Motivation Despite the remarkable advances in sequencing and computational techniques, noise in the data and complexity of the underlying biological mechanisms render deconvolution of the phylogenetic relationships between cancer mutations difficult. Besides that, the majority of the existing datasets consist of bulk sequencing data of single tumor sample of an individual. Accurate inference of the phylogenetic order of mutations is particularly challenging in these cases and the existing methods are faced with several theoretical limitations. To overcome these limitations, new methods are required for integrating and harnessing the full potential of the existing data. Results We introduce a method called Hintra for intra-tumor heterogeneity detection. Hintra integrates sequencing data for a cohort of tumors and infers tumor phylogeny for each individual based on the evolutionary information shared between different tumors. Through an iterative process, Hintra learns the repeating evolutionary patterns and uses this information for resolving the phylogenetic ambiguities of individual tumors. The results of synthetic experiments show an improved performance compared to two state-of-the-art methods. The experimental results with a recent Breast Cancer dataset are consistent with the existing knowledge and provide potentially interesting findings. Availability and implementation The source code for Hintra is available at https://github.com/sahandk/HINTRA.
Cancer is driven by genetic mutations that dysregulate pathways important for proper cell function. Therefore, discovering these cancer pathways and their dysregulation order is key to understanding and treating cancer. However, the heterogeneity of mutations between different individuals makes this challenging and requires that cancer progression is studied in a subtype-specific way. To address this challenge, we provide a mathematical model, called Subtype-specific Pathway Linear Progression Model (SPM), that simultaneously captures cancer subtypes and pathways and order of dysregulation of the pathways within each subtype. Experiments with synthetic data indicate the robustness of SPM to problem specifics including noise compared to an existing method. Moreover, experimental results on glioblastoma multiforme and colorectal adenocarcinoma show the consistency of SPM’s results with the existing knowledge and its superiority to an existing method in certain cases. The implementation of our method is available at https://github.com/Dalton386/SPM.
The question of answering queries over ML predictions has been gaining attention in the database community. This question is challenging because finding high quality answers by invoking an oracle such as a human expert or an expensive deep neural network model on every single item in the DB and then applying the query, can be prohibitive. We develop a novel unified framework for approximate query answering by leveraging a proxy to minimize the oracle usage of finding high quality answers for both Precision-Target (PT) and Recall-Target (RT) queries. Our framework uses a judicious combination of invoking the expensive oracle on data samples and applying the cheap proxy on the DB objects. It relies on two assumptions. Under the P roxy Q uality assumption, we develop two algorithms: PQA that efficiently finds high quality answers with high probability and no oracle calls, and PQE, a heuristic extension that achieves empirically good performance with a small number of oracle calls. Alternatively, under the C ore S et C losure assumption, we develop two algorithms: CSC that efficiently returns high quality answers with high probability and minimal oracle usage, and CSE, which extends it to more general settings. Our extensive experiments on five real-world datasets on both query types, PT and RT, demonstrate that our algorithms outperform the state-of-the-art and achieve high result quality with provable statistical guarantees.
The question of answering queries over ML predictions has been gaining attention in the database community. This question is challenging because the cost of finding high quality answers corresponds to invoking an oracle such as a human expert or an expensive deep neural network model on every single item in the DB and then applying the query. We develop a novel unified framework for approximate query answering by leveraging a proxy to minimize the oracle usage of finding high quality answers for both Precision-Target (PT) and Recall-Target (RT) queries. Our framework uses a judicious combination of invoking the expensive oracle on data samples and applying the cheap proxy on the objects in the DB. It relies on two assumptions. Under the Proxy Quality assumption, proxy quality can be quantified in a probabilistic manner w.r.t. the oracle. This allows us to develop two algorithms: PQA that efficiently finds high quality answers with high probability and no oracle calls, and PQE, a heuristic extension that achieves empirically good performance with a small number of oracle calls. Alternatively, under the Core Set Closure assumption, we develop two algorithms: CSC that efficiently returns high quality answers with high probability and minimal oracle usage, and CSE, which extends it to more general settings. Our extensive experiments on five real-world datasets on both query types, PT and RT, demonstrate that our algorithms outperform the state-of-the-art and achieve high result quality with provable statistical guarantees.
Cancer is driven by genetic mutations that dysregulate pathways important for proper cell function. Therefore, discovering these cancer pathways and their dysregulation order is key to understanding and treating cancer. However, the heterogeneity of mutations between different individuals makes this challenging and requires that cancer progression is studied in a subtypespecific way. To address this challenge, we provide a mathematical model, called Subtype-specific Pathway Linear Progression Model (SPM), that simultaneously captures cancer subtypes and pathways and order of dysregulation of the pathways within each subtype. Experiments with synthetic data indicate the robustness of SPM to problem specifics including noise compared to an existing method. Moreover, experimental results on glioblastoma multiforme and colorectal adenocarcinoma show the consistency of SPM's results with the existing knowledge and its superiority to an existing method in certain cases. The implementation of our method is available at https://github.com/Dalton386/SPM.
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