# Simplicity within biological complexity

arXiv: https://arxiv.org/abs/2405.09595 · HTML: https://mlsanity.com/paper/2405.09595/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 49 of its 223 references that are in the map.
- First posted on arXiv 15 May 2024.

## Builds on (most cited first, 30 of 49)

- [Semi-Supervised Classification with Graph Convolutional Networks](https://mlsanity.com/paper/1609.02907/) (2016)
- [Efficient Estimation of Word Representations in Vector Space](https://mlsanity.com/paper/1301.3781/) (2013)
- [Neural Message Passing for Quantum Chemistry](https://mlsanity.com/paper/1704.01212/) (2017)
- [Distributed Representations of Words and Phrases and their Compositionality](https://mlsanity.com/paper/1310.4546/) (2013)
- [node2vec: Scalable Feature Learning for Networks](https://mlsanity.com/paper/1607.00653/) (2016)
- [A Survey on Hallucination in Large Language Models: Principles, Taxonomy, Challenges, and Open Questions](https://mlsanity.com/paper/2311.05232/) (2023)
- [Graph Neural Networks: A Review of Methods and Applications](https://mlsanity.com/paper/1812.08434/) (2018)
- [DeepWalk: Online Learning of Social Representations](https://mlsanity.com/paper/1403.6652/) (2014)
- [Google's Neural Machine Translation System: Bridging the Gap between Human and Machine Translation](https://mlsanity.com/paper/1609.08144/) (2016)
- [Variational Graph Auto-Encoders](https://mlsanity.com/paper/1611.07308/) (2016)
- [Hierarchical Graph Representation Learning with Differentiable Pooling](https://mlsanity.com/paper/1806.08804/) (2018)
- [Distributed Representations of Sentences and Documents](https://mlsanity.com/paper/1405.4053/) (2014)
- [LINE: Large-scale Information Network Embedding](https://mlsanity.com/paper/1503.03578/) (2015)
- [Deep Learning on Graphs: A Survey](https://mlsanity.com/paper/1812.04202/) (2018)
- [A Structured Self-attentive Sentence Embedding](https://mlsanity.com/paper/1703.03130/) (2017)
- [Improving Graph Neural Network Expressivity via Subgraph Isomorphism Counting](https://mlsanity.com/paper/2006.09252/) (2020)
- [Estimating the intrinsic dimension of datasets by a minimal neighborhood information](https://mlsanity.com/paper/1803.06992/) (2018)
- [Network Embedding as Matrix Factorization: Unifying DeepWalk, LINE, PTE, and node2vec](https://mlsanity.com/paper/1710.02971/) (2017)
- [Graph Embedding Techniques, Applications, and Performance: A Survey](https://mlsanity.com/paper/1705.02801/) (2017)
- [Deep Reinforcement Learning for De-Novo Drug Design](https://mlsanity.com/paper/1711.10907/) (2017)
- [A Survey on Network Embedding](https://mlsanity.com/paper/1711.08752/) (2017)
- [DeID-GPT: Zero-shot Medical Text De-Identification by GPT-4](https://mlsanity.com/paper/2303.11032/) (2023)
- [PersLay: A Neural Network Layer for Persistence Diagrams and New Graph Topological Signatures](https://mlsanity.com/paper/1904.09378/) (2019)
- [Deep Learning with Topological Signatures](https://mlsanity.com/paper/1707.04041/) (2017)
- [Geometric Deep Learning on Molecular Representations](https://mlsanity.com/paper/2107.12375/) (2021)
- [Learning Structural Node Embeddings Via Diffusion Wavelets](https://mlsanity.com/paper/1710.10321/) (2017)
- [PTE: Predictive Text Embedding through Large-scale Heterogeneous Text Networks](https://mlsanity.com/paper/1508.00200/) (2015)
- [Graph Representation Learning in Biomedicine](https://mlsanity.com/paper/2104.04883/) (2021)
- [LLMCarbon: Modeling the end-to-end Carbon Footprint of Large Language Models](https://mlsanity.com/paper/2309.14393/) (2023)
- [Graph Filtration Learning](https://mlsanity.com/paper/1905.10996/) (2019)

## Abstract (arXiv)

Heterogeneous, interconnected, systems-level, molecular data have become increasingly available and key in precision medicine. We need to utilize them to better stratify patients into risk groups, discover new biomarkers and targets, repurpose known and discover new drugs to personalize medical treatment. Existing methodologies are limited and a paradigm shift is needed to achieve quantitative and qualitative breakthroughs. In this perspective paper, we survey the literature and argue for the development of a comprehensive, general framework for embedding of multi-scale molecular network data that would enable their explainable exploitation in precision medicine in linear time. Network embedding methods map nodes to points in low-dimensional space, so that proximity in the learned space reflects the network's topology-function relationships. They have recently achieved unprecedented performance on hard problems of utilizing few omic data in various biomedical applications. However, research thus far has been limited to special variants of the problems and data, with the performance depending on the underlying topology-function network biology hypotheses, the biomedical applications and evaluation metrics. The availability of multi-omic data, modern graph embedding paradigms and compute power call for a creation and training of efficient, explainable and controllable models, having no potentially dangerous, unexpected behaviour, that make a qualitative breakthrough. We propose to develop a general, comprehensive embedding framework for multi-omic network data, from models to efficient and scalable software implementation, and to apply it to biomedical informatics. It will lead to a paradigm shift in computational and biomedical understanding of data and diseases that will open up ways to solving some of the major bottlenecks in precision medicine and other domains.