Unlocking adaptive digital pathology through dynamic feature learning

Foundation models have revolutionized the paradigm of digital pathology, as they leverage general-purpose features to emulate real-world pathological practices, enabling the quantitative analysis of critical histological patterns and the dissection of cancer-specific signals. However, these static general features constrain the flexibility and pathological relevance in the ever-evolving needs of clinical applications, hindering the broad use of the current models. Here we introduce PathFiT, a dynamic feature learning method that can be effortlessly plugged into various pathology foundation models to unlock their adaptability. Meanwhile, PathFiT performs seamless implementation across diverse pathology applications regardless of downstream specificity. To validate PathFiT, we construct a digital pathology benchmark with over 20 terabytes of Internet and real-world data comprising 28 H\&E-stained tasks and 7 specialized imaging tasks including Masson's Trichrome staining and immunofluorescence images. By applying PathFiT to the representative pathology foundation models, we demonstrate state-of-the-art performance on 34 out of 35 tasks, with significant improvements on 23 tasks and outperforming by 10.20% on specialized imaging tasks. The superior performance and versatility of PathFiT open up new avenues in computational pathology.

Diagnostic Text-guided Representation Learning in Hierarchical Classification for Pathological Whole Slide Image

With the development of digital imaging in medical microscopy, artificial intelligent-based analysis of pathological whole slide images (WSIs) provides a powerful tool for cancer diagnosis. Limited by the expensive cost of pixel-level annotation, current research primarily focuses on representation learning with slide-level labels, showing success in various downstream tasks. However, given the diversity of lesion types and the complex relationships between each other, these techniques still deserve further exploration in addressing advanced pathology tasks. To this end, we introduce the concept of hierarchical pathological image classification and propose a representation learning called PathTree. PathTree considers the multi-classification of diseases as a binary tree structure. Each category is represented as a professional pathological text description, which messages information with a tree-like encoder. The interactive text features are then used to guide the aggregation of hierarchical multiple representations. PathTree uses slide-text similarity to obtain probability scores and introduces two extra tree specific losses to further constrain the association between texts and slides. Through extensive experiments on three challenging hierarchical classification datasets: in-house cryosectioned lung tissue lesion identification, public prostate cancer grade assessment, and public breast cancer subtyping, our proposed PathTree is consistently competitive compared to the state-of-the-art methods and provides a new perspective on the deep learning-assisted solution for more complex WSI classification.

GALA: Geometry-Aware Local Adaptive Grids for Detailed 3D Generation

We propose GALA, a novel representation of 3D shapes that (i) excels at capturing and reproducing complex geometry and surface details, (ii) is computationally efficient, and (iii) lends itself to 3D generative modelling with modern, diffusion-based schemes. The key idea of GALA is to exploit both the global sparsity of surfaces within a 3D volume and their local surface properties. Sparsity is promoted by covering only the 3D object boundaries, not empty space, with an ensemble of tree root voxels. Each voxel contains an octree to further limit storage and compute to regions that contain surfaces. Adaptivity is achieved by fitting one local and geometry-aware coordinate frame in each non-empty leaf node. Adjusting the orientation of the local grid, as well as the anisotropic scales of its axes, to the local surface shape greatly increases the amount of detail that can be stored in a given amount of memory, which in turn allows for quantization without loss of quality. With our optimized C++/CUDA implementation, GALA can be fitted to an object in less than 10 seconds. Moreover, the representation can efficiently be flattened and manipulated with transformer networks. We provide a cascaded generation pipeline capable of generating 3D shapes with great geometric detail.

Agent Aggregator with Mask Denoise Mechanism for Histopathology Whole Slide Image Analysis

Histopathology analysis is the gold standard for medical diagnosis. Accurate classification of whole slide images (WSIs) and region-of-interests (ROIs) localization can assist pathologists in diagnosis. The gigapixel resolution of WSI and the absence of fine-grained annotations make direct classification and analysis challenging. In weakly supervised learning, multiple instance learning (MIL) presents a promising approach for WSI classification. The prevailing strategy is to use attention mechanisms to measure instance importance for classification. However, attention mechanisms fail to capture inter-instance information, and self-attention causes quadratic computational complexity. To address these challenges, we propose AMD-MIL, an agent aggregator with a mask denoise mechanism. The agent token acts as an intermediate variable between the query and key for computing instance importance. Mask and denoising matrices, mapped from agents-aggregated value, dynamically mask low-contribution representations and eliminate noise. AMD-MIL achieves better attention allocation by adjusting feature representations, capturing micro-metastases in cancer, and improving interpretability. Extensive experiments on CAMELYON-16, CAMELYON-17, TCGA-KIDNEY, and TCGA-LUNG show AMD-MIL's superiority over state-of-the-art methods.

Gene Regulatory Network Inference from Pre-trained Single-Cell Transcriptomics Transformer with Joint Graph Learning

Inferring gene regulatory networks (GRNs) from single-cell RNA sequencing (scRNA-seq) data is a complex challenge that requires capturing the intricate relationships between genes and their regulatory interactions. In this study, we tackle this challenge by leveraging the single-cell BERT-based pre-trained transformer model (scBERT), trained on extensive unlabeled scRNA-seq data, to augment structured biological knowledge from existing GRNs. We introduce a novel joint graph learning approach that combines the rich contextual representations learned by pre-trained single-cell language models with the structured knowledge encoded in GRNs using graph neural networks (GNNs). By integrating these two modalities, our approach effectively reasons over boththe gene expression level constraints provided by the scRNA-seq data and the structured biological knowledge inherent in GRNs. We evaluate our method on human cell benchmark datasets from the BEELINE study with cell type-specific ground truth networks. The results demonstrate superior performance over current state-of-the-art baselines, offering a deeper understanding of cellular regulatory mechanisms.

SweepNet: Unsupervised Learning Shape Abstraction via Neural Sweepers

Shape abstraction is an important task for simplifying complex geometric structures while retaining essential features. Sweep surfaces, commonly found in human-made objects, aid in this process by effectively capturing and representing object geometry, thereby facilitating abstraction. In this paper, we introduce \papername, a novel approach to shape abstraction through sweep surfaces. We propose an effective parameterization for sweep surfaces, utilizing superellipses for profile representation and B-spline curves for the axis. This compact representation, requiring as few as 14 float numbers, facilitates intuitive and interactive editing while preserving shape details effectively. Additionally, by introducing a differentiable neural sweeper and an encoder-decoder architecture, we demonstrate the ability to predict sweep surface representations without supervision. We show the superiority of our model through several quantitative and qualitative experiments throughout the paper. Our code is available at https://mingrui-zhao.github.io/SweepNet/

Asymmetrical estimator for training grey-box deep photonic neural networks

Physical neural networks (PNNs) are emerging paradigms for neural network acceleration due to their high-bandwidth, in-propagation analogue processing. Despite the advantages of PNN for inference, training remains a challenge. The imperfect information of the physical transformation means the failure of conventional gradient-based updates from backpropagation (BP). Here, we present the asymmetrical training (AT) method, which treats the PNN structure as a grey box. AT performs training while only knowing the last layer output and neuron topological connectivity of a deep neural network structure, not requiring information about the physical control-transformation mapping. We experimentally demonstrated the AT method on deep grey-box PNNs implemented by uncalibrated photonic integrated circuits (PICs), improving the classification accuracy of Iris flower and modified MNIST hand-written digits from random guessing to near theoretical maximum. We also showcased the consistently enhanced performance of AT over BP for different datasets, including MNIST, fashion-MNIST, and Kuzushiji-MNIST. The AT method demonstrated successful training with minimal hardware overhead and reduced computational overhead, serving as a robust light-weight training alternative to fully explore the advantages of physical computation.

EASI-Tex: Edge-Aware Mesh Texturing from Single Image

We present a novel approach for single-image mesh texturing, which employs a diffusion model with judicious conditioning to seamlessly transfer an object's texture from a single RGB image to a given 3D mesh object. We do not assume that the two objects belong to the same category, and even if they do, there can be significant discrepancies in their geometry and part proportions. Our method aims to rectify the discrepancies by conditioning a pre-trained Stable Diffusion generator with edges describing the mesh through ControlNet, and features extracted from the input image using IP-Adapter to generate textures that respect the underlying geometry of the mesh and the input texture without any optimization or training. We also introduce Image Inversion, a novel technique to quickly personalize the diffusion model for a single concept using a single image, for cases where the pre-trained IP-Adapter falls short in capturing all the details from the input image faithfully. Experimental results demonstrate the efficiency and effectiveness of our edge-aware single-image mesh texturing approach, coined EASI-Tex, in preserving the details of the input texture on diverse 3D objects, while respecting their geometry.

AnaMoDiff: 2D Analogical Motion Diffusion via Disentangled Denoising

We present AnaMoDiff, a novel diffusion-based method for 2D motion analogies that is applied to raw, unannotated videos of articulated characters. Our goal is to accurately transfer motions from a 2D driving video onto a source character, with its identity, in terms of appearance and natural movement, well preserved, even when there may be significant discrepancies between the source and driving characters in their part proportions and movement speed and styles. Our diffusion model transfers the input motion via a latent optical flow (LOF) network operating in a noised latent space, which is spatially aware, efficient to process compared to the original RGB videos, and artifact-resistant through the diffusion denoising process even amid dense movements. To accomplish both motion analogy and identity preservation, we train our denoising model in a feature-disentangled manner, operating at two noise levels. While identity-revealing features of the source are learned via conventional noise injection, motion features are learned from LOF-warped videos by only injecting noise with large values, with the stipulation that motion properties involving pose and limbs are encoded by higher-level features. Experiments demonstrate that our method achieves the best trade-off between motion analogy and identity preservation.

Slice3D: Multi-Slice, Occlusion-Revealing, Single View 3D Reconstruction

We introduce multi-slice reasoning, a new notion for single-view 3D reconstruction which challenges the current and prevailing belief that multi-view synthesis is the most natural conduit between single-view and 3D. Our key observation is that object slicing is more advantageous than altering views to reveal occluded structures. Specifically, slicing is more occlusion-revealing since it can peel through any occluders without obstruction. In the limit, i.e., with infinitely many slices, it is guaranteed to unveil all hidden object parts. We realize our idea by developing Slice3D, a novel method for single-view 3D reconstruction which first predicts multi-slice images from a single RGB image and then integrates the slices into a 3D model using a coordinate-based transformer network for signed distance prediction. The slice images can be regressed or generated, both through a U-Net based network. For the former, we inject a learnable slice indicator code to designate each decoded image into a spatial slice location, while the slice generator is a denoising diffusion model operating on the entirety of slice images stacked on the input channels. We conduct extensive evaluation against state-of-the-art alternatives to demonstrate superiority of our method, especially in recovering complex and severely occluded shape structures, amid ambiguities. All Slice3D results were produced by networks trained on a single Nvidia A40 GPU, with an inference time less than 20 seconds.