Related papers: Learning Embeddings from Cancer Mutation Sets for …

Is there really much more to say about sparse autoencoders (SAEs)? Autoencoders in general, and SAEs in particular, represent deep architectures that are capable of modeling low-dimensional latent structure in data. Such structure could…

Somatic mutations in cancer can be viewed as a mixture distribution of several mutational signatures, which can be inferred using non-negative matrix factorization (NMF). Mutational signatures have previously been parametrized using either…

Cancer diagnosis, prognosis, and therapeutic response predictions are based on morphological information from histology slides and molecular profiles from genomic data. However, most deep learning-based objective outcome prediction and…

Variational Auto-Encoders (VAEs) are capable of learning latent representations for high dimensional data. However, due to the i.i.d. assumption, VAEs only optimize the singleton variational distributions and fail to account for the…

Human cancers present a significant public health challenge and require the discovery of novel drugs through translational research. Transcriptomics profiling data that describes molecular activities in tumors and cancer cell lines are…

We propose a novel algorithm for quantizing continuous latent representations in trained models. Our approach applies to deep probabilistic models, such as variational autoencoders (VAEs), and enables both data and model compression. Unlike…

Self-supervised learning has revolutionized medical imaging by enabling efficient and generalizable feature extraction from large-scale unlabeled datasets. Recently, self-supervised foundation models have been extended to three-dimensional…

Radiotherapists require accurate registration of MR/CT images to effectively use information from both modalities. In a typical registration pipeline, rigid or affine transformations are applied to roughly align the fixed and moving images…

Computational pathology relies on effective representation learning to support cancer research and precision medicine. Although self-supervised learning has driven major progress at the patch and whole-slide image levels, representation…

One of the most challenges in medical imaging is the lack of data and annotated data. It is proven that classical segmentation methods such as U-NET are useful but still limited due to the lack of annotated data. Using a weakly supervised…

Changes in the number of copies of certain parts of the genome, known as copy number alterations (CNAs), due to somatic mutation processes are a hallmark of many cancers. This genomic complexity is known to be associated with poorer…

In this paper we propose Structuring AutoEncoders (SAE). SAEs are neural networks which learn a low dimensional representation of data which are additionally enriched with a desired structure in this low dimensional space. While traditional…

Generative learning is a powerful tool for representation learning, and shows particular promise for problems in biomedical imaging. However, in this context, sampling from the distribution is secondary to finding representations of real…

Motivation: Despite advances in the computational analysis of high-throughput molecular profiling assays (e.g. transcriptomics), a dichotomy exists between methods that are simple and interpretable, and ones that are complex but with lower…

Sparse autoencoders (SAEs) have recently emerged as pivotal tools for introspection into large language models. SAEs can uncover high-quality, interpretable features at different levels of granularity and enable targeted steering of the…

Whole-slide images are central to digital pathology, yet their extreme size and scarce annotations make self-supervised learning essential. Masked Autoencoders (MAEs) with Vision Transformer backbones have recently shown strong potential…

Microscopic examination of slides prepared from tissue samples is the primary tool for detecting and classifying cancerous lesions, a process that is time-consuming and requires the expertise of experienced pathologists. Recent advances in…

We propose a new method that employs transfer learning techniques to effectively correct sampling selection errors introduced by sparse annotations during supervised learning for automated tumor segmentation. The practicality of current…

Deep learning has gained significant attention in medical image segmentation. However, the limited availability of annotated training data presents a challenge to achieving accurate results. In efforts to overcome this challenge, data…

We propose a new deep learning method for tumour segmentation when dealing with missing imaging modalities. Instead of producing one network for each possible subset of observed modalities or using arithmetic operations to combine feature…