# TimelyGPT: Extrapolatable Transformer Pre-training for Long-term Time-Series Forecasting in Healthcare

arXiv: https://arxiv.org/abs/2312.00817 · HTML: https://mlsanity.com/paper/2312.00817/

## Key facts

- Cited by 4 papers in the map (data through 14 Oct 2026).
- Builds on 48 of its 73 references that are in the map.
- First posted on arXiv 29 Nov 2023.

## Builds on (most cited first, 30 of 48)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [Language Models are Few-Shot Learners](https://mlsanity.com/paper/2005.14165/) (2020)
- [Exploring the Limits of Transfer Learning with a Unified Text-to-Text Transformer](https://mlsanity.com/paper/1910.10683/) (2019)
- [LLaMA: Open and Efficient Foundation Language Models](https://mlsanity.com/paper/2302.13971/) (2023)
- [Scaling Laws for Neural Language Models](https://mlsanity.com/paper/2001.08361/) (2020)
- [RoFormer: Enhanced Transformer with Rotary Position Embedding](https://mlsanity.com/paper/2104.09864/) (2021)
- [Robust Speech Recognition via Large-Scale Weak Supervision](https://mlsanity.com/paper/2212.04356/) (2022)
- [XLNet: Generalized Autoregressive Pretraining for Language Understanding](https://mlsanity.com/paper/1906.08237/) (2019)
- [Efficiently Modeling Long Sequences with Structured State Spaces](https://mlsanity.com/paper/2111.00396/) (2021)
- [Xception: Deep Learning with Depthwise Separable Convolutions](https://mlsanity.com/paper/1610.02357/) (2016)
- [Informer: Beyond Efficient Transformer for Long Sequence Time-Series Forecasting](https://mlsanity.com/paper/2012.07436/) (2020)
- [A Time Series is Worth 64 Words: Long-term Forecasting with Transformers](https://mlsanity.com/paper/2211.14730/) (2022)
- [Transformers are RNNs: Fast Autoregressive Transformers with Linear Attention](https://mlsanity.com/paper/2006.16236/) (2020)
- [Conformer: Convolution-augmented Transformer for Speech Recognition](https://mlsanity.com/paper/2005.08100/) (2020)
- [Transformer-XL: Attentive Language Models Beyond a Fixed-Length Context](https://mlsanity.com/paper/1901.02860/) (2019)
- [Autoformer: Decomposition Transformers with Auto-Correlation for Long-Term Series Forecasting](https://mlsanity.com/paper/2106.13008/) (2021)
- [MLP-Mixer: An all-MLP Architecture for Vision](https://mlsanity.com/paper/2105.01601/) (2021)
- [Are Transformers Effective for Time Series Forecasting?](https://mlsanity.com/paper/2205.13504/) (2022)
- [FEDformer: Frequency Enhanced Decomposed Transformer for Long-term Series Forecasting](https://mlsanity.com/paper/2201.12740/) (2022)
- [Self-Attention with Relative Position Representations](https://mlsanity.com/paper/1803.02155/) (2018)
- [Train Short, Test Long: Attention with Linear Biases Enables Input Length Extrapolation](https://mlsanity.com/paper/2108.12409/) (2021)
- [TimesNet: Temporal 2D-Variation Modeling for General Time Series Analysis](https://mlsanity.com/paper/2210.02186/) (2022)
- [Scaling Vision Transformers](https://mlsanity.com/paper/2106.04560/) (2021)
- [RWKV: Reinventing RNNs for the Transformer Era](https://mlsanity.com/paper/2305.13048/) (2023)
- [The RefinedWeb Dataset for Falcon LLM: Outperforming Curated Corpora with Web Data, and Web Data Only](https://mlsanity.com/paper/2306.01116/) (2023)
- [Retentive Network: A Successor to Transformer for Large Language Models](https://mlsanity.com/paper/2307.08621/) (2023)
- [Recurrent Neural Networks for Multivariate Time Series with Missing Values](https://mlsanity.com/paper/1606.01865/) (2016)
- [TS2Vec: Towards Universal Representation of Time Series](https://mlsanity.com/paper/2106.10466/) (2021)
- [A Transformer-based Framework for Multivariate Time Series Representation Learning](https://mlsanity.com/paper/2010.02803/) (2020)
- [Hyena Hierarchy: Towards Larger Convolutional Language Models](https://mlsanity.com/paper/2302.10866/) (2023)

## Built on by (most cited first, 4 of 4)

- [Medical world models in healthcare: foundations, applications, and challenges for trustworthy clinical translation](https://mlsanity.com/paper/2607.25242/) (2026)
- [TrajGPT: Irregular Time-Series Representation Learning for Health Trajectory Analysis](https://mlsanity.com/paper/2410.02133/) (2024)
- [Transformer-Based Multi-Modal Temporal Embeddings for Explainable Metabolic Phenotyping in Type 1 Diabetes](https://mlsanity.com/paper/2601.04299/) (2026)
- [SMI: Ontology-Grounded Semantic IDs for Hierarchy-Aware Medical Concept Representation](https://mlsanity.com/paper/2610.18672/) (2026)

## Abstract (arXiv)

Large-scale pre-trained models (PTMs) such as BERT and GPT have recently achieved great success in Natural Language Processing and Computer Vision domains. However, the development of PTMs on healthcare time-series data is lagging behind.This underscores the limitations of the existing transformer-based architectures, particularly their scalability to handle large-scale time series and ability to capture long-term temporal dependencies. In this study, we present Timely Generative Pre-trained Transformer (TimelyGPT). TimelyGPT employs an extrapolatable position (xPos) embedding to encode trend and periodic patterns into time-series representations. It also integrates recurrent attention and temporal convolution modules to effectively capture global-local temporal dependencies. We evaluated TimelyGPT on two large-scale healthcare time series datasets corresponding to continuous biosignals and irregularly-sampled time series, respectively. Our experiments show that during pre-training, TimelyGPT excels in learning time-series representations from continuously monitored biosignals and irregularly-sampled time series data commonly observed in longitudinal electronic health records (EHRs). In forecasting continuous biosignals, TimelyGPT achieves accurate extrapolation up to 6,000 timesteps of body temperature during the sleep stage transition, given a short look-up window (i.e., prompt) containing only 2,000 timesteps. For irregularly-sampled time series, TimelyGPT with a proposed time-specific inference demonstrates high top recall scores in predicting future diagnoses using early diagnostic records, effectively handling irregular intervals between clinical records. Together, we envision TimelyGPT to be useful in a broad spectrum of health domains, including long-term patient health state forecasting and patient risk trajectory prediction.