To achieve joint matrix factorization, we construct an objective function which aims to minimize the factorization error, with constraints on the scale of the condition-specific components and the similarity between condition-specific gene modules. We propose an algorithm based on block coordinate ...
However, interpreting the individual parts remains a challenge. To address this challenge, we extend methods for differential expression analysis by allowing cells to have partial membership to multiple groups. We call this grade of membership differential expression (GoM DE). We illustrate the ...
As connectomics advances, it will become commonplace to know far more about the structure of a nervous system than about its function. The starting point for many investigations will become neuronal wiring diagrams, which will be interpreted to make theo
www.nature.com/tp ORIGINAL ARTICLE BECon: a tool for interpreting DNA methylation findings from blood in the context of brain RD Edgar1,2, MJ Jones1,2, MJ Meaney3,4,5, G Turecki6 and MS Kobor1,2,5 Tissue differences are one of the largest contributors to variability in the human ...
1. Interpreting Forms of RepresentationVisual order as concretized worldview – Erwin Panofsky’sPerspective as Symbolic FormDescribed by W.J.T. Mitchell as an “epic of visuality”, Panofsky’s essay on per-spective, originally published in 1927,1is a concentrated synthesis of the his-tory ...
To evaluate the performance of Moonlight, we compared its machine-learning approach to two state-of-the-art methods for the detection of cancer driver genes: 20/20+66and OncodriveRole67. We chose these methods for their popularity, ease of implementation, and similarity to Moonlight’s machine...
There is an increasing interest in the use of Deep Learning (DL) based methods as a supporting analytical framework in oncology. However, most direct applications of DL will deliver models with limited transparency and explainability, which constrain the
To evaluate the performance of Moonlight, we compared its machine-learning approach to two state-of-the-art methods for the detection of cancer driver genes: 20/20+66and OncodriveRole67. We chose these methods for their popularity, ease of implementation, and similarity to Moonlight’s machine...
In this way, the semantic similarity (and difference) between NLSR terms can be interpreted by examining fuzzy membership degrees. Each of the elements in (𝜇1, 𝜇2,…,𝜇𝑘)(μ1, μ2,…,μk) can take a non-zero value to measure the degree of geometric representation belonging to...
As the similarity between geographical units indicates that they belong to the same functional region, the number of subspaces can also be inferred as five based on the number of darker blocks. Figure 3. Visualization of the similarity matrix. Non-zero entries in the matrix are painted black, ...