Spatial transcriptomics (ST) is a novel technology that enables the observation of gene expression at the resolution of individual spots within pathological tissues. ST quantifies the expression of tens of thousands of genes in a tissue section; however, heavy observational noise is often introduced during measurement. In prior studies, to ensure meaningful assessment, both training and evaluation have been restricted to only a small subset of highly variable genes, and genes outside this subset have also been excluded from the training process. However, since there are likely co-expression relationships between genes, low-expression genes may still contribute to the estimation of the evaluation target. In this paper, we propose Auxiliary Gene Learning (AGL) that utilizes the benefit of the ignored genes by reformulating their expression estimation as auxiliary tasks and training them jointly with the primary tasks. To effectively leverage auxiliary genes, we must select a subset of auxiliary genes that positively influence the prediction of the target genes. However, this is a challenging optimization problem due to the vast number of possible combinations. To overcome this challenge, we propose Prior-Knowledge-Based Differentiable Top-k Gene Selection via Bi-level Optimization (DkGSB), a method that ranks genes by leveraging prior knowledge and relaxes the combinatorial selection problem into a differentiable top-k selection problem. The experiments confirm the effectiveness of incorporating auxiliary genes and show that the proposed method outperforms conventional auxiliary task learning approaches.

Active learning (AL) is a label-efficient machine learning paradigm that focuses on selectively annotating high-value instances to maximize learning efficiency. Its effectiveness can be further enhanced by incorporating weak supervision, which uses rough yet cost-effective annotations instead of exact (i.e., full) but expensive annotations. We introduce a novel AL framework, Instance-wise Supervision-Level Optimization (ISO), which not only selects the instances to annotate but also determines their optimal annotation level within a fixed annotation budget. Its optimization criterion leverages the value-to-cost ratio (VCR) of each instance while ensuring diversity among the selected instances. In classification experiments, ISO consistently outperforms traditional AL methods and surpasses a state-of-the-art AL approach that combines full and weak supervision, achieving higher accuracy at a lower overall cost. This code is available at https://github.com/matsuo-shinnosuke/ISOAL.

Domain shift is a significant challenge in machine learning, particularly in medical applications where data distributions differ across institutions due to variations in data collection practices, equipment, and procedures. This can degrade performance when models trained on source domain data are applied to the target domain. Domain adaptation methods have been widely studied to address this issue, but most struggle when class proportions between the source and target domains differ. In this paper, we propose a weakly-supervised domain adaptation method that leverages class proportion information from the target domain, which is often accessible in medical datasets through prior knowledge or statistical reports. Our method assigns pseudo-labels to the unlabeled target data based on class proportion (called proportion-constrained pseudo-labeling), improving performance without the need for additional annotations. Experiments on two endoscopic datasets demonstrate that our method outperforms semi-supervised domain adaptation techniques, even when 5% of the target domain is labeled. Additionally, the experimental results with noisy proportion labels highlight the robustness of our method, further demonstrating its effectiveness in real-world application scenarios.

This paper tackles the problem of the worst-class error rate, instead of the standard error rate averaged over all classes. For example, a three-class classification task with class-wise error rates of 10%, 10%, and 40% has a worst-class error rate of 40%, whereas the average is 20% under the class-balanced condition. The worst-class error is important in many applications. For example, in a medical image classification task, it would not be acceptable for the malignant tumor class to have a 40% error rate, while the benign and healthy classes have a 10% error rates. To avoid overfitting in worst-class error minimization using Deep Neural Networks (DNNs), we design a problem formulation for bounding the worst-class error instead of achieving zero worst-class error. Moreover, to correctly bound the worst-class error, we propose a boosting approach which ensembles DNNs. We give training and generalization worst-class-error bound. Experimental results show that the algorithm lowers worst-class test error rates while avoiding overfitting to the training set.

Learning from label proportions (LLP) is a kind of weakly supervised learning that trains an instance-level classifier from label proportions of bags, which consist of sets of instances without using instance labels. A challenge in LLP arises when the number of instances in a bag (bag size) is numerous, making the traditional LLP methods difficult due to GPU memory limitations. This study aims to develop an LLP method capable of learning from bags with large sizes. In our method, smaller bags (mini-bags) are generated by sampling instances from large-sized bags (original bags), and these mini-bags are used in place of the original bags. However, the proportion of a mini-bag is unknown and differs from that of the original bag, leading to overfitting. To address this issue, we propose a perturbation method for the proportion labels of sampled mini-bags to mitigate overfitting to noisy label proportions. This perturbation is added based on the multivariate hypergeometric distribution, which is statistically modeled. Additionally, loss weighting is implemented to reduce the negative impact of proportions sampled from the tail of the distribution. Experimental results demonstrate that the proportion label perturbation and loss weighting achieve classification accuracy comparable to that obtained without sampling. Our codes are available at https://github.com/stainlessnight/LLP-LargeBags.

The paper proposes a novel problem in multi-class Multiple-Instance Learning (MIL) called Learning from the Majority Label (LML). In LML, the majority class of instances in a bag is assigned as the bag’s label. LML aims to classify instances using bag-level majority classes. This problem is valuable in various applications. Existing MIL methods are unsuitable for LML due to aggregating confidences, which may lead to inconsistency between the bag-level label and the label obtained by counting the number of instances for each class. This may lead to incorrect instance-level classification. We propose a counting network trained to produce the bag-level majority labels estimated by counting the number of instances for each class. This led to the consistency of the majority class between the network outputs and one obtained by counting the number of instances. Experimental results show that our counting network outperforms conventional MIL methods on four datasets1.

This paper proposes a novel and efficient method for Learning from Label Proportions (LLP), whose goal is to train a classifier only by using the class label proportions of instance sets, called bags. We propose a novel LLP method based on an online pseudo-labeling method with regret minimization. As opposed to the previous LLP methods, the proposed method effectively works even if the bag sizes are large. We demonstrate the effectiveness of the proposed method using some benchmark datasets.

Learning from label proportions (LLP) is a promising weakly supervised learning problem. In LLP, a set of instances (bag) has label proportions, but no instance-level labels are given. LLP aims to train an instance-level classifier by using the label proportions of the bag. In this paper, we propose a bag-level data augmentation method for LLP called MixBag, based on the key observation from our preliminary experiments; that the instance-level classification accuracy improves as the number of labeled bags increases even though the total number of instances is fixed. We also propose a confidence interval loss designed based on statistical theory to use the augmented bags effectively. To the best of our knowledge, this is the first attempt to propose bag-level data augmentation for LLP. The advantage of MixBag is that it can be applied to instance-level data augmentation techniques and any LLP method that uses the proportion loss. Experimental results demonstrate this advantage and the effectiveness of our method.

Data augmentation is a technique to improve the generalization ability of machine learning methods by increasing the size of the dataset. However, since every augmentation method is not equally effective for every dataset, you need to select an appropriate method carefully. We propose a neural network that dynamically selects the best combination of data augmentation methods using a Gating Network and a mutually beneficial feature consistency loss. The Gating Network is able to control how much of each data augmentation is used for the representation within the network. The feature consistency loss gives a constraint that augmented features from the same input pattern should be in similar. In the experiments, we demonstrate the effectiveness of the proposed method on the 12 largest time-series datasets from 2018 UCR Time Series Archive and reveal the relationships between the data augmentation methods through analysis of the proposed method.

Oftentimes, patterns can be represented through different modalities. For example, leaf data can be in the form of images or contours. Handwritten characters can also be either online or offline. To exploit this fact, we propose the use of self-augmentation and combine it with multi-modal feature embedding. In order to take advantage of the complementary information from the different modalities, the self-augmented multi-modal feature embedding employs a shared feature space. Through experimental results on classification with online handwriting and leaf images, we demonstrate that the proposed method can create effective embeddings.