# Gene Incremental Learning for Single-Cell Transcriptomics

arXiv: https://arxiv.org/abs/2511.13762 · HTML: https://mlsanity.com/paper/2511.13762/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 14 of its 48 references that are in the map.
- First posted on arXiv 14 Nov 2025.

## Builds on (most cited first, 14 of 14)

- [Adam: A Method for Stochastic Optimization](https://mlsanity.com/paper/1412.6980/) (2014)
- [Distilling the Knowledge in a Neural Network](https://mlsanity.com/paper/1503.02531/) (2015)
- [iCaRL: Incremental Classifier and Representation Learning](https://mlsanity.com/paper/1611.07725/) (2016)
- [Large Scale Incremental Learning](https://mlsanity.com/paper/1905.13260/) (2019)
- [An Empirical Investigation of Catastrophic Forgetting in Gradient-Based Neural Networks](https://mlsanity.com/paper/1312.6211/) (2013)
- [End-to-End Incremental Learning](https://mlsanity.com/paper/1807.09536/) (2018)
- [Learning under Concept Drift: A Review](https://mlsanity.com/paper/2004.05785/) (2020)
- [Class-incremental learning: survey and performance evaluation on image classification](https://mlsanity.com/paper/2010.15277/) (2020)
- [Maintaining Discrimination and Fairness in Class Incremental Learning](https://mlsanity.com/paper/1911.07053/) (2019)
- [Class-incremental Learning via Deep Model Consolidation](https://mlsanity.com/paper/1903.07864/) (2019)
- [Distilling Causal Effect of Data in Class-Incremental Learning](https://mlsanity.com/paper/2103.01737/) (2021)
- [Class-Incremental Learning by Knowledge Distillation with Adaptive Feature Consolidation](https://mlsanity.com/paper/2204.00895/) (2022)
- [LFPT5: A Unified Framework for Lifelong Few-shot Language Learning Based on Prompt Tuning of T5](https://mlsanity.com/paper/2110.07298/) (2021)
- [Towards continual task learning in artificial neural networks: current approaches and insights from neuroscience](https://mlsanity.com/paper/2112.14146/) (2021)

## Abstract (arXiv)

Classes, as fundamental elements of Computer Vision, have been extensively studied within incremental learning frameworks. In contrast, tokens, which play essential roles in many research fields, exhibit similar characteristics of growth, yet investigations into their incremental learning remain significantly scarce. This research gap primarily stems from the holistic nature of tokens in language, which imposes significant challenges on the design of incremental learning frameworks for them. To overcome this obstacle, in this work, we turn to a type of token, gene, for a large-scale biological dataset--single-cell transcriptomics--to formulate a pipeline for gene incremental learning and establish corresponding evaluations. We found that the forgetting problem also exists in gene incremental learning, thus we adapted existing class incremental learning methods to mitigate the forgetting of genes. Through extensive experiments, we demonstrated the soundness of our framework design and evaluations, as well as the effectiveness of our method adaptations. Finally, we provide a complete benchmark for gene incremental learning in single-cell transcriptomics.