Network pharmacology: towards the artificial intelligence-based precision traditional Chinese medicine

P Zhang, D Zhang, W Zhou, L Wang… - Briefings in …, 2024 - academic.oup.com
Network pharmacology (NP) provides a new methodological perspective for understanding
traditional medicine from a holistic perspective, giving rise to frontiers such as traditional …

FOCAL: Contrastive learning for multimodal time-series sensing signals in factorized orthogonal latent space

S Liu, T Kimura, D Liu, R Wang, J Li… - Advances in …, 2024 - proceedings.neurips.cc
This paper proposes a novel contrastive learning framework, called FOCAL, for extracting
comprehensive features from multimodal time-series sensing signals through self …

Mapping the Multiscale Proteomic Organization of Cellular and Disease Phenotypes

A Cesnik, LV Schaffer, I Gaur, M Jain… - Annual Review of …, 2024 - annualreviews.org
While the primary sequences of human proteins have been cataloged for over a decade,
determining how these are organized into a dynamic collection of multiprotein assemblies …

Mapping cells through time and space with moscot

D Klein, G Palla, M Lange, M Klein, Z Piran, M Gander… - bioRxiv, 2023 - biorxiv.org
Single-cell genomics technologies enable multimodal profiling of millions of cells across
temporal and spatial dimensions. Experimental limitations prevent the measurement of all …

Joint variational autoencoders for multimodal imputation and embedding

N Cohen Kalafut, X Huang, D Wang - Nature Machine Intelligence, 2023 - nature.com
Single-cell multimodal datasets have measured various characteristics of individual cells,
enabling a deep understanding of cellular and molecular mechanisms. However …

[HTML][HTML] TMO-Net: an explainable pretrained multi-omics model for multi-task learning in oncology

F Wang, Z Zhuang, F Gao, R He… - Genome …, 2024 - genomebiology.biomedcentral.com
Cancer is a complex disease composing systemic alterations in multiple scales. In this study,
we develop the Tumor Multi-Omics pre-trained Network (TMO-Net) that integrates multi …

[HTML][HTML] scButterfly: a versatile single-cell cross-modality translation method via dual-aligned variational autoencoders

Y Cao, X Zhao, S Tang, Q Jiang, S Li, S Li… - Nature …, 2024 - nature.com
Recent advancements for simultaneously profiling multi-omics modalities within individual
cells have enabled the interrogation of cellular heterogeneity and molecular hierarchy …

A denoised multi-omics integration framework for cancer subtype classification and survival prediction

J Pang, B Liang, R Ding, Q Yan… - Briefings in …, 2023 - academic.oup.com
The availability of high-throughput sequencing data creates opportunities to
comprehensively understand human diseases as well as challenges to train machine …

[HTML][HTML] ScLinear predicts protein abundance at single-cell resolution

D Hanhart, F Gossi, MA Rapsomaniki… - Communications …, 2024 - nature.com
Single-cell multi-omics have transformed biomedical research and present exciting machine
learning opportunities. We present scLinear, a linear regression-based approach that …

Comprehensive View Embedding Learning for Single-Cell Multimodal Integration

Z Tang, J Huang, G Chen, CYC Chen - Proceedings of the AAAI …, 2024 - ojs.aaai.org
Motivation: Advances in single-cell measurement techniques provide rich multimodal data,
which helps us to explore the life state of cells more deeply. However, multimodal …