizer (learning rate ≈
1e-4) and significant data augmentation to imitate scanner variability in the Phase A (Preclinical Supervised
Training). Phase B (Domain Adaptation) involves freezing task heads and training the encoder with increasing
adversarial loss weight (λ) to reduce domain discrimination [5, 7]. Phase C (Human Fine-tuning) applies the
model to limited labeled human data, refining predictions and confirming transferred characteristics against
clinical biomarkers [6]. For ROIs or global representations, feature extraction generates latent embeddings.
These embeddings can be utilized in regression or classification models, such as linear regression and random
model evaluation is performed across both domains. Segmentation performance is quantified using Dice
coefficient and voxel-wise ROC metrics, while outcome prediction is evaluated by R², MAE, or AUC for
preclinical data. Through assessing reduction in Maximum Mean Discrepancy (MMD) and by measuring
correlations between predicted embeddings and human clinical biomarkers using Pearson or Spearman
coefficients cross-domain adaptation is validated. Permutation tests and false discovery rate (FDR) correction
across multiple ROIs verify the sequence. Grad-CAM and integrated gradients are employed to visualize
salient regions driving the model’s predictions for explainability and uncertainty estimation, [8]. Monte Carlo
dropout or deep ensemble techniques estimates the uncertainty and confidence intervals. In order to determine
biological plausibility, saliency maps are compared to histology and PET patterns. Practically, investigation
can start with a small number of critical ROIs, such as the hippocampus, entorhinal cortex, and posterior
cingulate cortex. Improvement of computing performance are achieved with lightweight 2D or ROI-patch
models. For consistency across imaging sites and species, instance or group normalization layers are chosen.
The strict separation of training and test participants, together with metadata-aware modeling, avoids data
leakage and bias.
Page 1962