Awesome-IML

An awesome collection of sources regarding Informed Machine Learning (IML)/Background Knowledge Integration (BKI).

Overview, Taxonomy and Surveys

Year	Title	Paper
2022	A review of some techniques for inclusion of domain-knowledge into deep neural networks	Link
2021	Informed Machine Learning - A Taxonomy and Survey of Integrating Prior Knowledge into Learning Systems	Link
2020	Integrating Machine Learning with Human Knowledge	Link
2024	Medical-informed machine learning: integrating prior knowledge into medical decision systems	Link
2024	Physics-informed machine learning: A comprehensive review on applications in anomaly detection and condition monitoring	Link

Datasets

Year	Title	Link
2021	The BioGRID database: A comprehensive biomedical resource of curated protein, genetic, and chemical interactions	Link
2020	miRDB: an online database for prediction of functional microRNA targets	Link

Tasks

Papers are categorized based on the task, more details are included in the table.

Classification

Title	Year	Knowledge Representation	Model	Task (specific)	Paper	Code
A multimodal graph neural network framework for cancer molecular subtype classification	2024	graph	GNN	cancer subtype classification	Link
Biologically informed deep learning to query gene programs in single-cell atlases	2023	binary matrix	Conditional variational autoencoders	single cell reference mapping	Link	Link
Cancer molecular subtype classification by graph convolutional networks on multi-omics data	2021	graph	GNN	cancer subtype classification	Link
PKGCN: prior knowledge enhanced graph convolutional network for graph-based semi-supervised learning	2019	graph	GNN	node classification	Link
Single-cell classification using graph convolutional networks	2021	graph	GNN	cell classification	Link	Link
Graph neural networks with multiple prior knowledge for multi-omics data analysis	2023	graph	GNN	cancer molecular subtype classification	Link
Prior Knowledge Guided Unsupervised Domain Adaptation	2022	human feedback	Predictive Model	unsupervised domain adaptation (UDA)	Link	Link
BaKGraSTeC: A Background Knowledge Graph Based Method for Short Text Classification	2020	knowledge graph	GNN	short text classification	Link
Learning beyond datasets: Knowledge Graph Augmented Neural Networks for Natural language Processing	2018	knowledge graph	NN	text classification	Link
Injecting Semantic Background Knowledge into Neural Networks using Graph Embeddings	2017	knowledge graph	NN	fraud detection	Link
The Deep Weight Prior	2019	propabilistic relations	Bayesian CNN		Link	Link
Prior-Enhanced Few-Shot Segmentation with Meta-Prototypes	2021	simulation results	Two-Stage Neural Network (Prior and Segmentation)	image segmentation	Link	Link
Interpretations are useful: penalizing explanations to align neural networks with prior knowledge	2020				Link	Link
Interpretable brain disease classification and relevance‑guided deep learning	2022		CNN	brain disease classification	Link	Link
Towards explainable oral cancer recognition: Screening on imperfect images via Informed Deep Learning and Case-Based Reasoning	2024	human feedback	RCNN	cancer recognition	Link	Link

Clustering

Title	Year	Knowledge Representation	Model	Task (specific)	Paper	Code
A framework for deep constrained clustering	2021	algebraic equation	autoencoder	constrained clustering	Link	Link

Feature Extraction

Title	Year	Knowledge Representation	Model	Task (specific)	Paper	Code
Hierarchy-based Image Embeddings for Semantic Image Retrieval	2019	graph	CNN	semantic image retrieval	Link	Link

Forecasting

Title	Year	Knowledge Representation	Model	Task (specific)	Paper	Code
Analyzing Koopman approaches to physics-informed machine learning for long-term sea-surface temperature forecasting	2021		Autoencoder	time series forecasting	Link	Link
Simulation-Informed Revenue Extrapolation with Confidence Estimate for Scaleup Companies Using Scarce Time-Series Data	2022			time series forecasting	Link	Link

Prediction

Title	Year	Knowledge Representation	Model	Task (specific)	Paper	Code
A Physics-informed Neural Network for Wind Turbine Main Bearing Fatigue	2020	differential equations	RNN	predictive maintenance	Link	Link
SimbaML (Simulation-Based ML)	2023	differential equations / simulation results	ODE	synthetic data generation	Link	Link
Utilizing Molecular Network Information via Graph Convolutional Neural Networks to Predict Metastatic Event in Breast Cancer	2019	graph	GNN	cancer prediction	Link
Knowledge-aware Attention Network for Protein-Protein Interaction Extraction	2019	Knowledge Base of Protein-Protein Pairs	Transformer	protein-protein interaction (PPI) extraction	Link	Link
Leveraging prior knowledge for protein–protein interaction extraction with memory network	2018	Knowledge Base of Protein-Protein Pairs	Memory Network Model	protein-protein interaction (PPI) extraction	Link	Link
KCRL: A Prior Knowledge Based Causal Discovery Framework with Reinforcement Learning	2022	knowledge graph	Transformer-Based Deep RL Agent	causal discovery	Link	Link
Knowledge Enhanced Graph Neural Networks for Graph Completion	2023	logic rules	GNN	graph completion	Link	Link
Inclusion of domain-knowledge into GNNs using mode-directed inverse entailment	2022	logic rules	GNN	drug discovery	Link
Incorporating symbolic domain knowledge into graph neural networks	2021	logic rules	GNN	drug discovery	Link	Link
Language Model Prior for Low-Resource Neural Machine Translation	2020	probabilistic relations	Transformer + LLM	neural machine translation (NMT)	Link	Link
Prior Knowledge Integration for Neural Machine Translation using Posterior Regularization	2017	probabilistic relations		neural machine translation (NMT)	Link	Link
Knowledge enhanced graph neural networks for explainable recommendation	2022	semantic knowledge?	GNN	recommendation	Link
Advancing Generalizable Remote Physiological Measurement through the Integration of Explicit and Implicit Prior Knowledge	2024	simulation results			Link	Link
Incorporating prior knowledge into regularized regression	2020		linear regression		Link	Link
Physics-informed neural networks: A deep learning framework for solving forward and inverse problems involving nonlinear partial differential equations	2019			solutions to partial differential equations	Link	Link
The impact of prior knowledge on causal structure learning	2023	knowledge graph		causal learning	Link

Regression

Title	Year	Knowledge Representation	Model	Task (specific)	Paper	Code
Regression Shrinkage and Selection Via the Lasso	1996	probabilistic relations	Linear Regression		Link
Feature-weighted elastic net: using “features of features” for better prediction	2020	Human Feedback, Feature Groups, Feature Importance	Linear Regression		Link
Adaptive penalization in high-dimensional regression and classification with external covariates using variational Bayes	2019	Feature Groups	Hierarchical Bayes		Link	Link

Elicitation

Title	Year	Knowledge Representation	Model	Task (specific)	Paper	Code
Prior knowledge elicitation: The past, present, and future	2023				Link