Deep Active Learning with Noise Stability

Uncertainty estimation for unlabeled data is crucial to active learning. With a deep neural network employed as the backbone model, the data selection process is highly challenging due to the potential over-confidence of the model inference. Existing methods resort to special learning fashions (e.g. adversarial) or auxiliary models to address this challenge. This tends to result in complex and inefficient pipelines, which would render the methods impractical. In this work, we propose a novel algorithm that leverages noise stability to estimate data uncertainty in a Single-Training Multi-Inference fashion. The key idea is to measure the output derivation from the original observation when the model parameters are randomly perturbed by noise. We provide theoretical analyses by leveraging the small Gaussian noise theory and demonstrate that our method favors a subset with large and diverse gradients. Despite its simplicity, our method outperforms the state-of-the-art active learning baselines in various tasks, including computer vision, natural language processing, and structural data analysis.

Dataset Pruning: Reducing Training Data by Examining Generalization Influence

The great success of deep learning heavily relies on increasingly larger training data, which comes at a price of huge computational and infrastructural costs. This poses crucial questions that, do all training data contribute to model's performance? How much does each individual training sample or a sub-training-set affect the model's generalization, and how to construct a smallest subset from the entire training data as a proxy training set without significantly sacrificing the model's performance? To answer these, we propose dataset pruning, an optimization-based sample selection method that can (1) examine the influence of removing a particular set of training samples on model's generalization ability with theoretical guarantee, and (2) construct a smallest subset of training data that yields strictly constrained generalization gap. The empirically observed generalization gap of dataset pruning is substantially consistent with our theoretical expectations. Furthermore, the proposed method prunes 40% training examples on the CIFAR-10 dataset, halves the convergence time with only 1.3% test accuracy decrease, which is superior to previous score-based sample selection methods.

Sparse Local Patch Transformer for Robust Face Alignment and Landmarks Inherent Relation Learning

Heatmap regression methods have dominated face alignment area in recent years while they ignore the inherent relation between different landmarks. In this paper, we propose a Sparse Local Patch Transformer (SLPT) for learning the inherent relation. The SLPT generates the representation of each single landmark from a local patch and aggregates them by an adaptive inherent relation based on the attention mechanism. The subpixel coordinate of each landmark is predicted independently based on the aggregated feature. Moreover, a coarse-to-fine framework is further introduced to incorporate with the SLPT, which enables the initial landmarks to gradually converge to the target facial landmarks using fine-grained features from dynamically resized local patches. Extensive experiments carried out on three popular benchmarks, including WFLW, 300W and COFW, demonstrate that the proposed method works at the state-of-the-art level with much less computational complexity by learning the inherent relation between facial landmarks. The code is available at the project website.

SHREC 2021: Classification in cryo-electron tomograms

Cryo-electron tomography (cryo-ET) is an imaging technique that allows three-dimensional visualization of macro-molecular assemblies under near-native conditions. Cryo-ET comes with a number of challenges, mainly low signal-to-noise and inability to obtain images from all angles. Computational methods are key to analyze cryo-electron tomograms. To promote innovation in computational methods, we generate a novel simulated dataset to benchmark different methods of localization and classification of biological macromolecules in tomograms. Our publicly available dataset contains ten tomographic reconstructions of simulated cell-like volumes. Each volume contains twelve different types of complexes, varying in size, function and structure. In this paper, we have evaluated seven different methods of finding and classifying proteins. Seven research groups present results obtained with learning-based methods and trained on the simulated dataset, as well as a baseline template matching (TM), a traditional method widely used in cryo-ET research. We show that learning-based approaches can achieve notably better localization and classification performance than TM. We also experimentally confirm that there is a negative relationship between particle size and performance for all methods.

Color Space-based HoVer-Net for Nuclei Instance Segmentation and Classification

Nuclei segmentation and classification is the first and most crucial step that is utilized for many different microscopy medical analysis applications. However, it suffers from many issues such as the segmentation of small objects, imbalance, and fine-grained differences between types of nuclei. In this paper, multiple different contributions were done tackling these problems present. Firstly, the recently released "ConvNeXt" was used as the encoder for HoVer-Net model since it leverages the key components of transformers that make them perform well. Secondly, to enhance the visual differences between nuclei, a multi-channel color space-based approach is used to aid the model in extracting distinguishing features. Thirdly, Unified Focal loss (UFL) was used to tackle the background-foreground imbalance. Finally, Sharpness-Aware Minimization (SAM) was used to ensure generalizability of the model. Overall, we were able to outperform the current state-of-the-art (SOTA), HoVer-Net, on the preliminary test set of the CoNiC Challenge 2022 by 12.489% mPQ+.

Distribution-aware Margin Calibration for Semantic Segmentation in Images

The Jaccard index, also known as Intersection-over-Union (IoU), is one of the most critical evaluation metrics in image semantic segmentation. However, direct optimization of IoU score is very difficult because the learning objective is neither differentiable nor decomposable. Although some algorithms have been proposed to optimize its surrogates, there is no guarantee provided for the generalization ability. In this paper, we propose a margin calibration method, which can be directly used as a learning objective, for an improved generalization of IoU over the data-distribution, underpinned by a rigid lower bound. This scheme theoretically ensures a better segmentation performance in terms of IoU score. We evaluated the effectiveness of the proposed margin calibration method on seven image datasets, showing substantial improvements in IoU score over other learning objectives using deep segmentation models.

Boosting Active Learning via Improving Test Performance

Central to active learning (AL) is what data should be selected for annotation. Existing works attempt to select highly uncertain or informative data for annotation. Nevertheless, it remains unclear how selected data impacts the test performance of the task model used in AL. In this work, we explore such an impact by theoretically proving that selecting unlabeled data of higher gradient norm leads to a lower upper bound of test loss, resulting in a better test performance. However, due to the lack of label information, directly computing gradient norm for unlabeled data is infeasible. To address this challenge, we propose two schemes, namely expected-gradnorm and entropy-gradnorm. The former computes the gradient norm by constructing an expected empirical loss while the latter constructs an unsupervised loss with entropy. Furthermore, we integrate the two schemes in a universal AL framework. We evaluate our method on classical image classification and semantic segmentation tasks. To demonstrate its competency in domain applications and its robustness to noise, we also validate our method on a cellular imaging analysis task, namely cryo-Electron Tomography subtomogram classification. Results demonstrate that our method achieves superior performance against the state-of-the-art. Our source code is available at https://github.com/xulabs/aitom

Cryo-shift: Reducing domain shift in cryo-electron subtomograms with unsupervised domain adaptation and randomization

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 to real experimental data will cause the trained models to perform poorly in predicting classes on real subtomograms. 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.

Objects in Semantic Topology

A more realistic object detection paradigm, Open-World Object Detection, has arisen increasing research interests in the community recently. A qualified open-world object detector can not only identify objects of known categories, but also discover unknown objects, and incrementally learn to categorize them when their annotations progressively arrive. Previous works rely on independent modules to recognize unknown categories and perform incremental learning, respectively. In this paper, we provide a unified perspective: Semantic Topology. During the life-long learning of an open-world object detector, all object instances from the same category are assigned to their corresponding pre-defined node in the semantic topology, including the `unknown' category. This constraint builds up discriminative feature representations and consistent relationships among objects, thus enabling the detector to distinguish unknown objects out of the known categories, as well as making learned features of known objects undistorted when learning new categories incrementally. Extensive experiments demonstrate that semantic topology, either randomly-generated or derived from a well-trained language model, could outperform the current state-of-the-art open-world object detectors by a large margin, e.g., the absolute open-set error is reduced from 7832 to 2546, exhibiting the inherent superiority of semantic topology on open-world object detection.