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Abstract Motivation While each cancer is the result of an isolated evolutionary process, there are repeated patterns in tumorigenesis defined by recurrent driver mutations and their temporal ordering. Such repeated evolutionary trajectories hold the potential to improve stratification of cancer patients into subtypes with distinct survival and therapy response profiles. However, current cancer phylogeny methods infer large solution spaces of plausible evolutionary histories from the same sequencing data, obfuscating repeated evolutionary patterns. Results To simultaneously resolve ambiguities in sequencing data and identify cancer subtypes, we propose to leverage common patterns of evolution found in patient cohorts. We first formulate the Multiple Choice Consensus Tree problem, which seeks to select a tumor tree for each patient and assign patients into clusters in such a way that maximizes consistency within each cluster of patient trees. We prove that this problem is NP-hard and develop a heuristic algorithm, Revealing Evolutionary Consensus Across Patients (RECAP), to solve this problem in practice. Finally, on simulated data, we show RECAP outperforms existing methods that do not account for patient subtypes. We then use RECAP to resolve ambiguities in patient trees and find repeated evolutionary trajectories in lung and breast cancer cohorts. Availability and implementation https://github.com/elkebir-group/RECAP. Supplementary information Supplementary data are available at Bioinformatics online. 

Document authors commonly use tables to support arguments presented in the text. But, because tables are usually separate from the main body text, readers must split their attention between different parts of the document. We present an interactive document reader that automatically links document text with corresponding table cells. Readers can select a sentence (or tables cells) and our reader highlights the relevant table cells (or sentences). We provide an automatic pipeline for extracting such references between sentence text and table cells for existing PDF documents that combines structural analysis of tables with natural language processing and rule-based matching. On a test corpus of 330 (sentence, table) pairs, our pipeline correctly extracts 48.8% of the references. An additional 30.5% contain only false negatives (FN) errors -- the reference is missing table cells. The remaining 20.7% contain false positives (FP) errors -- the reference includes extraneous table cells and could therefore mislead readers. A user study finds that despite such errors, our interactive document reader helps readers match sentences with corresponding table cells more accurately and quickly than a baseline document reader.