Foundation models alter medical data science workflow, challenging veridical data science principles.
problem Foundation models disrupt traditional data science practices in medicine.
method Critically examined the medical foundation model lifecycle and its deviation from veridical data science principles.
result Foundation models challenge veridical data science principles of predictability, computability, and stability.
This chapter introduces reproducibility in machine learning for medical imaging.
problem Lack of reproducibility in machine learning for medical imaging.
method Distinguishes and defines types of reproducibility, outlines requirements, and discusses utility.
result Discussion on benefits and a plea for a non-dogmatic approach to reproducibility.
Data science models, although successful in a number of commercial domains, have had limited applicability in scientific problems involving complex physical phenomena. Theory-guided data science (TGDS) is an emerging paradigm that aims to leverage the wealth of scientific knowledge for improving the effectiveness of da…
Survey on understanding neural networks for medical applications.
problem Black-box nature of deep neural networks hinders their use in critical applications.
method Comprehensive review of interpretability studies in neural networks.
result Interpretability research is crucial for the acceptance of neural networks in medical diagnosis.
This guide explains statistical distances for evaluating generative models.
problem Evaluating the quality of samples from generative models.
method Four statistical distances: SW, C2ST, MMD, FID.
result Different distances can yield varying results on similar data.
CAggNet improves medical image segmentation by fusing coarse and fine features.
problem Medical image segmentation accuracy and efficiency.
method Crossing Aggregation Network with nested skip connections and weighted aggregation.
result CAggNet achieves more accurate and efficient segmentation compared to existing methods.
The paper investigates deep neural networks for medical imaging applications, providing interpretable results.
problem Uninterpretable decisions made by deep neural networks in medical imaging applications.
method Investigation of deep neural networks for malaria, diabetic retinopathy, brain tumor, and tuberculosis detection in various imaging modalities. Visualization of class activation mappings provided.
result Visualization of class activation mappings enhances understanding of deep neural networks and aids doctors in decision-making.
Teaches reproducible research to medical students and postgrads.
problem Lack of reproducibility in medical research practices.
method Designed and delivered a lecture series on reproducible research.
result Encountered practical obstacles in reproducing a published analysis.
3D dataset for intracranial aneurysms aids deep learning applications.
problem Lack of 3D medical datasets for deep learning.
method Developed an open-access 3D dataset, IntrA, for intracranial aneurysms.
result Demonstrated the challenges and performance of 3D medical datasets.
Sparse learning has been shown to be effective in solving many real-world problems. Finding sparse representations is a fundamentally important topic in many fields of science including signal processing, computer vision, genome study and medical imaging. One important issue in applying sparse representation is to find…
Review of clustering methods for functional data across various fields.
problem Identify heterogeneous morphological patterns in continuous functions.
method Comprehensive review and systematic taxonomy of existing methods.
result Proposes a new taxonomy linking functional data clustering to conventional multivariate methods.
TorchIO simplifies medical image processing for deep learning.
problem Challenges in processing medical images like MRI and CT.
method Efficient loading, preprocessing, augmentation, and patch-based sampling.
result Enables researchers to focus on deep learning experiments.
Novel method converts time series data into functional data for high dimensional classification.
problem Small sample size problem in high dimensional time series data.
method Classwise Functional Principal Component Analysis (PCA) followed by Bayesian linear classifier.
result Demonstrated efficacy on synthetic and real data sets.
Bandit algorithms optimize treatment decisions for precision medicine.
problem Optimizing treatment decisions for individual patients based on genetic or molecular profiling.
method Contextual bandit algorithms that consider patient characteristics.
result Bandit algorithms are useful for mobile health and digital phenotyping.
Matrices of (approximate) low rank are pervasive in data science, appearing in recommender systems, movie preferences, topic models, medical records, and genomics. While there is a vast literature on how to exploit low rank structure in these datasets, there is less attention on explaining why the low rank structure ap…
Widely-used public benchmarks are of huge importance to computer vision and machine learning research, especially with the computational resources required to reproduce state of the art results quickly becoming untenable. In medical image computing, the wide variety of image modalities and problem formulations yields a…
At this moment, databanks worldwide contain brain images of previously unimaginable numbers. Combined with developments in data science, these massive data provide the potential to better understand the genetic underpinnings of brain diseases. However, different datasets, which are stored at different institutions, can…
Bayesian inference corrects bias in supervised learning datasets.
problem Correcting bias in supervised machine learning datasets.
method Bayesian inference framework to adjust posterior distribution.
result Improved model fitting to original dataset.
This paper investigates robust and efficient DR/RDR estimators for WATEs.
problem Lack of systematic investigation into robustness and efficiency conditions for WATE estimation.
method Proposes three RDR estimators using semiparametric efficient influence function and double/debiased machine learning.
result Demonstrates the practical relevance of the methods in medical and social sciences.
Automated system extracts medication regimens from medical conversations.
problem Extract relevant medication information from medical conversations.
method QA task approach, combined QA and Information Extraction, data augmentation, public embeddings, pretraining.
result Improved accuracy in extracting dosage and frequency from 54.28 and 37.13 to 89.57 and 45.94.
Privacy-preserving deep learning for medical data across distributed platforms.
problem Data leakage in medical platforms.
method Separates hidden layers; first layer local, others centralized for training.
result Improved learning performance with all data used during training.
PHOTONAI simplifies machine learning model development in Python.
problem Rapid and efficient machine learning model development.
method Unified framework combining algorithms from different toolboxes, automating repetitive tasks.
result Achieves state-of-the-art solution in medical machine learning.
Representation learning (RL) plays an important role in extracting proper representations from complex medical data for various analyzing tasks, such as patient grouping, clinical endpoint prediction and medication recommendation. Medical data can be divided into two typical categories, outpatient and inpatient, that h…
Data science teams collaborate extensively, using various tools and stakeholders.
problem Lack of understanding in how data science workers collaborate in practice.
method Conducted an online survey with 183 data science workers.
result Data science teams are highly collaborative and use multiple tools and stakeholders.
Paper proposes a new method to handle missing data in medical records using sequential variational autoencoders.
problem Missing data in medical records due to sensor off-times and uneven data collection.
method Sequential variational autoencoders (VAEs) with a new methodology called Shi-VAE.
result Shi-VAE achieves the best performance in terms of both metrics compared to state-of-the-art methods.
Improves medication name inference for telemedicine and conversational agents.
problem Challenges in mapping user-friendly medication names to standardized ones.
method Entity-boosted two-tower neural network for ranking SMN to DMP.
result State-of-the-art results achieved with improved attention-based ranking.
Causal inference from observational data is the goal of many data analyses in the health and social sciences. However, academic statistics has often frowned upon data analyses with a causal objective. The introduction of the term "data science" provides a historic opportunity to redefine data analysis in such a way tha…
IDA adapts to non-iid data in federated learning for medical imaging.
problem Statistical heterogeneity in federated learning data, especially in medical imaging.
method IDA (Inverse Distance Aggregation) is a novel adaptive weighting approach for clients based on meta-information.
result IDA outperforms Federated Averaging in handling unbalanced and non-iid data in federated learning.
The treatment effects of medications play a key role in guiding medical prescriptions. They are usually assessed with randomized controlled trials (RCTs), which are expensive. Recently, large-scale electronic health records (EHRs) have become available, opening up new opportunities for more cost-effective assessments. …
Data Science is currently a popular field of science attracting expertise from very diverse backgrounds. Current learning practices need to acknowledge this and adapt to it. This paper summarises some experiences relating to such learning approaches from teaching a postgraduate Data Science module, and draws some learn…
Automatic representation learning of key entities in electronic health record (EHR) data is a critical step for healthcare informatics that turns heterogeneous medical records into structured and actionable information. Here we propose ME2Vec, an algorithmic framework for learning low-dimensional vectors of the most co…
This study applies neural models to automatically recognize medical entities from natural language.
problem Automated recognition of medical entities from natural language is complex and time-consuming.
method Utilizes deep neural sequence models trained on a large dataset of death certificates.
result Deep neural models can efficiently recognize medical entities from natural language.
Proposes a new method for medical diagnosis using network-based representation learning.
problem Improving medical diagnosis accuracy through better data representation.
method Heterogeneous network-based model and modified metapath2vec algorithm for learning latent node representations.
result Significant performance boost in symptom/disease classification and disease prediction tasks.
Enhances medical code predictions for multi-morbidity patients using text classification.
problem Improving accuracy in predicting medical codes for patients with multiple illnesses.
method Used machine learning techniques, including multi-label medical text classification, to enhance predictions.
result High dimensional embeddings pre-trained on health data significantly improve multi-label classification performance.
Defines data science as a natural ecosystem with challenges and missions.
problem Challenges and missions in data science due to 5D complexities and data life cycle phases.
method Systemic and data-centric view of data science as a fusion of data universe and its challenges, formalizing a general-purpose architecture.
result Essential data science as a natural ecosystem integrating specific disciplines and high-impact applications.
Machine learning constructs problem-based medical records from electronic health records.
problem Difficulty in finding relevant medical information for clinical questions.
method Knowledge base completion using machine learning on electronic health records.
result Automatic construction of problem-based groupings of medications, procedures, and lab tests.
Hierarchical-CPI improves variable importance measurement for medical data.
problem Limited interpretability of complex medical models.
method Hierarchical-CPI measures conditional variable importance with statistical control, handling correlated data.
result Hierarchical-CPI outperforms existing methods in medical datasets.
This paper reviews deep learning methods for handling irregularly sampled medical time series data.
problem Handling irregularly sampled medical time series data for personalized treatment and precise diagnosis.
method Summarizes and compares deep learning methods categorized by technology and task.
result Achieved good results in data imputation and downstream tasks.
This paper addresses privacy in federated learning for medical imaging by estimating model uncertainty.
problem Privacy concerns in federated learning for medical imaging.
method Federated Learning (FL) for collaborative model training while preserving patient data privacy.
result Accurate uncertainty estimation in federated learning for medical imaging.
RL algorithms with medical integration improve personalized treatment recommendations.
problem Developing effective personalized treatment strategies for chronic diseases.
method Integrating medical knowledge into RL algorithms for DTR.
result Enhanced treatment recommendations with increased confidence.
New research finds uncertainty estimation techniques fail to reliably detect abnormal medical cases.
problem Uncertainty estimation does not reliably detect out-of-distribution patients in medical tabular data.
method A series of tests on various uncertainty estimation techniques on real-world medical data.
result Almost all techniques fail to identify out-of-distribution patients, contradicting earlier findings.
ML methods improve planetary science data analysis.
problem Insufficient use of ML in planetary science.
method Ten recommendations for integrating ML in planetary science.
result Expanding planetary science insights from large datasets.
With the expeditious advancement of information technologies, health-related data presented unprecedented potentials for medical and health discoveries but at the same time significant challenges for machine learning techniques both in terms of size and complexity. Those challenges include: the structured data with var…
Generative Adversarial Networks (GANs) and their extensions have carved open many exciting ways to tackle well known and challenging medical image analysis problems such as medical image de-noising, reconstruction, segmentation, data simulation, detection or classification. Furthermore, their ability to synthesize imag…
Data science enhances knot theory by analyzing invariant relations.
problem Understanding the complex relations between knot invariants.
method Topological data analysis applied to knot theory.
result New insights into long-standing conjectures about knots.
Deep learning algorithms produces state-of-the-art results for different machine learning and computer vision tasks. To perform well on a given task, these algorithms require large dataset for training. However, deep learning algorithms lack generalization and suffer from over-fitting whenever trained on small dataset,…
The paper uses geometric methods to classify medical data histograms.
problem Classifying medical data histograms for disease diagnosis.
method Information geometry of beta distributions for comparing and classifying histograms.
result Geometric tools, particularly negatively curved Fisher information, enable unique mean calculation and K-means classification.
Framework harmonizes EHR data across institutions for better analysis.
problem Heterogeneity of medical codes and terminologies hinder EHR data analysis.
method MASH (Multi-source Automated Structured Hierarchy) uses neural optimal transport and learned hyperbolic embeddings to align and structure EHR data.
result MASH generates interpretable hierarchical graphs for unstructured local laboratory codes.