SC-MIL: Sparsely Coded Multiple Instance Learning for Whole Slide Image Classification

Multiple Instance Learning (MIL) has been widely used in weakly supervised whole slide image (WSI) classification. Typical MIL methods include a feature embedding part that embeds the instances into features via a pre-trained feature extractor and the MIL aggregator that combines instance embeddings into predictions. The current focus has been directed toward improving these parts by refining the feature embeddings through self-supervised pre-training and modeling the correlations between instances separately. In this paper, we proposed a sparsely coded MIL (SC-MIL) that addresses those two aspects at the same time by leveraging sparse dictionary learning. The sparse dictionary learning captures the similarities of instances by expressing them as a sparse linear combination of atoms in an over-complete dictionary. In addition, imposing sparsity help enhance the instance feature embeddings by suppressing irrelevant instances while retaining the most relevant ones. To make the conventional sparse coding algorithm compatible with deep learning, we unrolled it into an SC module by leveraging deep unrolling. The proposed SC module can be incorporated into any existing MIL framework in a plug-and-play manner with an acceptable computation cost. The experimental results on multiple datasets demonstrated that the proposed SC module could substantially boost the performance of state-of-the-art MIL methods. The codes are available at \href{https://github.com/sotiraslab/SCMIL.git}{https://github.com/sotiraslab/SCMIL.git}.

SC-VAE: Sparse Coding-based Variational Autoencoder

Learning rich data representations from unlabeled data is a key challenge towards applying deep learning algorithms in downstream supervised tasks. Several variants of variational autoencoders have been proposed to learn compact data representaitons by encoding high-dimensional data in a lower dimensional space. Two main classes of VAEs methods may be distinguished depending on the characteristics of the meta-priors that are enforced in the representation learning step. The first class of methods derives a continuous encoding by assuming a static prior distribution in the latent space. The second class of methods learns instead a discrete latent representation using vector quantization (VQ) along with a codebook. However, both classes of methods suffer from certain challenges, which may lead to suboptimal image reconstruction results. The first class of methods suffers from posterior collapse, whereas the second class of methods suffers from codebook collapse. To address these challenges, we introduce a new VAE variant, termed SC-VAE (sparse coding-based VAE), which integrates sparse coding within variational autoencoder framework. Instead of learning a continuous or discrete latent representation, the proposed method learns a sparse data representation that consists of a linear combination of a small number of learned atoms. The sparse coding problem is solved using a learnable version of the iterative shrinkage thresholding algorithm (ISTA). Experiments on two image datasets demonstrate that our model can achieve improved image reconstruction results compared to state-of-the-art methods. Moreover, the use of learned sparse code vectors allows us to perform downstream task like coarse image segmentation through clustering image patches.

TLR: Transfer Latent Representation for Unsupervised Domain Adaptation

Domain adaptation refers to the process of learning prediction models in a target domain by making use of data from a source domain. Many classic methods solve the domain adaptation problem by establishing a common latent space, which may cause the loss of many important properties across both domains. In this manuscript, we develop a novel method, transfer latent representation (TLR), to learn a better latent space. Specifically, we design an objective function based on a simple linear autoencoder to derive the latent representations of both domains. The encoder in the autoencoder aims to project the data of both domains into a robust latent space. Besides, the decoder imposes an additional constraint to reconstruct the original data, which can preserve the common properties of both domains and reduce the noise that causes domain shift. Experiments on cross-domain tasks demonstrate the advantages of TLR over competing methods.