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Register a new userRobust Nucleus Detection with Partially Labeled Exemplars
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Quantitative analysis of cell nuclei in microscopic images is an essential yet challenging source of biological and pathological information. The major challenge is accurate detection and segmentation of densely packed nuclei in images acquired under a variety of conditions. Mask R-CNN-based methods have achieved state-of-the-art nucleus segmentation. However, the current pipeline requires fully annotated training images, which are time consuming to create and sometimes noisy. Importantly, nuclei often appear similar within the same image. This similarity could be utilized to segment nuclei with only partially labeled training examples. We propose a simple yet effective region-proposal module for the current Mask R-CNN pipeline to perform few-exemplar learning. To capture the similarities between unlabeled regions and labeled nuclei, we apply decomposed self-attention to learned features. On the self-attention map, we observe strong activation at the centers and edges of all nuclei, including unlabeled nuclei. On this basis, our region-proposal module propagates partial annotations to the whole image and proposes effective bounding boxes for the bounding box-regression and binary mask-generation modules. Our method effectively learns from unlabeled regions thereby improving detection performance. We test our method with various nuclear images. When trained with only 1/4 of the nuclei annotated, our approach retains a detection accuracy comparable to that from training with fully annotated data. Moreover, our method can serve as a bootstrapping step to create full annotations of datasets, iteratively generating and correcting annotations until a predetermined coverage and accuracy are reached. The source code is available at https://github.com/feng-lab/nuclei.
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In many applications labeled data is not readily available, and needs to be collected via pain-staking human supervision. We propose a rule-exemplar method for collecting human supervision to combine the efficiency of rules with the quality of instance labels. The supervision is coupled such that it is both natural for humans and synergistic for learning. We propose a training algorithm that jointly denoises rules via latent coverage variables, and trains the model through a soft implication loss over the coverage and label variables. The denoised rules and trained model are used jointly for inference. Empirical evaluation on five different tasks shows that (1) our algorithm is more accurate than several existing methods of learning from a mix of clean and noisy supervision, and (2) the coupled rule-exemplar supervision is effective in denoising rules.
Facial landmark detection aims to localize the anatomically defined points of human faces. In this paper, we study facial landmark detection from partially labeled facial images. A typical approach is to (1) train a detector on the labeled images; (2) generate new training samples using this detectors prediction as pseudo labels of unlabeled images; (3) retrain the detector on the labeled samples and partial pseudo labeled samples. In this way, the detector can learn from both labeled and unlabeled data to become robust. In this paper, we propose an interaction mechanism between a teacher and two students to generate more reliable pseudo labels for unlabeled data, which are beneficial to semi-supervised facial landmark detection. Specifically, the two students are instantiated as dual detectors. The teacher learns to judge the quality of the pseudo labels generated by the students and filter out unqualified samples before the retraining stage. In this way, the student detectors get feedback from their teacher and are retrained by premium data generated by itself. Since the two students are trained by different samples, a combination of their predictions will be more robust as the final prediction compared to either prediction. Extensive experiments on 300-W and AFLW benchmarks show that the interactions between teacher and students contribute to better utilization of the unlabeled data and achieves state-of-the-art performance.
We apply the network Lasso to classify partially labeled data points which are characterized by high-dimensional feature vectors. In order to learn an accurate classifier from limited amounts of labeled data, we borrow statistical strength, via an intrinsic network structure, across the dataset. The resulting logistic network Lasso amounts to a regularized empirical risk minimization problem using the total variation of a classifier as a regularizer. This minimization problem is a non-smooth convex optimization problem which we solve using a primal-dual splitting method. This method is appealing for big data applications as it can be implemented as a highly scalable message passing algorithm.
Motivation: Capillary electrophoresis (CE) of nucleic acids is a workhorse technology underlying high-throughput genome analysis and large-scale chemical mapping for nucleic acid structural inference. Despite the wide availability of CE-based instruments, there remain challenges in leveraging their full power for quantitative analysis of RNA and DNA structure, thermodynamics, and kinetics. In particular, the slow rate and poor automation of available analysis tools have bottlenecked a new generation of studies involving hundreds of CE profiles per experiment. Results: We propose a computational method called high-throughput robust analysis for capillary electrophoresis (HiTRACE) to automate the key tasks in large-scale nucleic acid CE analysis, including the profile alignment that has heretofore been a rate-limiting step in the highest throughput experiments. We illustrate the application of HiTRACE on thirteen data sets representing 4 different RNAs, three chemical modification strategies, and up to 480 single mutant variants; the largest data sets each include 87,360 bands. By applying a series of robust dynamic programming algorithms, HiTRACE outperforms prior tools in terms of alignment and fitting quality, as assessed by measures including the correlation between quantified band intensities between replicate data sets. Furthermore, while the smallest of these data sets required 7 to 10 hours of manual intervention using prior approaches, HiTRACE quantitation of even the largest data sets herein was achieved in 3 to 12 minutes. The HiTRACE method therefore resolves a critical barrier to the efficient and accurate analysis of nucleic acid structure in experiments involving tens of thousands of electrophoretic bands.
Attribute reduction is one of the most important research topics in the theory of rough sets, and many rough sets-based attribute reduction methods have thus been presented. However, most of them are specifically designed for dealing with either labeled data or unlabeled data, while many real-world applications come in the form of partial supervision. In this paper, we propose a rough sets-based semi-supervised attribute reduction method for partially labeled data. Particularly, with the aid of prior class distribution information about data, we first develop a simple yet effective strategy to produce the proxy labels for unlabeled data. Then the concept of information granularity is integrated into the information-theoretic measure, based on which, a novel granular conditional entropy measure is proposed, and its monotonicity is proved in theory. Furthermore, a fast heuristic algorithm is provided to generate the optimal reduct of partially labeled data, which could accelerate the process of attribute reduction by removing irrelevant examples and excluding redundant attributes simultaneously. Extensive experiments conducted on UCI data sets demonstrate that the proposed semi-supervised attribute reduction method is promising and even compares favourably with the supervised methods on labeled data and unlabeled data with true labels in terms of classification performance.
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