README
Optum Relevant Papers:
A list of papers that is related to the Patient Like Me Project
- A study into patient similarity through representation learning from medical records
- Automated Cardiovascular Record Retrieval by Multimodal Learning between Electrocardiogram and Clinical Report
- Problems and challenges in patient information retrieval: a descriptive study.
- Is Cosine-Similarity of Embeddings Really About Similarity?
- ReMatch: Retrieval Enhanced Schema Matching with LLMs
- karpathy knn vs svm for similarity search
- Re-evaluating Word Mover’s Distance
- METEOR: An Automatic Metric for MT Evaluation with Improved Correlation with Human Judgments
- Predicting the Progression of Chronic Kidney Disease: A Systematic Review of Artificial Intelligence and Machine Learning Approaches
- Matching patients to clinical trials with large language models
- Time Series Classification using Dynamic Time Warping K-Nearest Neighbours
- IEEE: Time Series Classification using Dynamic Time Warping K-Nearest Neighbours
A list of papers that is related to disease onset using Language Model technolgoies
Optum Relevant Tutorials
Diffusion Papers
- Simplified and Generalized Masked Diffusion for Discrete Data
- Large Language Models are Powerful EHR Encoders
Causal Inference Papers
- TABPFN: A TRANSFORMER THAT SOLVES SMALL TABULAR CLASSIFICATION PROBLEMS IN A SECOND
- TRANSFORMERS CAN DO BAYESIAN INFERENCE
- LC-PFN: Efficient Bayesian Learning Curve Extrapolation using Prior-Data Fitted Networks
- TabPFN Blog
- Learning Latent Structural Causal Models
- ForecastPFN: Synthetically-Trained Zero-Shot Forecasting
- Uncertainty-Aware Dynamic Fusion for Multimodal Clinical Prediction Tasks
EHR related Paper
- Value of the Electronic Medical Record for Hospital Care: Update From the Literature
- Revisiting the MIMIC-IV Benchmark: Experiments Using Language Models for Electronic Health Records
- Health-LLM: Large Language Models for Health Prediction via Wearable Sensor Data
- Generalization—a key challenge for responsible AI in patient-facing clinical applications
- Disorder-Free Data Are All You Need — Inverse Supervised Learning for Broad-Spectrum Head Disorder Detection
- EHRAgent: Code Empowers Large Language Models for Few-shot Complex Tabular Reasoning on Electronic Health Records
- Evaluation and mitigation of the limitations of large language models in clinical decision-making
- Matching Patients to Clinical Trials using LLaMA 2 Embeddings and Siamese Neural Network
- A multi-center study on the adaptability of a shared foundation model for electronic health records
- Clinical-Longformer and Clinical-BigBird: Transformers for long clinical sequences
- MDS-ED: Multimodal Decision Support in the Emergency Department -- a Benchmark Dataset for Diagnoses and Deterioration Prediction in Emergency Medicine
- Segment Anything in Medical Images and Videos: Benchmark and Deployment
- GRAPH TRANSFORMERS ON EHRS: BETTER REPRESENTATION IMPROVES DOWNSTREAM PERFORMANCE
- Medical Graph RAG: Towards Safe Medical Large Language Model via Graph Retrieval-Augmented Generation
- A generalist vision–language foundation model for diverse biomedical tasks
- Harnessing the power of longitudinal medical imaging for eye disease prognosis using Transformer-based sequence modeling
- EHRFlow: A Large Language Model-Driven Iterative Multi-Agent Electronic Health Record Data Analysis Workflow
- An open-source framework for end-to-end analysis of electronic health record data
- General-Purpose Retrieval-Enhanced Medical Prediction Model Using Near-Infinite History
- Zero shot health trajectory prediction using transformer
- Unified Clinical Vocabulary Embeddings for Advancing Precision Medicine
- An evaluation framework for clinical useof large language models in patientinteraction tasks
- Development and Validation of a Machine Learning Algorithm to Classify Lower Urinary Tract Symptoms
- Data from the All of Us research program reinforces existence of activity inequality
- Med-Real2Sim: Non-Invasive Medical Digital Twins using Physics-Informed Self-Supervised Learning
- Context Clues: Evaluating Long Context Models for Clinical Prediction Tasks on EHR Data
- Asclepius-R : Clinical Large Language Model Built On MIMIC-III Discharge Summaries
- KIT-LSTM: Knowledge-guided Time-aware LSTM for Continuous Clinical Risk Prediction
- Predicting sex from retinal fundus photographs using automated deep learning
- Future-Guided Pretraining via Time-to-Event Supervision for 3D Medical Imaging
- Uncertainty Quantification for Clinical Outcome Predictions with (Large) Language Models
- Hospitalization prediction from the emergency department using computer vision AI with short patient video clips
- MedRAX: Medical Reasoning Agent for Chest X-ray
- 3D Foundation AI Model for Generalizable Disease Detection in Head Computed Tomography
- Multimodal Medical Code Tokenizer
- Large language models are less effective at clinical prediction tasks than locally trained machine learning models
- TIMER: Temporal Instruction Modeling and Evaluation for Longitudinal Clinical Records
- Frequent but fragmented: use of note templates to document outpatient visits at an academic health center
- Standardization of Emergency Department Clinical Note Templates: A Retrospective Analysis across an Integrated Health System
- Exploring Scaling Laws for EHR Foundation Models
- A multimodal vision foundation model for clinical dermatology
- Foundation Models for Clinical Records at Health System Scale
- Foundation models for electronic health records: representation dynamics and transferability
Other Misc./Methods Papers/Deep Learning Papers
A list of papers I am reading.
- Scaling Laws for Downstream Task Performance of Large Language Models
- ImageBind: One Embedding Space To Bind Them All
- AnyMAL: An Efficient and Scalable Any-Modality Augmented Language Model
- Transformers Can Do Arithmetic with the Right Embeddings
- LLM2Vec: Large Language Models Are Secretly Powerful Text Encoders
- LoRA: Low-Rank Adaptation of Large Language Models
- RAFT: Adapting Language Model to Domain Specific RAG
- A Closer Look at AUROC and AUPRC under Class Imbalance
- The Era of 1-bit LLMs: All Large Language Models are in 1.58 Bits
- All-in-one simulation-based inference
- No New Net
- tree of thought
- Q-Sparse: All Large Language Models can be Fully Sparsely-Activated
- Reuse, Don't Retrain: A Recipe for Continued Pretraining of Language Models
- FasterViT: Fast Vision Transformers with Hierarchical Attention
- Few-shot Adaptation to Distribution Shifts By Mixing Source and Target Embeddings
- SparseCL: Sparse Contrastive Learning for Contradiction Retrieval
- Cell2Sentence: Teaching Large Language Models the Language of Biology
- Concept BottleNeck Models
- The AI Scientist: Towards Fully Automated Open-Ended Scientific Discovery
- How Well Can Vision Language Models See Image Details?
- The Data Addition Dilemma
- Bayesian Learning via Stochastic Gradient Langevin Dynamics
- HeAR- Health Acoustic Representations
- Uncertainty Quantification with Pre-trained Language Models: A Large-Scale Empirical Analysis
- Improving model calibration with accuracy versus uncertainty optimization
- Larger and more instructable language models become less reliable
- Why did the Model Fail?": Attributing Model Performance Changes to Distribution Shifts
- DISCOVERYWORLD: A Virtual Environment for Developing and Evaluating Automated Scientific Discovery Agents
- A Comprehensive Survey on Graph Neural Networks
- A Probabilistic Inference Approach to Inference-Time Scaling of LLMs using Particle-Based Monte Carlo Methods
- One Model to learn them all
- Toward a Theory of Tokenization in LLMs
- A Brief Review of Deep Multi-task Learning and Auxiliary Task Learning
- Generating Realistic Tabular Data with Large Language Models
- Foundation Models in Electrocardiogram: A Review
- The Super Weight in Large Language Models
- BERTs are Generative In-Context Learners
- The Virtual Lab: AI Agents Design New SARS-CoV-2 Nanobodies with Experimental Validation
- Large Language Model Influence on Diagnostic Reasoning A Randomized Clinical Trial
- Finding "Good Views" of Electrocardiogram Signals for Inferring Abnormalities in Cardiac Condition
- Superhuman performance of a large language model on the reasoning tasks of a physician
- Transformer2: Self-adaptive LLMs
- Accurate predictions on small data with a tabular foundation model
- Hallucinations Can Improve Large Language Models in Drug Discovery
- DeepSeek-R1: Incentivizing Reasoning Capability in LLMs via Reinforcement Learning
- SFT Memorizes, RL Generalizes: A Comparative Study of Foundation Model Post-training
- The Pitfalls of Memorization: When Memorization Hurts Generalization
- Leveraging Domain Knowledge for Efficient Reward Modeling in RLHF: A Case-Study in E-Commerce Opinion Summarization
- DogeRM: Equipping Reward Models with Domain Knowledge through Model Merging
- A Comparison of Multi-task learning and Single-task learning Approaches
- Quantifying Uncertainty in Answers from any Language Model and Enhancing their Trustworthiness
- Deep Learning is Not So Mysterious or Different
- A Comprehensive Benchmark of Machine and Deep Learning Across Diverse Tabular Datasets
- FoNE: Precise Single-Token Number Embeddings via Fourier Features
- NoProp: Training Neural Networks without Back-propagation or Forward-propagation
- When Bad Data Leads to Good Models
- Convergent Learning: Do different neural networks learn the same representations?
- Harnessing the Universal Geometry of Embeddings
- When accurate prediction models yield harmful self-fulfilling prophecies
- CellVoyager: AI CompBio Agent Generates New Insights by Autonomously Analyzing Biological Data
Contributors
Simonlee711
123 commits
Similar repos
README
Optum Relevant Papers:
A list of papers that is related to the Patient Like Me Project
- A study into patient similarity through representation learning from medical records
- Automated Cardiovascular Record Retrieval by Multimodal Learning between Electrocardiogram and Clinical Report
- Problems and challenges in patient information retrieval: a descriptive study.
- Is Cosine-Similarity of Embeddings Really About Similarity?
- ReMatch: Retrieval Enhanced Schema Matching with LLMs
- karpathy knn vs svm for similarity search
- Re-evaluating Word Mover’s Distance
- METEOR: An Automatic Metric for MT Evaluation with Improved Correlation with Human Judgments
- Predicting the Progression of Chronic Kidney Disease: A Systematic Review of Artificial Intelligence and Machine Learning Approaches
- Matching patients to clinical trials with large language models
- Time Series Classification using Dynamic Time Warping K-Nearest Neighbours
- IEEE: Time Series Classification using Dynamic Time Warping K-Nearest Neighbours
A list of papers that is related to disease onset using Language Model technolgoies
Optum Relevant Tutorials
Diffusion Papers
- Simplified and Generalized Masked Diffusion for Discrete Data
- Large Language Models are Powerful EHR Encoders
Causal Inference Papers
- TABPFN: A TRANSFORMER THAT SOLVES SMALL TABULAR CLASSIFICATION PROBLEMS IN A SECOND
- TRANSFORMERS CAN DO BAYESIAN INFERENCE
- LC-PFN: Efficient Bayesian Learning Curve Extrapolation using Prior-Data Fitted Networks
- TabPFN Blog
- Learning Latent Structural Causal Models
- ForecastPFN: Synthetically-Trained Zero-Shot Forecasting
- Uncertainty-Aware Dynamic Fusion for Multimodal Clinical Prediction Tasks
EHR related Paper
- Value of the Electronic Medical Record for Hospital Care: Update From the Literature
- Revisiting the MIMIC-IV Benchmark: Experiments Using Language Models for Electronic Health Records
- Health-LLM: Large Language Models for Health Prediction via Wearable Sensor Data
- Generalization—a key challenge for responsible AI in patient-facing clinical applications
- Disorder-Free Data Are All You Need — Inverse Supervised Learning for Broad-Spectrum Head Disorder Detection
- EHRAgent: Code Empowers Large Language Models for Few-shot Complex Tabular Reasoning on Electronic Health Records
- Evaluation and mitigation of the limitations of large language models in clinical decision-making
- Matching Patients to Clinical Trials using LLaMA 2 Embeddings and Siamese Neural Network
- A multi-center study on the adaptability of a shared foundation model for electronic health records
- Clinical-Longformer and Clinical-BigBird: Transformers for long clinical sequences
- MDS-ED: Multimodal Decision Support in the Emergency Department -- a Benchmark Dataset for Diagnoses and Deterioration Prediction in Emergency Medicine
- Segment Anything in Medical Images and Videos: Benchmark and Deployment
- GRAPH TRANSFORMERS ON EHRS: BETTER REPRESENTATION IMPROVES DOWNSTREAM PERFORMANCE
- Medical Graph RAG: Towards Safe Medical Large Language Model via Graph Retrieval-Augmented Generation
- A generalist vision–language foundation model for diverse biomedical tasks
- Harnessing the power of longitudinal medical imaging for eye disease prognosis using Transformer-based sequence modeling
- EHRFlow: A Large Language Model-Driven Iterative Multi-Agent Electronic Health Record Data Analysis Workflow
- An open-source framework for end-to-end analysis of electronic health record data
- General-Purpose Retrieval-Enhanced Medical Prediction Model Using Near-Infinite History
- Zero shot health trajectory prediction using transformer
- Unified Clinical Vocabulary Embeddings for Advancing Precision Medicine
- An evaluation framework for clinical useof large language models in patientinteraction tasks
- Development and Validation of a Machine Learning Algorithm to Classify Lower Urinary Tract Symptoms
- Data from the All of Us research program reinforces existence of activity inequality
- Med-Real2Sim: Non-Invasive Medical Digital Twins using Physics-Informed Self-Supervised Learning
- Context Clues: Evaluating Long Context Models for Clinical Prediction Tasks on EHR Data
- Asclepius-R : Clinical Large Language Model Built On MIMIC-III Discharge Summaries
- KIT-LSTM: Knowledge-guided Time-aware LSTM for Continuous Clinical Risk Prediction
- Predicting sex from retinal fundus photographs using automated deep learning
- Future-Guided Pretraining via Time-to-Event Supervision for 3D Medical Imaging
- Uncertainty Quantification for Clinical Outcome Predictions with (Large) Language Models
- Hospitalization prediction from the emergency department using computer vision AI with short patient video clips
- MedRAX: Medical Reasoning Agent for Chest X-ray
- 3D Foundation AI Model for Generalizable Disease Detection in Head Computed Tomography
- Multimodal Medical Code Tokenizer
- Large language models are less effective at clinical prediction tasks than locally trained machine learning models
- TIMER: Temporal Instruction Modeling and Evaluation for Longitudinal Clinical Records
- Frequent but fragmented: use of note templates to document outpatient visits at an academic health center
- Standardization of Emergency Department Clinical Note Templates: A Retrospective Analysis across an Integrated Health System
- Exploring Scaling Laws for EHR Foundation Models
- A multimodal vision foundation model for clinical dermatology
- Foundation Models for Clinical Records at Health System Scale
- Foundation models for electronic health records: representation dynamics and transferability
Other Misc./Methods Papers/Deep Learning Papers
A list of papers I am reading.
- Scaling Laws for Downstream Task Performance of Large Language Models
- ImageBind: One Embedding Space To Bind Them All
- AnyMAL: An Efficient and Scalable Any-Modality Augmented Language Model
- Transformers Can Do Arithmetic with the Right Embeddings
- LLM2Vec: Large Language Models Are Secretly Powerful Text Encoders
- LoRA: Low-Rank Adaptation of Large Language Models
- RAFT: Adapting Language Model to Domain Specific RAG
- A Closer Look at AUROC and AUPRC under Class Imbalance
- The Era of 1-bit LLMs: All Large Language Models are in 1.58 Bits
- All-in-one simulation-based inference
- No New Net
- tree of thought
- Q-Sparse: All Large Language Models can be Fully Sparsely-Activated
- Reuse, Don't Retrain: A Recipe for Continued Pretraining of Language Models
- FasterViT: Fast Vision Transformers with Hierarchical Attention
- Few-shot Adaptation to Distribution Shifts By Mixing Source and Target Embeddings
- SparseCL: Sparse Contrastive Learning for Contradiction Retrieval
- Cell2Sentence: Teaching Large Language Models the Language of Biology
- Concept BottleNeck Models
- The AI Scientist: Towards Fully Automated Open-Ended Scientific Discovery
- How Well Can Vision Language Models See Image Details?
- The Data Addition Dilemma
- Bayesian Learning via Stochastic Gradient Langevin Dynamics
- HeAR- Health Acoustic Representations
- Uncertainty Quantification with Pre-trained Language Models: A Large-Scale Empirical Analysis
- Improving model calibration with accuracy versus uncertainty optimization
- Larger and more instructable language models become less reliable
- Why did the Model Fail?": Attributing Model Performance Changes to Distribution Shifts
- DISCOVERYWORLD: A Virtual Environment for Developing and Evaluating Automated Scientific Discovery Agents
- A Comprehensive Survey on Graph Neural Networks
- A Probabilistic Inference Approach to Inference-Time Scaling of LLMs using Particle-Based Monte Carlo Methods
- One Model to learn them all
- Toward a Theory of Tokenization in LLMs
- A Brief Review of Deep Multi-task Learning and Auxiliary Task Learning
- Generating Realistic Tabular Data with Large Language Models
- Foundation Models in Electrocardiogram: A Review
- The Super Weight in Large Language Models
- BERTs are Generative In-Context Learners
- The Virtual Lab: AI Agents Design New SARS-CoV-2 Nanobodies with Experimental Validation
- Large Language Model Influence on Diagnostic Reasoning A Randomized Clinical Trial
- Finding "Good Views" of Electrocardiogram Signals for Inferring Abnormalities in Cardiac Condition
- Superhuman performance of a large language model on the reasoning tasks of a physician
- Transformer2: Self-adaptive LLMs
- Accurate predictions on small data with a tabular foundation model
- Hallucinations Can Improve Large Language Models in Drug Discovery
- DeepSeek-R1: Incentivizing Reasoning Capability in LLMs via Reinforcement Learning
- SFT Memorizes, RL Generalizes: A Comparative Study of Foundation Model Post-training
- The Pitfalls of Memorization: When Memorization Hurts Generalization
- Leveraging Domain Knowledge for Efficient Reward Modeling in RLHF: A Case-Study in E-Commerce Opinion Summarization
- DogeRM: Equipping Reward Models with Domain Knowledge through Model Merging
- A Comparison of Multi-task learning and Single-task learning Approaches
- Quantifying Uncertainty in Answers from any Language Model and Enhancing their Trustworthiness
- Deep Learning is Not So Mysterious or Different
- A Comprehensive Benchmark of Machine and Deep Learning Across Diverse Tabular Datasets
- FoNE: Precise Single-Token Number Embeddings via Fourier Features
- NoProp: Training Neural Networks without Back-propagation or Forward-propagation
- When Bad Data Leads to Good Models
- Convergent Learning: Do different neural networks learn the same representations?
- Harnessing the Universal Geometry of Embeddings
- When accurate prediction models yield harmful self-fulfilling prophecies
- CellVoyager: AI CompBio Agent Generates New Insights by Autonomously Analyzing Biological Data
Similar repos
Contributors
Simonlee711
123 commits