Precision oncology, the genetic sequencing of tumors to identify druggable targets, has emerged as the standard of care in the treatment of many cancers. Nonetheless, due to the pace of therapy development and variability in patient information, designing effective protocols for individual treatment assignment in a sam…
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48 results for “Precision Oncology”
New methods use RL and DA to improve dosing precision and reduce side effects.
problem Improving precision and safety of anticancer drug dosing.
method Bayesian data assimilation and reinforcement learning.
result Significantly reduces incidence of severe side effects.
AI framework uses multi-omics data to personalize cancer treatment suggestions.
problem Leveraging AI for personalized cancer treatment based on complex patient characteristics.
method Modular machine learning framework trained on diverse multi-omics technologies.
result Superior performance in personalized counterfactual treatment suggestions.
The genomic profile underlying an individual tumor can be highly informative in the creation of a personalized cancer treatment strategy for a given patient; a practice known as precision oncology. This involves next generation sequencing of a tumor sample and the subsequent identification of genomic aberrations, such …
Bayesian model predicts oncology demand trends with high accuracy.
problem Accurate forecasting of oncology demand for resource planning.
method Boosting-based Bayesian conjugate models for Poisson process.
result Model outperforms other methods in trend detection accuracy.
New framework for managing medical risks using convex responses.
problem Medical risk management and dosing optimization.
method Analyzes convex and concave dose-response functions, defines antifragility.
result Proposes a mathematical framework for integrating nonlinearities in oncology.
Graphical models have gained a lot of attention recently as a tool for learning and representing dependencies among variables in multivariate data. Often, domain scientists are looking specifically for differences among the dependency networks of different conditions or populations (e.g. differences between regulatory …
Analysis of somatic mutation profiles from cancer patients is essential in the development of cancer research. However, the low frequency of most mutations and the varying rates of mutations across patients makes the data extremely challenging to statistically analyze as well as difficult to use in classification probl…
Aim: To review how machine learning (ML) is applied to imaging biomarkers in neuro-oncology, in particular for diagnosis, prognosis, and treatment response monitoring. Materials and Methods: The PubMed and MEDLINE databases were searched for articles published before September 2018 using relevant search terms. The sear…
Over the past decades, both critical care and cancer care have improved substantially. Due to increased cancer-specific survival, we hypothesized that both the number of cancer patients admitted to the ICU and overall survival have increased since the millennium change. MIMIC-III, a freely accessible critical care data…
The complexity of human cancer often results in significant heterogeneity in response to treatment. Precision medicine offers potential to improve patient outcomes by leveraging this heterogeneity. Individualized treatment rules (ITRs) formalize precision medicine as maps from the patient covariate space into the space…
AI in Pharma for Personalized Sequential Decision-Making: Methods, Applications and Opportunitiesstat.ME
AI enhances personalized drug development and decision-making in pharma.
problem Traditional drug development lacks personalized treatment plans.
method Application of AI in drug discovery, clinical trials, and post-marketing assessment.
result AI improves personalized medicine, optimizing health outcomes.
Generative AI models improve clinical trial data by generating survival outcomes.
problem Generating valid survival outcomes for clinical trials with synthetic data.
method A variational autoencoder (VAE) that jointly generates mixed-type covariates and survival outcomes.
result The method outperforms GAN baselines on fidelity, utility, and privacy metrics.
The emerging field of precision oncology relies on the accurate pinpointing of alterations in the molecular profile of a tumor to provide personalized targeted treatments. Current methodologies in the field commonly include the application of next generation sequencing technologies to a tumor sample, followed by the id…
Q-learning adapted to find near-equivalent treatment strategies.
problem Finding optimal treatment sequences in dynamic treatment regimes.
method Introducing a worst-value tolerance criterion to find sets of near-equivalent policies.
result Constructs families of near-equivalent treatment strategies.
We have applied a little-known data transformation to subsets of the Surveillance, Epidemiology, and End Results (SEER) publically available data of the National Cancer Institute (NCI) to make it suitable input to standard machine learning classifiers. This transformation properly treats the right-censored data in the …
Reinforcement learning algorithms are gaining popularity in fields in which optimal scheduling is important, and oncology is not an exception. The complex and uncertain dynamics of cancer limit the performance of traditional model-based scheduling strategies like Optimal Control. Motivated by the recent success of mode…
In this manuscript we analyze a data set containing information on children with Hodgkin Lymphoma (HL) enrolled on a clinical trial. Treatments received and survival status were collected together with other covariates such as demographics and clinical measurements. Our main task is to explore the potential of machine …
auton-survival simplifies survival analysis for healthcare data.
problem Handling censored time-to-event data in healthcare.
method Open-source package for survival regression, adjustment, counterfactual estimation, phenotyping, and treatment effects.
result Demonstrates auton-survival's ability to support complex health and epidemiological questions.
Develops regression trees for estimating cumulative incidence curves in competing risks.
problem Estimating cumulative incidence functions in competing risks settings.
method Uses augmented estimators of the Brier score risk to build and prune regression trees.
result Demonstrates the utility of the proposed methods through simulation studies and real data.
The ability to accurately classify disease subtypes is of vital importance, especially in oncology where this capability could have a life saving impact. Here we report a classification between two subtypes of non-small cell lung cancer, namely Adeno- carcinoma vs Squamous cell carcinoma. The data consists of approxima…
Flow cytometry is often used to characterize the malignant cells in leukemia and lymphoma patients, traced to the level of the individual cell. Typically, flow cytometric data analysis is performed through a series of 2-dimensional projections onto the axes of the data set. Through the years, clinicians have determined…
Detects changes in brain signal topology to predict epileptic seizures.
problem Anomaly detection in EEG signals for epilepsy.
method Extends signature theory to detect changes in topological structure of EEG signals.
result Detection of precursor phenomena to epileptic seizures.
Challenge aims to develop automated meningioma MRI segmentation models.
problem Lack of automated, objective tools for meningioma assessment.
method Develop and evaluate models on largest annotated dataset.
result Improved care of patients with meningioma through automated segmentation.
Analysis of histopathology slides is a critical step for many diagnoses, and in particular in oncology where it defines the gold standard. In the case of digital histopathological analysis, highly trained pathologists must review vast whole-slide-images of extreme digital resolution ( pixels) across multiple…
Machine Learning (ML) is proving extremely beneficial in many healthcare applications. In pediatric oncology, retrospective studies that investigate the relationship between treatment and late adverse effects still rely on simple heuristics. To assess the effects of radiation therapy, treatment plans are typically simu…
DeePathology: Deep Multi-Task Learning for Inferring Molecular Pathology from Cancer Transcriptomestat.ML
Despite great advances, molecular cancer pathology is often limited to the use of a small number of biomarkers rather than the whole transcriptome, partly due to computational challenges. Here, we introduce a novel architecture of Deep Neural Networks (DNNs) that is capable of simultaneous inference of various properti…
Shared Keyboard: An improved Bayesian design for phase I clinical trials via Beta kernel processstat.AP
Shared Keyboard design improves phase I clinical trials by borrowing information across doses.
problem Interim decisions based on current dose data may overlook signals from neighboring doses.
method Bayesian model-assisted design using Beta kernel process with kernel-weighted pseudo-counts.
result Significant improvements in identifying maximum tolerated dose and safety.
DECAT framework evaluates multimodal models for shared biology, detecting confounders and false positives.
problem Determining if multimodal models learn shared biology or just confounders.
method DECAT framework classifies multimodal representations into four diagnostic scenarios using null-referenced metrics.
result DECAT detects confounders and false positives in multimodal models, improving with larger cohorts and stronger representations.
MEC-Cox: A Machine-Learning-Assisted Generalized Entropy Calibration Method for Estimating ATT Marginal Hazard-Ratio
problem Estimating ATT marginal hazard-ratio in externally controlled survival trials
method Machine-learning-assisted generalized entropy calibration for IPW Cox regression
result Reduces bias, increases efficiency, and improves coverage
A key goal of computational personalized medicine is to systematically utilize genomic and other molecular features of samples to predict drug responses for a previously unseen sample. Such predictions are valuable for developing hypotheses for selecting therapies tailored for individual patients. This is especially va…
Paper presents a method for identifying isotope envelopes in MALDI-ToF data.
problem Deisotoping of isotopic peaks in MALDI-ToF molecular imaging data.
method Uses Mamdani-Assilan fuzzy system and spatial maps of molecular distribution to identify isotope envelopes.
result Proposed method detects overlapping envelopes and analyzes large data sets.
Low precision weights, activations, and gradients have been proposed as a way to improve the computational efficiency and memory footprint of deep neural networks. Recently, low precision networks have even shown to be more robust to adversarial attacks. However, typical implementations of low precision DNNs use unifor…
Mixed-precision CA-SGD for generalized linear models on GPUs
problem SGD communication bottleneck
method Mixed-precision CA-SGD
result Matches FP32 SGD loss within 0.5% on various problems
Paper explores low-precision SGLD for neural networks, reducing costs without sacrificing performance.
problem Infeasibility of low-precision sampling in large-scale scenarios.
method Developed low-precision SGLD with quantization function and full-precision gradient accumulators.
result Low-precision SGLD achieves comparable performance to full-precision SGLD with only 8 bits.
Proposes ConRad model for lung cancer classification using radiomics and interpretable machine learning.
problem Lack of interpretability in deep neural networks for cancer diagnosis.
method Integration of radiomics and DNN-predicted biomarkers in interpretable classifiers (ConRad).
result ConRad models outperform CNNs in five-fold cross-validation.
Post-training quantization method using multiple low-precision points achieves higher precision for critical weights.
problem Discretizing pre-trained deep neural networks without re-training.
method Multipoint quantization with efficient greedy selection and adaptive point number.
result Outperforms state-of-the-art methods on ImageNet classification and PASCAL VOC object detection.
Low precision operations can provide scalability, memory savings, portability, and energy efficiency. This paper proposes SWALP, an approach to low precision training that averages low-precision SGD iterates with a modified learning rate schedule. SWALP is easy to implement and can match the performance of full-precisi…
This paper improves low-precision sampling using SGHMC for deep learning models.
problem Enhancing training efficiency of deep neural networks with low-precision training.
method Investigates low-precision sampling via Stochastic Gradient Hamiltonian Monte Carlo (SGHMC) for both log-concave and non-log-concave distributions.
result Low-precision SGHMC achieves quadratic improvement in error compared to SGLD for non-log-concave distributions.
Low-precision computation is often used to lower the time and energy cost of machine learning, and recently hardware accelerators have been developed to support it. Still, it has been used primarily for inference - not training. Previous low-precision training algorithms suffered from a fundamental tradeoff: as the num…
Efficient Bitwidth Search optimizes neural network quantization for better performance.
problem Finding optimal bitwidth for weights and activations of each layer efficiently.
method EBS algorithm reusing meta weights and binary decomposition for efficient mixed precision convolution.
result Mixed precision QNN outperforms uniform bitwidth and other techniques on CIFAR10 and ImageNet.
Deep neural networks have enabled progress in a wide variety of applications. Growing the size of the neural network typically results in improved accuracy. As model sizes grow, the memory and compute requirements for training these models also increases. We introduce a technique to train deep neural networks using hal…
The study examines how class imbalance affects precision-recall curves.
problem Understanding how precision changes with class imbalance ratios.
method Analyzes the relationship between precision, class imbalance ratio, and true/false positive rates.
result Predicts changes in precision-recall curves and other measures with class imbalance ratios.
It is well-known that the precision of data, hyperparameters, and internal representations employed in learning systems directly impacts its energy, throughput, and latency. The precision requirements for the training algorithm are also important for systems that learn on-the-fly. Prior work has shown that the data and…
This paper introduces a new method to train normalizing flows using precision-recall divergences.
problem Training generative models with mode dropping and low-quality samples.
method Introduces PR-divergences and proposes a novel generative model to minimize precision-recall trade-offs.
result Normalizing flows can be trained to achieve specific precision-recall trade-offs using PR-divergences.
A framework estimates multiple precision matrices with shared structures.
problem Estimating multiple precision matrices with shared structures.
method Penalized likelihood framework with iterative algorithm alternating between convex and clustering problems.
result The method outperforms competitors and performs similarly to methods using prior information.
Efforts to reduce the numerical precision of computations in deep learning training have yielded systems that aggressively quantize weights and activations, yet employ wide high-precision accumulators for partial sums in inner-product operations to preserve the quality of convergence. The absence of any framework to an…
Paper explores reducing precision in SVM for faster text classification.
problem Efficiency in multi-class text classification training.
method Comparison of SVM trained with reduced precision (16-bit, half) vs original.
result Reduced precision training maintains text classification accuracy.