Study examines biases in clinical word embeddings, revealing performance gaps across groups.
problem Biases in clinical word embeddings leading to performance differences across groups.
method Pretrained BERT models on MIMIC-III, fill-in-the-blank method, fairness evaluation on clinical tasks.
result Classifiers trained from BERT representations exhibit statistically significant differences in performance across groups.
Improved language model for French clinical reports achieves state-of-the-art performance in medical NLP tasks.
problem Lack of specialized language models for French clinical reports.
method Adapted a general pre-trained language model (CamemBERT) to French clinical reports using a corpus of 21M reports.
result Pretrained and fine-tuned models improved F1-score by 3 percentage points on APMed task.
Information in electronic health records (EHR), such as clinical narratives, examination reports, lab measurements, demographics, and other patient encounter entries, can be transformed into appropriate data representations that can be used for downstream clinical machine learning tasks using representation learning. L…
Improved AI lung ultrasound segmentation using expert confidence values.
problem Label uncertainty in lung ultrasound due to subjective interpretation by radiologists.
method Designing a data annotation protocol capturing expert confidence, training AI on binarized labels with confidence thresholds.
result Improved AI segmentation and better clinical outcomes (e.g., S/F oxygenation ratio estimation, patient readmission prediction).
Study improves healthcare time series imputation by considering structured missingness.
problem Structured missingness in clinical data impacts time series imputation models.
method Analysis of different masking strategies on imputation methods using PhysioNet Challenge 2012 dataset.
result Masking choices significantly affect imputation accuracy and clinical prediction.
Bayesian approach for handling incomplete clinical data.
problem Challenges in machine learning with multimodal, incomplete clinical data.
method Generative and discriminative learning, semi-supervised strategy, imputation of missing views.
result Automatic imputation of missing views and robust inference across different data sources.
Self-supervised learning improves ECG classification performance.
problem Label scarcity in clinical 12-lead ECG data.
method Adapted self-supervised methods to ECG domain, focusing on contrastive representations and latent forecasting.
result Contrastive predictive coding adaptation yields linear evaluation performance only 0.5% below supervised performance.
Electronic Health Records (EHRs) have been heavily used to predict various downstream clinical tasks such as readmission or mortality. One of the modalities in EHRs, clinical notes, has not been fully explored for these tasks due to its unstructured and inexplicable nature. Although recent advances in deep learning (DL…
Effective modeling of electronic health records presents many challenges as they contain large amounts of irregularity most of which are due to the varying procedures and diagnosis a patient may have. Despite the recent progress in machine learning, unsupervised learning remains largely at open, especially in the healt…
A new metric FRD improves comparing medical images.
problem Comparing medical images for distribution or domain differences.
method Developed a new metric FRD using standardized radiomic features.
result FRD outperforms other metrics in various medical imaging applications.
CASCADE improves uncertainty communication in Parkinson's disease medication management.
problem Uncertainty in clinical decision-making for Parkinson's disease patients.
method CASCADE uses a novel conformal prediction framework to adaptively scale prediction intervals based on classification uncertainty.
result CASCADE produces more efficient and robust prediction intervals for Parkinson's disease patients.
A benchmark evaluates ioUS-to-MR synthesis methods for brain tumor surgery.
problem Difficult interpretation of ioUS images for brain tumor surgery.
method Six generators trained under four inference regimes and two targets on public data.
result SynDiff-2.5D best preserved downstream segmentation (U_Dice=0.55).
PanRep learns universal node embeddings for heterogeneous graphs.
problem Learning universal node embeddings for heterogeneous graphs.
method Graph Neural Network (GNN) model with four decoders capturing different properties.
result PanRep outperforms unsupervised and supervised methods in node classification and link prediction.
Over half a million individuals are diagnosed with head and neck cancer each year worldwide. Radiotherapy is an important curative treatment for this disease, but it requires manual time consuming delineation of radio-sensitive organs at risk (OARs). This planning process can delay treatment, while also introducing int…
Stein-Encoder isolates genetic signals in multi-modal biomedical data.
problem Integration of high-dimensional genomic data with clinical data obscures genetic predictive impact.
method White-box supervised framework using Stein's method and residualization.
result Stein-Encoder improves predictive accuracy and reveals specific biological mechanisms.
Self-supervised metric learning boosts downstream tasks in multi-view data.
problem Improving distance-based downstream tasks without labeled data.
method Developed a statistical framework to study self-supervised metric learning in multi-view data.
result Self-supervised metric learning improves target distances for various downstream tasks.
Paper defines and solves a problem in representation learning to ensure fairness with high confidence.
problem Learning fair representations with high confidence guarantees for all downstream tasks.
method Formally defines the problem, introduces FRG framework, proves high probability fairness, and demonstrates effectiveness empirically.
result FRG framework provides high-confidence guarantees for limiting unfairness across all downstream models and tasks.
Study shows how pretraining robustness transfers to downstream tasks.
problem Understanding how robustness is transferred from pretraining to downstream tasks.
method Theoretical analysis and practical validation of robustness constraints.
result Robustness of a linear predictor on downstream tasks can be constrained by the robustness of its underlying representation.
Analysis of pretrained models' effectiveness in downstream tasks.
problem Understanding why pretrained models perform well in NLP tasks.
method Analyzed head and prompt tuning approaches using latent variable models.
result Prompt tuning provides stronger guarantees than head tuning.
This paper characterizes VAE training pathologies and their effects on tasks.
problem Characterizing VAE training pathologies and their impact on downstream tasks.
method Concretely characterizing conditions for VAE training pathologies and their connection to specific downstream tasks.
result Connects VAE training pathologies to specific downstream tasks like learning compressed and disentangled representations, adversarial robustness, and semi-supervised learning.
Study shows scaling up models doesn't always improve downstream tasks.
problem Understanding why scaling up models doesn't always improve downstream performance.
method Systematic study of 4800 experiments on various models, analyzing performance on 20 downstream tasks.
result Performance on downstream tasks saturates as model size increases, revealing a nonlinear relationship.
UBM transfers bias mitigation from upstream to downstream tasks efficiently.
problem Bias in fine-tuned language models across various tasks.
method Apply bias mitigation to an upstream model, then fine-tune a downstream model on this mitigated model.
result UBM effects transfer to new downstream tasks, creating less biased models.
This study examines how the size and alignment of pretraining data affect the performance of large language models on downstream tasks.
problem Understanding how the size and alignment of pretraining data impact the performance of large language models on downstream tasks.
method Investigated the scaling behavior of large language models in a transfer learning setting, focusing on machine translation tasks.
result The size of the finetuning dataset and the distribution alignment between pretraining and downstream data significantly influence the scaling behavior of downstream performance.
Machine learning is bringing a paradigm shift to healthcare by changing the process of disease diagnosis and prognosis in clinics and hospitals. This development equips doctors and medical staff with tools to evaluate their hypotheses and hence make more precise decisions. Although most current research in the literatu…
Theoretical analysis shows pretext-based self-supervised learning can be boosted by downstream data under certain conditions.
problem Theoretical analysis of pretext-based self-supervised learning and downstream data refinement.
method Theoretical analysis and experiments on synthetic and real-world datasets.
result Theoretical lower bounds and experiments show that downstream data refinement can boost or hurt performance depending on conditions.
Extracting information from electronic health records (EHR) is a challenging task since it requires prior knowledge of the reports and some natural language processing algorithm (NLP). With the growing number of EHR implementations, such knowledge is increasingly challenging to obtain in an efficient manner. We address…
Enhances performance on downstream tasks using multi-domain data.
problem Improving performance on tasks with limited downstream data.
method Deep transfer learning framework leveraging shared and domain-specific features.
result Significantly improves convergence rate for learning Lipschitz functions.
Mask-reconstruction pretraining helps in downstream tasks by capturing more semantic features.
problem How mask-reconstruction pretraining helps in downstream tasks and why it surpasses supervised learning.
method Theoretical analysis and experimental validation of mask-reconstruction pretraining (MRP) on auto-encoders.
result MRP provably captures more semantic features than supervised learning, leading to better performance in downstream tasks.
New model captures patient-level EHR data efficiently.
problem Irregular EHR code timing and lack of temporal structure.
method Latent factor point process model with Fourier-Eigen embedding.
result Efficiently captures subgroup-specific temporal patterns.
Language models help text classification tasks by predicting next words.
problem Lack of theoretical understanding of why language models perform well on downstream tasks.
method Mathematical study of the connection between next word prediction and text classification, formalizing it and quantifying the benefit.
result Language models that are ε-optimal in cross-entropy learn features that can solve classification tasks with linear approximation.
This work optimizes alignment and uniformity of features on a hypersphere for better downstream performance.
problem Improving the performance of contrastive representation learning.
method Identifying and optimizing alignment and uniformity of features on a hypersphere.
result Directly optimizing alignment and uniformity leads to comparable or better performance than contrastive learning.
New framework explains how larger pre-trained models reduce downstream learning sample complexity.
problem Understanding why larger pre-trained models reduce sample complexity in downstream tasks.
method Introducing a novel framework called Caulking inspired by PEFT methods.
result Improved pre-trained models provably decrease downstream task sample complexity.
This paper reports on Qwant Research contribution to tasks 2 and 3 of the DEFT 2019's challenge, focusing on French clinical cases analysis. Task 2 is a task on semantic similarity between clinical cases and discussions. For this task, we propose an approach based on language models and evaluate the impact on the resul…
Evaluating the clinical similarities between pairwise patients is a fundamental problem in healthcare informatics. A proper patient similarity measure enables various downstream applications, such as cohort study and treatment comparative effectiveness research. One major carrier for conducting patient similarity resea…
BrainCast predicts whole-brain fMRI time series from short scans.
problem Short scans reduce fMRI data quality and statistical power.
method Spatio-temporal forecasting framework for fMRI time series.
result BrainCast improves fMRI time series quality and prediction.
This work proposes a new pre-processing method for supervised learning to improve fairness without sacrificing utility.
problem Improving fairness in supervised learning without compromising model performance.
method Task-tailored pre-processing approach that balances fairness and utility.
result The proposed method preserves consistent trade-offs among multiple downstream models and improves fairness in computer vision tasks.
Framework fine-tunes foundation models with semi-supervised learning for downstream tasks and latent spaces.
problem Training foundation models with limited labelled data.
method Mutual information decomposition for downstream and latent spaces, semi-supervised fine-tuning.
result Significant improvements in classification tasks under low-labelled conditions.
Drug similarity has been studied to support downstream clinical tasks such as inferring novel properties of drugs (e.g. side effects, indications, interactions) from known properties. The growing availability of new types of drug features brings the opportunity of learning a more comprehensive and accurate drug similar…
Proposes a new metric to quantify the difference between neural network representations based on downstream task performance.
problem The lack of a consistent metric to measure the difference between neural network representations.
method Introduced the Transferred Discrepancy (TD) metric, which evaluates the difference between representations based on their performance on downstream tasks.
result TD provides fine-grained information for various downstream tasks and can evaluate the effectiveness of different training strategies.
TaskMet learns a metric to improve model performance on unseen tasks.
problem Deep models trained on one task may struggle on another task due to conflicting objectives.
method TaskMet learns a metric in the prediction space to balance task and prediction losses.
result TaskMet achieves better performance on downstream tasks without altering the prediction model.
Optimal Word2Vec hyper-parameters improve NLP tasks.
problem Finding the best Word2Vec hyper-parameters for NLP tasks.
method Empirical evaluation of various hyper-parameter combinations on NLP tasks.
result The best hyper-parameters vary by task, and high analogy scores don't always correlate with performance.
In this chapter, we provide a brief overview of applying machine learning techniques for clinical prediction tasks. We begin with a quick introduction to the concepts of machine learning and outline some of the most common machine learning algorithms. Next, we demonstrate how to apply the algorithms with appropriate to…
Proposes a novel imputation network for clinical time series data.
problem Missing value imputation in clinical time series data with sparsity, irregularity, and high-dimensionality.
method Variational-recurrent imputation network that considers correlated features, temporal dynamics, and uncertainty.
result The proposed method outperformed state-of-the-art methods on real-world EHR datasets.
New framework analyzes why more negative samples improve self-supervised learning performance.
problem Inconsistency between theoretical degradation and empirical improvement of downstream supervised tasks with more negative samples.
method Coupon collector's problem framework to analyze self-supervised representation learning with more negative samples.
result Bound can implicitly incorporate supervised loss in self-supervised loss by increasing negative samples.
Action-BED: Task-Driven Bayesian Experimental Design
problem Bayesian experimental design with doubly intractable objectives
method Formulating BED in terms of expected future loss (EFL) and optimising it with stochastic gradients
result Simplified and task-driven framework for BED
Minimal variations guide unsupervised learning for better downstream tasks.
problem Efficiently describing raw data for various future tasks.
method Minimal variations as a guiding principle for unsupervised representation learning.
result Unveiling minimal variations as a principle behind unsupervised learning.
Self-supervised learning improves few-shot classification and segmentation on point clouds.
problem Efficiently learn from limited labeled data in point cloud applications.
method Hierarchical cover-tree partitioning for self-supervised pre-training; restricted to support set for few-shot learning.
result Self-supervised learning significantly improves downstream classification and segmentation accuracy.
SFM generates smooth functional data without exposing real data.
problem Challenges in statistical analysis of functional data.
method Copula framework and smooth flow construction.
result SFM produces high-quality synthetic functional data.