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Interpretable deep learning models for translational medicine

用于转化医学的可解释深度学习模型

基本信息

批准号：
10579895
负责人：
XINGHUA LU
金额：
$ 31.37万
依托单位：
UNIVERSITY OF PITTSBURGH AT PITTSBURGH
依托单位国家：
美国
项目类别：
财政年份：
2015
资助国家：
美国
起止时间：
2015-04-01 至 2025-03-31
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10579895
关键词：
Affect Algorithms Antineoplastic Agents Big Data Biological Cancer Patient Cancer cell line Cell model Cell physiology Cells Chemicals Data Disease Event Gene Expression Genetic Genetic Transcription Grain Human Immune Evasion Immunotherapy Individual Information Theory Intervention Knowledge Learning Libraries Malignant Neoplasms Maps Messenger RNA Methodology MicroRNAs Mining Modeling Molecular Monitor Nature Network-based Organoids Outcome Paper Pathologic Pathway interactions Patients Phenotype Physiological Publishing Research Research Personnel Side Signal Pathway Signal Transduction Signaling Molecule Structure System Systems Biology Techniques Technology The Cancer Genome Atlas Training Translational Research United States National Institutes of Health Yeasts biological systems cancer cell cancer therapy cell behavior data modeling deep field survey deep learning deep learning algorithm deep learning model design drug sensitivity experience genome-wide innovation inquiry-based learning insight learning algorithm learning strategy machine learning algorithm machine learning method novel pharmacologic pre-clinical precision medicine precision oncology predicting response prevent response single-cell RNA sequencing success theories tool transcription factor transcriptome transcriptomics translational applications translational impact translational medicine transmission process treatment response tumor tumor microenvironment

项目摘要

Understanding the state of cellular signaling systems provides insights to how cells behave under physiological and pathological conditions. Cellular signaling systems are organized as hierarchy (cascade) and signals of a molecular is often compositionally encoded to control cellular processes, such as gene expression. This project aims to develop advanced deep learning models (DLMs) to simulate cellular signaling systems based on gene expression data. In last 3 years, the project has made significant progresses, but the challenges remain. Importantly, contemporary DLMs behave as “black boxes”, in that it is difficult to interpret how signals are encoded and how to interpret which signal a hidden node represent in a DLM. This black-box nature prevents researchers from gaining biological insights using DLMs, even though these models can be much superior in modeling data than other types of models in many tasks, e.g., predicting drug sensitivity of cancer cells. In this competitive renewal, we propose to develop novel DLMs and innovative inference algorithms to train “interpretable” DLMs and apply them in translational research. The proposed research is innovative and of high significance in several perspectives: 1) Our novel DLMs and algorithms take advantage of big data resulting from systematic chemical/genetic perturbations of cellular signaling machinery, so that we can use the perturbation condition as side information to reveal how signals are encoded in a DLM. 2) We integrate principles of causal inference and information theory with deep learning method to make DLMs interpretable. As results, that researchers can gain mechanistic insights from such models. 3) Innovative application of interpretable DLMs will advance translational research. For example, we will train interpretable DLMs to model cellular signaling at the level of single cells and use this information investigate inter-cellular interactions among cells in tumor microenvironment to shed light on immune evasion mechanisms of cancers. We will also use information derived from interpretable DLMs to predict cancer cell drug sensitivity. We anticipate that our study will bring forth significant advances not only in deep learning methodology but also in precision medicine.

了解细胞信号系统的状态可以深入了解细胞在生理条件下的行为。和病理条件。细胞信号系统被组织为层次结构（级联）和信号的一个分子通常在组成上编码以控制细胞过程，例如基因表达。这该项目旨在开发先进的深度学习模型（DLM），以模拟基于基因表达数据。在过去的3年里，该项目取得了重大进展，但挑战保持。重要的是，当代的DLMs表现为“黑匣子”，因为很难解释信号是如何产生的。以及如何解释隐藏节点在DLM中表示哪个信号。这种黑箱性质阻止研究人员使用DLMs获得生物学见解，即使这些模型可能非常复杂，在许多任务中上级其他类型的模型，例如，预测癌症的药物敏感性细胞在这个竞争性的更新，我们建议开发新的DLMs和创新的推理算法，训练“可解释的”DLM并将其应用于翻译研究。拟议的研究具有创新性，在几个方面具有重要意义：1）我们的新型DLM和算法利用大数据由于细胞信号机制的系统性化学/遗传扰动，因此我们可以使用扰动条件作为边信息，以揭示信号如何在DLM中编码。2)我们整合因果推理和信息理论的原理与深度学习方法，使DLM可解释。因此，研究人员可以从这些模型中获得机理的见解。3)创新应用可解释的DLM将促进翻译研究。例如，我们将训练可解释的DLM来建模在单细胞水平上的细胞信号传导，并利用这些信息研究细胞间的相互作用在肿瘤微环境中的细胞之间，以阐明癌症的免疫逃避机制。我们还将使用来自可解释的DLMs的信息来预测癌细胞药物敏感性。我们预计，这项研究不仅将在深度学习方法学方面取得重大进展，还将在精准医学方面取得重大进展。

项目成果

期刊论文数量（17）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

Toward multimodal signal detection of adverse drug reactions.

DOI：
10.1016/j.jbi.2017.10.013
发表时间：
2017-12
期刊：
Journal of biomedical informatics
影响因子：
4.5
作者：
Harpaz R;DuMouchel W;Schuemie M;Bodenreider O;Friedman C;Horvitz E;Ripple A;Sorbello A;White RW;Winnenburg R;Shah NH
通讯作者：
Shah NH

A signal-based method for finding driver modules of breast cancer metastasis to the lung.

一种基于信号的方法，用于发现肺癌转移的驱动器模块。

DOI：
10.1038/s41598-017-09951-2
发表时间：
2017-08-30
期刊：
Scientific reports
影响因子：
4.6
作者：
Yan G;Chen V;Lu X;Lu S
通讯作者：
Lu S

A Novel Bayesian Framework Infers Driver Activation States and Reveals Pathway-Oriented Molecular Subtypes in Head and Neck Cancer.

DOI：
10.3390/cancers14194825
发表时间：
2022-10-03
期刊：
CANCERS
影响因子：
5.2
作者：
Liu, Zhengping;Cai, Chunhui;Ma, Xiaojun;Liu, Jinling;Chen, Lujia;Lui, Vivian Wai Yan;Cooper, Gregory F.;Lu, Xinghua
通讯作者：
Lu, Xinghua

Leveraging MEDLINE indexing for pharmacovigilance - Inherent limitations and mitigation strategies.

DOI：
10.1016/j.jbi.2015.08.022
发表时间：
2015-10
期刊：
Journal of biomedical informatics
影响因子：
4.5
作者：
Winnenburg R;Sorbello A;Ripple A;Harpaz R;Tonning J;Szarfman A;Francis H;Bodenreider O
通讯作者：
Bodenreider O

Revealing the Impact of Genomic Alterations on Cancer Cell Signaling with an Interpretable Deep Learning Model.