Learning Curves for Drug Response Prediction in Cancer Cell Lines
Argonne National Laboratory（阿贡国家实验室）；University of Chicago（芝加哥大学）；Frederick National Laboratory for Cancer Research（弗雷德里克国家癌症研究实验室）；Leidos Biomedical Research, Inc.（Leidos生物医学研究公司）
Alexander Partin, Thomas Brettin, Yvonne A. Evrard, Yitan Zhu, Hyunseung Yoo, Fangfang Xia, Songhao Jiang, Austin Clyde, Maulik Shukla, Michael Fonstein, James … 展开作者
Alexander Partin, Thomas Brettin, Yvonne A. Evrard, Yitan Zhu, Hyunseung Yoo, Fangfang Xia, Songhao Jiang, Austin Clyde, Maulik Shukla, Michael Fonstein, James H. Doroshow, Rick Stevens
Motivated by the size of cell line drug sensitivity data, researchers have been developing machine learning (ML) models for predicting drug response to advance cancer treatment. As drug sensitivity studies continue generating data, a common question is whether the proposed predictors can further improve the generalization performance with more training data. We utilize empirical learning curves for evaluating and comparing the data scaling properties of two neural networks (NNs) and two gradient boosting decision tree (GBDT) models trained on four drug screening datasets. The learning curves are accurately fitted to a power law model, providing a framework for assessing the data scaling behavior of these predictors. The curves demonstrate that no single model dominates in terms of prediction performance across all datasets and training sizes, suggesting that the shape of these curves depends on the unique model-dataset pair. The multi-input NN (mNN), in which gene expressions and molecular drug descriptors are input into separate subnetworks, outperforms a single-input NN (sNN), where the cell and drug features are concatenated for the input layer. In contrast, a GBDT with hyperparameter tuning exhibits superior performance as compared with both NNs at the lower range of training sizes for two of the datasets, whereas the mNN performs better at the higher range of training sizes. Moreover, the trajectory of the curves suggests that increasing the sample size is expected to further improve prediction scores of both NNs. These observations demonstrate the benefit of using learning curves to evaluate predictors, providing a broader perspective on the overall data scaling characteristics. The fitted power law curves provide a forward-looking performance metric and can serve as a co-design tool to guide experimental biologists and computational scientists in the design of future experiments.
Large variability between cell lines brings a difficult optimization problem of drug selection for cancer therapy. Standard approaches use prediction of value for this purpose, corresponding e.g. to expected value of their distribution. This article shows superiority of working on, predicting the entire probability distributions - proposing basic tools for this purpose. We are mostly interested in the best drug in their batch to be tested - proper optimization of their selection for extreme statistics requires knowledge of the entire probability distributions, which for distributions of drug p…
Argonne National Laboratory（阿贡国家实验室）；The University of Chicago（芝加哥大学）
Cancer claims millions of lives yearly worldwide. While many therapies have been made available in recent years, by in large cancer remains unsolved. Exploiting computational predictive models to study and treat cancer holds great promise in improving drug development and personalized design of treatment plans, ultimately suppressing tumors, alleviating suffering, and prolonging lives of patients. A wave of recent papers demonstrates promising results in predicting cancer response to drug treatments while utilizing deep learning methods. These papers investigate diverse data representations, n…
Predicting clinical outcomes to anti-cancer drugs on a personalized basis is challenging in cancer treatment due to the heterogeneity of tumors. Traditional computational efforts have been made to model the effect of drug response on individual samples depicted by their molecular profile, yet overfitting occurs because of the high dimension for omics data, hindering models from clinical application. Recent research shows that deep learning is a promising approach to build drug response models by learning alignment patterns between drugs and samples. However, existing studies employed the simpl…
Argonne National Laboratory（阿贡国家实验室）；Leidos Biomedical Research, Inc.（莱多斯生物医学研究公司）；National Cancer Institute（美国国家癌症研究所）；The University of Chicago（芝加哥大学）
Transfer learning has been shown to be effective in many applications in which training data for the target problem are limited but data for a related (source) problem are abundant. In this paper, we apply transfer learning to the prediction of anti-cancer drug response. Previous transfer learning studies for drug response prediction focused on building models that predict the response of tumor cells to a specific drug treatment. We target the more challenging task of building general prediction models that can make predictions for both new tumor cells and new drugs. We apply the classic trans…
Enhancing drug and cell line representations via contrastive learning for improved anti-cancer drug prioritization
The Ohio State University（俄亥俄州立大学）；Biomedical Informatics Department, The Ohio State University（俄亥俄州立大学生物医学信息学系）；Computer Science and Engineering Department, The Ohio State University（俄亥俄州立大学计算机科学与工程系）；Translational Data Analytics Institute, The Ohio State University（俄亥俄州立大学转化数据分析研究所）
IBM Research – Zurich（IBM苏黎世研究院）；Institute für Molekulare Systembiologie（分子系统生物学研究所）
We present the Network-based Biased Tree Ensembles (NetBiTE) method for drug sensitivity prediction and drug sensitivity biomarker identification in cancer using a combination of prior knowledge and gene expression data. Our devised method consists of a biased tree ensemble that is built according to a probabilistic bias weight distribution. The bias weight distribution is obtained from the assignment of high weights to the drug targets and propagating the assigned weights over a protein-protein interaction network such as STRING. The propagation of weights, defines neighborhoods of influence …
SDIVF R&D Centre（SDIVF研发中心）；The Chinese University of Hong Kong（香港中文大学）
Understanding the phenotypic drug response on cancer cell lines plays a vital rule in anti-cancer drug discovery and re-purposing. The Genomics of Drug Sensitivity in Cancer (GDSC) database provides open data for researchers in phenotypic screening to test their models and methods. Previously, most research in these areas starts from the fingerprints or features of drugs, instead of their structures. In this paper, we introduce a model for phenotypic screening, which is called twin Convolutional Neural Network for drugs in SMILES format (tCNNS). tCNNS is comprised of CNN input channels for dru…
Centrum Wiskunde & Informatica（数学与计算机科学中心）；Utrecht University（乌得勒支大学）；Massachusetts General Hospital（麻省总医院）；Harvard Medical School（哈佛医学院）；Maastricht University Medical Centre+（马斯特里赫特大学医学中心+）
Personalizing drug prescriptions in cancer care based on genomic information requires associating genomic markers with treatment effects. This is an unsolved challenge requiring genomic patient data in yet unavailable volumes as well as appropriate quantitative methods. We attempt to solve this challenge for an experimental proxy for which sufficient data is available: 42 drugs tested on 1018 cancer cell lines. Our goal is to develop a method to identify the drug that is most promising based on a cell line's genomic information. For this, we need to identify for each drug the machine learning …
TransCDR: a deep learning model for enhancing the generalizability of cancer drug response prediction through transfer learning and multimodal data fusion for drug representation
Shanghai Medical College, Fudan University（复旦大学上海医学院）；Shanghai Institute of Stem Cell Research and Clinical Translation（上海干细胞研究与临床转化研究院）；Shanghai World Foreign Language Academy（上海世界外国语中学）
University of Chicago（芝加哥大学）；Argonne National Laboratory（阿贡国家实验室）；Frederick National Laboratory for Cancer Research（弗雷德里克国家癌症研究实验室）
By combining various cancer cell line (CCL) drug screening panels, the size of the data has grown significantly to begin understanding how advances in deep learning can advance drug response predictions. In this paper we train >35,000 neural network models, sweeping over common featurization techniques. We found the RNA-seq to be highly redundant and informative even with subsets larger than 128 features. We found the inclusion of single nucleotide polymorphisms (SNPs) coded as count matrices improved model performance significantly, and no substantial difference in model performance with resp…
The emergence of acquired drug resistance in cancer represents a major barrier to treatment success. While research has traditionally focused on genetic sources of resistance, recent findings suggest that cancer cells can acquire transient resistant phenotypes via epigenetic modifications and other non-genetic mechanisms. Although these resistant phenotypes are eventually relinquished by individual cells, they can temporarily 'save' the tumor from extinction and enable the emergence of more permanent resistance mechanisms. These observations have generated interest in the potential of epigenet…
Modern cancer -omics and pharmacological data hold great promise in precision cancer medicine for developing individualized patient treatments. However, high heterogeneity and noise in such data pose challenges for predicting the response of cancer cell lines to therapeutic drugs accurately. As a result, arbitrary human judgment calls are rampant throughout the predictive modeling pipeline. In this work, we develop a transparent stability-driven pipeline for drug response interpretable predictions, or staDRIP, which builds upon the PCS framework for veridical data science (Yu and Kumbier, 2020…
Institute of Molecular Systems Biology, ETH Zürich（苏黎世联邦理工学院分子系统生物学研究所）
In this work, we propose two novel methodologies to study temporal and morphological phenotypic effects caused by different experimental conditions using imaging data. As a proof of concept, we apply them to analyze drug effects in 2D cancer cell cultures. We train a convolutional autoencoder on 1M images dataset with random augmentations and multi-crops to use as feature extractor. We systematically compare it to the pretrained state-of-the-art models. We further use the feature extractor in two ways. First, we apply distance-based analysis and dynamic time warping to cluster temporal pattern…
Cancer is one of the most common diseases worldwide, posing a serious threat to human health and leading to the deaths of a large number of people. It was observed during the drug administration in chemotherapy that immune cells, cancer cells and normal cells are killed or at least seriously injured and also in order to keep dosage of the drug at specific level in body, drug should be delivered in specific time and dosage. Therefore, to address these problems, a decision-making process is needed to identify the most appropriate treatment for cancer cases which causes killing of cancer cells by…
Permutation invariant multi-output Gaussian Processes for drug combination prediction in cancer
MRC Biostatistics Unit, University of Cambridge（剑桥大学医学研究委员会生物统计学单元）；Oslo Centre for Biostatistics and Epidemiology (OCBE), University of Oslo（奥斯陆大学奥斯陆生物统计学与流行病学中心）；Broad Institute of MIT & Harvard（麻省理工学院与哈佛大学博德研究所）；CRUK Cambridge Centre Ovarian Programme（英国癌症研究剑桥中心卵巢项目）；Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID)（剑桥治疗免疫学与传染病研究所）
Evaluating the Effectiveness of Artificial Intelligence in Predicting Adverse Drug Reactions among Cancer Patients: A Systematic Review and Meta-Analysis
National Polytechnic School of Oran - Maurice Audin（奥兰国家理工学院 - 莫里斯·奥丹）
To enable personalized cancer treatment, machine learning models have been developed to predict drug response as a function of tumor and drug features. However, most algorithm development efforts have relied on cross validation within a single study to assess model accuracy. While an essential first step, cross validation within a biological data set typically provides an overly optimistic estimate of the prediction performance on independent test sets. To provide a more rigorous assessment of model generalizability between different studies, we use machine learning to analyze five publicly av…
Recent clinical trials have shown that the adaptive drug therapy can be more efficient than a standard MTD-based policy in treatment of cancer patients. The adaptive therapy paradigm is not based on a preset schedule; instead, the doses are administered based on the current state of tumor. But the adaptive treatment policies examined so far have been largely ad hoc. In this paper we propose a method for systematically optimizing the rules of adaptive policies based on an Evolutionary Game Theory model of cancer dynamics. Given a set of treatment objectives, we use the framework of dynamic prog…
University of Virginia（弗吉尼亚大学）；McGill University（麦吉尔大学）
Predicting the response of cancer cells to drugs is an important problem in pharmacogenomics. Recent efforts in generation of large scale datasets profiling gene expression and drug sensitivity in cell lines have provided a unique opportunity to study this problem. However, one major challenge is the small number of samples (cell lines) compared to the number of features (genes) even in these large datasets. We propose a collaborative filtering (CF) like algorithm for modeling gene-drug relationship to identify patients most likely to benefit from a treatment. Due to the correlation of gene ex…
Intercellular heterogeneity is a major obstacle to successful precision medicine. Single-cell RNA sequencing (scRNA-seq) technology has enabled in-depth analysis of intercellular heterogeneity in various diseases. However, its full potential for precision medicine has yet to be reached. Towards this, we propose a new drug recommendation system called: A Single-cell Guided Pipeline to Aid Repurposing of Drugs (ASGARD). ASGARD defines a novel drug score predicting drugs by considering all cell clusters to address the intercellular heterogeneity within each patient. We tested ASGARD on multiple d…
VQSynery: Robust Drug Synergy Prediction With Vector Quantization Mechanism
School of Data Science and Engineering（数据科学与工程学院）；East China Normal University（华东师范大学）；School of Medicine（医学院）；College of Design&Engineering（设计与工程学院）；National University of Singapore（新加坡国立大学）
University of Glasgow（格拉斯哥大学）；MBZUAI（穆罕默德·本·扎耶德人工智能大学）；Neurosurgery, Brigham and Women’s Hospital（布莱根和妇女医院神经外科）；University of New South Wales（新南威尔士大学）；Illinois Institute of Technology（伊利诺伊理工学院）；University of North Carolina at Chapel Hill（北卡罗来纳大学教堂山分校）；Harvard Medical School（哈佛医学院）
StateXDiff: Cell State-Contextualized Multimodal Diffusion for Single-Cell Perturbation Prediction
College of Future Technology（未来技术学院）；College of Informatics, Huazhong Agricultural University（华中农业大学信息学院）；Department of Clinical Neurosciences, University of Cambridge（剑桥大学临床神经科学系）
Adaptive High-Level Tight Control of Prostate Cancer: A Path from From Terminal Disease to Chronic Condition
Scripps and Pitzer Colleges, Claremont Colleges Consortium（斯克里普斯学院和皮策学院，克莱蒙特学院联盟）；Princeton University（普林斯顿大学）；Scripps College（斯克里普斯学院）；Cancer Ecology Center, The Brady Urological Institute, Johns Hopkins School of Medicine（约翰霍普金斯医学院布雷泌尿研究所癌症生态学中心）；Moffitt Cancer Center（莫菲特癌症中心）；Johns Hopkins University（约翰霍普金斯大学）；Bloomberg School of Public Health, Johns Hopkins University（约翰霍普金斯大学布隆伯格公共卫生学院）；Department of Chemical and Biomolecular Engineering, John Hopkins University（约翰霍普金斯大学生物化学工程系）
