skip to main content


This content will become publicly available on June 18, 2025

Title: Knowledge transfer from macro-world to micro-world: enhancing 3D Cryo-ET classification through fine-tuning video-based deep models
Abstract Motivation

Deep learning models have achieved remarkable success in a wide range of natural-world tasks, such as vision, language, and speech recognition. These accomplishments are largely attributed to the availability of open-source large-scale datasets. More importantly, pre-trained foundational model learnings exhibit a surprising degree of transferability to downstream tasks, enabling efficient learning even with limited training examples. However, the application of such natural-domain models to the domain of tiny Cryo-Electron Tomography (Cryo-ET) images has been a relatively unexplored frontier. This research is motivated by the intuition that 3D Cryo-ET voxel data can be conceptually viewed as a sequence of progressively evolving video frames.

Results

Leveraging the above insight, we propose a novel approach that involves the utilization of 3D models pre-trained on large-scale video datasets to enhance Cryo-ET subtomogram classification. Our experiments, conducted on both simulated and real Cryo-ET datasets, reveal compelling results. The use of video initialization not only demonstrates improvements in classification accuracy but also substantially reduces training costs. Further analyses provide additional evidence of the value of video initialization in enhancing subtomogram feature extraction. Additionally, we observe that video initialization yields similar positive effects when applied to medical 3D classification tasks, underscoring the potential of cross-domain knowledge transfer from video-based models to advance the state-of-the-art in a wide range of biological and medical data types.

Availability and implementation

https://github.com/xulabs/aitom.

 
more » « less
Award ID(s):
1949629 2211597
NSF-PAR ID:
10537930
Author(s) / Creator(s):
; ;
Editor(s):
Peng, Hanchuan
Publisher / Repository:
Oxford University Press
Date Published:
Journal Name:
Bioinformatics
Volume:
40
Issue:
7
ISSN:
1367-4811
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. Abstract Motivation

    Cryo-Electron Tomography (cryo-ET) is a 3D imaging technology that enables the visualization of subcellular structures in situ at near-atomic resolution. Cellular cryo-ET images help in resolving the structures of macromolecules and determining their spatial relationship in a single cell, which has broad significance in cell and structural biology. Subtomogram classification and recognition constitute a primary step in the systematic recovery of these macromolecular structures. Supervised deep learning methods have been proven to be highly accurate and efficient for subtomogram classification, but suffer from limited applicability due to scarcity of annotated data. While generating simulated data for training supervised models is a potential solution, a sizeable difference in the image intensity distribution in generated data as compared with real experimental data will cause the trained models to perform poorly in predicting classes on real subtomograms.

    Results

    In this work, we present Cryo-Shift, a fully unsupervised domain adaptation and randomization framework for deep learning-based cross-domain subtomogram classification. We use unsupervised multi-adversarial domain adaption to reduce the domain shift between features of simulated and experimental data. We develop a network-driven domain randomization procedure with ‘warp’ modules to alter the simulated data and help the classifier generalize better on experimental data. We do not use any labeled experimental data to train our model, whereas some of the existing alternative approaches require labeled experimental samples for cross-domain classification. Nevertheless, Cryo-Shift outperforms the existing alternative approaches in cross-domain subtomogram classification in extensive evaluation studies demonstrated herein using both simulated and experimental data.

    Availabilityand implementation

    https://github.com/xulabs/aitom.

    Supplementary information

    Supplementary data are available at Bioinformatics online.

     
    more » « less
  2. Elofsson, Arne (Ed.)
    Abstract Motivation Cryoelectron tomography (cryo-ET) visualizes structure and spatial organization of macromolecules and their interactions with other subcellular components inside single cells in the close-to-native state at submolecular resolution. Such information is critical for the accurate understanding of cellular processes. However, subtomogram classification remains one of the major challenges for the systematic recognition and recovery of the macromolecule structures in cryo-ET because of imaging limits and data quantity. Recently, deep learning has significantly improved the throughput and accuracy of large-scale subtomogram classification. However, often it is difficult to get enough high-quality annotated subtomogram data for supervised training due to the enormous expense of labeling. To tackle this problem, it is beneficial to utilize another already annotated dataset to assist the training process. However, due to the discrepancy of image intensity distribution between source domain and target domain, the model trained on subtomograms in source domain may perform poorly in predicting subtomogram classes in the target domain. Results In this article, we adapt a few shot domain adaptation method for deep learning-based cross-domain subtomogram classification. The essential idea of our method consists of two parts: (i) take full advantage of the distribution of plentiful unlabeled target domain data, and (ii) exploit the correlation between the whole source domain dataset and few labeled target domain data. Experiments conducted on simulated and real datasets show that our method achieves significant improvement on cross domain subtomogram classification compared with baseline methods. Availability and implementation Software is available online https://github.com/xulabs/aitom. Supplementary information Supplementary data are available at Bioinformatics online. 
    more » « less
  3. Xu, Jinbo (Ed.)
    Abstract Motivation Cryo-Electron Tomography (cryo-ET) is a 3D bioimaging tool that visualizes the structural and spatial organization of macromolecules at a near-native state in single cells, which has broad applications in life science. However, the systematic structural recognition and recovery of macromolecules captured by cryo-ET are difficult due to high structural complexity and imaging limits. Deep learning-based subtomogram classification has played critical roles for such tasks. As supervised approaches, however, their performance relies on sufficient and laborious annotation on a large training dataset. Results To alleviate this major labeling burden, we proposed a Hybrid Active Learning (HAL) framework for querying subtomograms for labeling from a large unlabeled subtomogram pool. Firstly, HAL adopts uncertainty sampling to select the subtomograms that have the most uncertain predictions. This strategy enforces the model to be aware of the inductive bias during classification and subtomogram selection, which satisfies the discriminativeness principle in AL literature. Moreover, to mitigate the sampling bias caused by such strategy, a discriminator is introduced to judge if a certain subtomogram is labeled or unlabeled and subsequently the model queries the subtomogram that have higher probabilities to be unlabeled. Such query strategy encourages to match the data distribution between the labeled and unlabeled subtomogram samples, which essentially encodes the representativeness criterion into the subtomogram selection process. Additionally, HAL introduces a subset sampling strategy to improve the diversity of the query set, so that the information overlap is decreased between the queried batches and the algorithmic efficiency is improved. Our experiments on subtomogram classification tasks using both simulated and real data demonstrate that we can achieve comparable testing performance (on average only 3% accuracy drop) by using less than 30% of the labeled subtomograms, which shows a very promising result for subtomogram classification task with limited labeling resources. Availability and implementation https://github.com/xulabs/aitom. Supplementary information Supplementary data are available at Bioinformatics online. 
    more » « less
  4. Abstract Purpose

    In order to produce a surgical gesture recognition system that can support a wide variety of procedures, either a very large annotated dataset must be acquired, or fitted models must generalize to new labels (so-called zero-shot capability). In this paper we investigate the feasibility of latter option.

    Methods

    Leveraging the bridge-prompt framework, we prompt-tune a pre-trained vision-text model (CLIP) for gesture recognition in surgical videos. This can utilize extensive outside video data such as text, but also make use of label meta-data and weakly supervised contrastive losses.

    Results

    Our experiments show that prompt-based video encoder outperforms standard encoders in surgical gesture recognition tasks. Notably, it displays strong performance in zero-shot scenarios, where gestures/tasks that were not provided during the encoder training phase are included in the prediction phase. Additionally, we measure the benefit of inclusion text descriptions in the feature extractor training schema.

    Conclusion

    Bridge-prompt and similar pre-trained + prompt-tuned video encoder models present significant visual representation for surgical robotics, especially in gesture recognition tasks. Given the diverse range of surgical tasks (gestures), the ability of these models to zero-shot transfer without the need for any task (gesture) specific retraining makes them invaluable.

     
    more » « less
  5. null (Ed.)
    Recent years have witnessed the enormous success of text representation learning in a wide range of text mining tasks. Earlier word embedding learning approaches represent words as fixed low-dimensional vectors to capture their semantics. The word embeddings so learned are used as the input features of task-specific models. Recently, pre-trained language models (PLMs), which learn universal language representations via pre-training Transformer-based neural models on large-scale text corpora, have revolutionized the natural language processing (NLP) field. Such pre-trained representations encode generic linguistic features that can be transferred to almost any text-related applications. PLMs outperform previous task-specific models in many applications as they only need to be fine-tuned on the target corpus instead of being trained from scratch. In this tutorial, we introduce recent advances in pre-trained text embeddings and language models, as well as their applications to a wide range of text mining tasks. Specifically, we first overview a set of recently developed self-supervised and weakly-supervised text embedding methods and pre-trained language models that serve as the fundamentals for downstream tasks. We then present several new methods based on pre-trained text embeddings and language models for various text mining applications such as topic discovery and text classification. We focus on methods that are weakly-supervised, domain-independent, language-agnostic, effective and scalable for mining and discovering structured knowledge from large-scale text corpora. Finally, we demonstrate with real world datasets how pre-trained text representations help mitigate the human annotation burden and facilitate automatic, accurate and efficient text analyses. 
    more » « less