Shankar Vembu
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View article: Crowd-sourced benchmarking of single-sample tumor subclonal reconstruction
Crowd-sourced benchmarking of single-sample tumor subclonal reconstruction Open
View article: Author Correction: Reconstructing evolutionary trajectories of mutation signature activities in cancer using TrackSig
Author Correction: Reconstructing evolutionary trajectories of mutation signature activities in cancer using TrackSig Open
View article: Author Correction: Inferring structural variant cancer cell fraction
Author Correction: Inferring structural variant cancer cell fraction Open
View article: Using error decay prediction to overcome practical issues of deep active learning for named entity recognition
Using error decay prediction to overcome practical issues of deep active learning for named entity recognition Open
View article: Inferring structural variant cancer cell fraction
Inferring structural variant cancer cell fraction Open
We present SVclone, a computational method for inferring the cancer cell fraction of structural variant (SV) breakpoints from whole-genome sequencing data. SVclone accurately determines the variant allele frequencies of both SV breakends, …
View article: Reconstructing evolutionary trajectories of mutation signature activities in cancer using TrackSig
Reconstructing evolutionary trajectories of mutation signature activities in cancer using TrackSig Open
View article: Overcoming Practical Issues of Deep Active Learning and its Applications on Named Entity Recognition.
Overcoming Practical Issues of Deep Active Learning and its Applications on Named Entity Recognition. Open
Existing deep active learning algorithms achieve impressive sampling efficiency on natural language processing tasks. However, they exhibit several weaknesses in practice, including (a) inability to use uncertainty sampling with black-box …
View article: Implementing Recommendation Algorithms in a Large-Scale Biomedical Science Knowledge Base
Implementing Recommendation Algorithms in a Large-Scale Biomedical Science Knowledge Base Open
The number of biomedical research articles published has doubled in the past 20 years. Search engine based systems naturally center around searching, but researchers may not have a clear goal in mind, or the goal may be expressed in a quer…
View article: Interactive Learning from Multiple Noisy Labels
Interactive Learning from Multiple Noisy Labels Open
Interactive learning is a process in which a machine learning algorithm is provided with meaningful, well-chosen examples as opposed to randomly chosen examples typical in standard supervised learning. In this paper, we propose a new metho…
View article: PhyloWGS: Reconstructing subclonal composition and evolution from whole-genome sequencing of tumors
PhyloWGS: Reconstructing subclonal composition and evolution from whole-genome sequencing of tumors Open