Dimitris Samaras

Varun Belagali, Saarthak Kapse, Pierre Marza et al.

The interpretation of small tiles in large whole slide images (WSI) often needs a larger image context. We introduce TICON, a transformer-based tile representation contextualizer that produces rich, contextualized embeddings for ''any'' application in computational pathology. Standard tile encoder-based pipelines, which extract embeddings of tiles stripped from their context, fail to model the rich slide-level information essential for both local and global tasks. Furthermore, different tile-encoders excel at different downstream tasks. Therefore, a unified model is needed to contextualize embeddings derived from ''any'' tile-level foundation model. TICON addresses this need with a single, shared encoder, pretrained using a masked modeling objective to simultaneously unify and contextualize representations from diverse tile-level pathology foundation models. Our experiments demonstrate that TICON-contextualized embeddings significantly improve performance across many different tasks, establishing new state-of-the-art results on tile-level benchmarks (i.e., HEST-Bench, THUNDER, CATCH) and slide-level benchmarks (i.e., Patho-Bench). Finally, we pretrain an aggregator on TICON to form a slide-level foundation model, using only 11K WSIs, outperforming SoTA slide-level foundation models pretrained with up to 350K WSIs.

Snehal Singh Tomar, Alexandros Graikos, Arjun Krishna et al.

Modern deep learning methods typically treat image sequences as large tensors of sequentially stacked frames. However, is this straightforward representation ideal given the current state-of-the-art (SoTA)? In this work, we address this question in the context of generative models and aim to devise a more effective way of modeling image sequence data. Observing the inefficiencies and bottlenecks of current SoTA image sequence generation methods, we showcase that rather than working with large tensors, we can improve the generation process by factorizing it into first generating the coarse sequence at low resolution and then refining the individual frames at high resolution. We train a generative model solely on grid images comprising subsampled frames. Yet, we learn to generate image sequences, using the strong self-attention mechanism of the Diffusion Transformer (DiT) to capture correlations between frames. In effect, our formulation extends a 2D image generator to operate as a low-resolution 3D image-sequence generator without introducing any architectural modifications. Subsequently, we super-resolve each frame individually to add the sequence-independent high-resolution details. This approach offers several advantages and can overcome key limitations of the SoTA in this domain. Compared to existing image sequence generation models, our method achieves superior synthesis quality and improved coherence across sequences. It also delivers high-fidelity generation of arbitrary-length sequences and increased efficiency in inference time and training data usage. Furthermore, our straightforward formulation enables our method to generalize effectively across diverse data domains, which typically require additional priors and supervision to model in a generative context. Our method consistently outperforms SoTA in quality and inference speed (at least twice-as-fast) across datasets.