Onur C. Koyun

Yongxin Guo, Hao Lu, Onur C. Koyun et al.

Multimodal learning that integrates genomics and histopathology has shown strong potential in cancer diagnosis, yet its clinical translation is hindered by the limited availability of paired histology-genomics data. Knowledge distillation (KD) offers a practical solution by transferring genomic supervision into histopathology models, enabling accurate inference using histology alone. However, existing KD methods rely on batch-local alignment, which introduces instability due to limited within-batch comparisons and ultimately degrades performance. To address these limitations, we propose Momentum Memory Knowledge Distillation (MoMKD), a cross-modal distillation framework driven by a momentum-updated memory. This memory aggregates genomic and histopathology information across batches, effectively enlarging the supervisory context available to each mini-batch. Furthermore, we decouple the gradients of the genomics and histology branches, preventing genomic signals from dominating histology feature learning during training and eliminating the modality-gap issue at inference time. Extensive experiments on the TCGA-BRCA benchmark (HER2, PR, and ODX classification tasks) and an independent in-house testing dataset demonstrate that MoMKD consistently outperforms state-of-the-art MIL and multimodal KD baselines, delivering strong performance and generalization under histology-only inference. Overall, MoMKD establishes a robust and generalizable knowledge distillation paradigm for computational pathology.

Hao Lu, Onur C. Koyun, Yongxin Guo et al.

Vector Quantization (VQ) underpins many modern generative frameworks such as VQ-VAE, VQ-GAN, and latent diffusion models. Yet, it suffers from the persistent problem of codebook collapse, where a large fraction of code vectors remains unused during training. This work provides a new theoretical explanation by identifying the nonstationary nature of encoder updates as the fundamental cause of this phenomenon. We show that as the encoder drifts, unselected code vectors fail to receive updates and gradually become inactive. To address this, we propose two new methods: Non-Stationary Vector Quantization (NSVQ), which propagates encoder drift to non-selected codes through a kernel-based rule, and Transformer-based Vector Quantization (TransVQ), which employs a lightweight mapping to adaptively transform the entire codebook while preserving convergence to the k-means solution. Experiments on the CelebA-HQ dataset demonstrate that both methods achieve near-complete codebook utilization and superior reconstruction quality compared to baseline VQ variants, providing a principled and scalable foundation for future VQ-based generative models. The code is available at: https://github.com/CAIR- LAB- WFUSM/NSVQ-TransVQ.git

Hao Lu, Onur C. Koyun, Yongxin Guo et al.

Vector-quantized autoencoders deliver high-fidelity latents but suffer inherent flaws: the quantizer is non-differentiable, requires straight-through hacks, and is prone to collapse. We address these issues at the root by replacing VQ with a simple, principled, and fully differentiable alternative: an online PCA bottleneck trained via Oja's rule. The resulting model, PCA-VAE, learns an orthogonal, variance-ordered latent basis without codebooks, commitment losses, or lookup noise. Despite its simplicity, PCA-VAE exceeds VQ-GAN and SimVQ in reconstruction quality on CelebAHQ while using 10-100x fewer latent bits. It also produces naturally interpretable dimensions (e.g., pose, lighting, gender cues) without adversarial regularization or disentanglement objectives. These results suggest that PCA is a viable replacement for VQ: mathematically grounded, stable, bit-efficient, and semantically structured, offering a new direction for generative models beyond vector quantization.