Anomaly detection in large datasets is essential in astronomy and computer vision. However, due to a scarcity of labelled data, it is often infeasible to apply supervised methods to anomaly detection. We present AnomalyMatch, an anomaly detection framework combining the semi-supervised FixMatch algorithm using EfficientNet classifiers with active learning. AnomalyMatch is tailored for large-scale applications and integrated into the ESA Datalabs science platform. In this method, we treat anomaly detection as a binary classification problem and efficiently utilise limited labelled and abundant unlabelled images for training. We enable active learning via a user interface for verification of high-confidence anomalies and correction of false positives. Evaluations on the GalaxyMNIST astronomical dataset and the miniImageNet natural-image benchmark under severe class imbalance display strong performance. Starting from five to ten labelled anomalies, we achieve an average AUROC of 0.96 (miniImageNet) and 0.89 (GalaxyMNIST), with respective AUPRC of 0.82 and 0.77. After three active learning cycles, anomalies are ranked with 76% (miniImageNet) to 94% (GalaxyMNIST) precision in the top 1% of the highest-ranking images by score. We compare to the established Astronomaly software on selected 'odd' galaxies from the 'Galaxy Zoo - The Galaxy Challenge' dataset, achieving comparable performance with an average AUROC of 0.83. Our results underscore the exceptional utility and scalability of this approach for anomaly discovery, highlighting the value of specialised approaches for domains characterised by severe label scarcity.

Active learning aims to efficiently build a labeled training set by strategically selecting samples to query labels from annotators. In this sequential process, each sample acquisition influences subsequent selections, causing dependencies among samples in the labeled set. However, these dependencies are overlooked during the model parameter estimation stage when updating the model using Maximum Likelihood Estimation (MLE), a conventional method that assumes independent and identically distributed (i.i.d.) data. We propose Dependency-aware MLE (DMLE), which corrects MLE within the active learning framework by addressing sample dependencies typically neglected due to the i.i.d. assumption, ensuring consistency with active learning principles in the model parameter estimation process. This improved method achieves superior performance across multiple benchmark datasets, reaching higher performance in earlier cycles compared to conventional MLE. Specifically, we observe average accuracy improvements of 6\%, 8.6\%, and 10.5\% for $k=1$, $k=5$, and $k=10$ respectively, after collecting the first 100 samples, where entropy is the acquisition function and $k$ is the query batch size acquired at every active learning cycle.

Accurate prediction and optimization of protein-protein binding affinity is crucial for therapeutic antibody development. Although machine learning-based prediction methods $\Delta\Delta G$ are suitable for large-scale mutant screening, they struggle to predict the effects of multiple mutations for targets without existing binders. Energy function-based methods, though more accurate, are time consuming and not ideal for large-scale screening. To address this, we propose an active learning workflow that efficiently trains a deep learning model to learn energy functions for specific targets, combining the advantages of both approaches. Our method integrates the RDE-Network deep learning model with Rosetta's energy function-based Flex ddG to efficiently explore mutants. In a case study targeting HER2-binding Trastuzumab mutants, our approach significantly improved the screening performance over random selection and demonstrated the ability to identify mutants with better binding properties without experimental $\Delta\Delta G$ data. This workflow advances computational antibody design by combining machine learning, physics-based computations, and active learning to achieve more efficient antibody development.

Binding affinity optimization is crucial in early-stage drug discovery. While numerous machine learning methods exist for predicting ligand potency, their comparative efficacy remains unclear. This study evaluates the performance of classical tree-based models and advanced neural networks in protein-ligand binding affinity prediction. Our comprehensive benchmarking encompasses 2D models utilizing ligand-only RDKit embeddings and Large Language Model (LLM) ligand representations, as well as 3D neural networks incorporating bound protein-ligand conformations. We assess these models across multiple standard datasets, examining various predictive scenarios including classification, ranking, regression, and active learning. Results indicate that simpler models can surpass more complex ones in specific tasks, while 3D models leveraging structural information become increasingly competitive with larger training datasets containing compounds with labelled affinity data against multiple targets. Pre-trained 3D models, by incorporating protein pocket environments, demonstrate significant advantages in data-scarce scenarios for specific binding pockets. Additionally, LLM pretraining on 2D ligand data enhances complex model performance, providing versatile embeddings that outperform traditional RDKit features in computational efficiency. Finally, we show that combining 2D and 3D model strengths improves active learning outcomes beyond current state-of-the-art approaches. These findings offer valuable insights for optimizing machine learning strategies in drug discovery pipelines.

Obtaining annotations for complex computer vision tasks such as object detection is an expensive and time-intense endeavor involving a large number of human workers or expert opinions. Reducing the amount of annotations required while maintaining algorithm performance is, therefore, desirable for machine learning practitioners and has been successfully achieved by active learning algorithms. However, it is not merely the amount of annotations which influences model performance but also the annotation quality. In practice, the oracles that are queried for new annotations frequently contain significant amounts of noise. Therefore, cleansing procedures are oftentimes necessary to review and correct given labels. This process is subject to the same budget as the initial annotation itself since it requires human workers or even domain experts. Here, we propose a composite active learning framework including a label review module for deep object detection. We show that utilizing part of the annotation budget to correct the noisy annotations partially in the active dataset leads to early improvements in model performance, especially when coupled with uncertainty-based query strategies. The precision of the label error proposals has a significant influence on the measured effect of the label review. In our experiments we achieve improvements of up to 4.5 mAP points of object detection performance by incorporating label reviews at equal annotation budget.

Previous work optimizes traditional active learning (AL) processes with incremental neural network architecture search (Active-iNAS) based on data complexity change, which improves the accuracy and learning efficiency. However, Active-iNAS trains several models and selects the model with the best generalization performance for querying the subsequent samples after each active learning cycle. The independent training processes lead to an insufferable computational budget, which is significantly inefficient and limits search flexibility and final performance. To address this issue, we propose a novel active strategy with the method called structured variational inference (SVI) or structured neural depth search (SNDS) whereby we could use the gradient descent method in neural network depth search during AL processes. At the same time, we theoretically demonstrate that the current VI-based methods based on the mean-field assumption could lead to poor performance. We apply our strategy using three querying techniques and three datasets and show that our strategy outperforms current methods.

Active learning selects informative samples for annotation within budget, which has proven efficient recently on object detection. However, the widely used active detection benchmarks conduct image-level evaluation, which is unrealistic in human workload estimation and biased towards crowded images. Furthermore, existing methods still perform image-level annotation, but equally scoring all targets within the same image incurs waste of budget and redundant labels. Having revealed above problems and limitations, we introduce a box-level active detection framework that controls a box-based budget per cycle, prioritizes informative targets and avoids redundancy for fair comparison and efficient application. Under the proposed box-level setting, we devise a novel pipeline, namely Complementary Pseudo Active Strategy (ComPAS). It exploits both human annotations and the model intelligence in a complementary fashion: an efficient input-end committee queries labels for informative objects only; meantime well-learned targets are identified by the model and compensated with pseudo-labels. ComPAS consistently outperforms 10 competitors under 4 settings in a unified codebase. With supervision from labeled data only, it achieves 100% supervised performance of VOC0712 with merely 19% box annotations. On the COCO dataset, it yields up to 4.3% mAP improvement over the second-best method. ComPAS also supports training with the unlabeled pool, where it surpasses 90% COCO supervised performance with 85% label reduction. Our source code is publicly available at https://github.com/lyumengyao/blad.

While deep learning succeeds in a wide range of tasks, it highly depends on the massive collection of annotated data which is expensive and time-consuming. To lower the cost of data annotation, active learning has been proposed to interactively query an oracle to annotate a small proportion of informative samples in an unlabeled dataset. Inspired by the fact that the samples with higher loss are usually more informative to the model than the samples with lower loss, in this paper we present a novel deep active learning approach that queries the oracle for data annotation when the unlabeled sample is believed to incorporate high loss. The core of our approach is a measurement Temporal Output Discrepancy (TOD) that estimates the sample loss by evaluating the discrepancy of outputs given by models at different optimization steps. Our theoretical investigation shows that TOD lower-bounds the accumulated sample loss thus it can be used to select informative unlabeled samples. On basis of TOD, we further develop an effective unlabeled data sampling strategy as well as an unsupervised learning criterion for active learning. Due to the simplicity of TOD, our methods are efficient, flexible, and task-agnostic. Extensive experimental results demonstrate that our approach achieves superior performances than the state-of-the-art active learning methods on image classification and semantic segmentation tasks. In addition, we show that TOD can be utilized to select the best model of potentially the highest testing accuracy from a pool of candidate models.

Obtaining human per-pixel labels for semantic segmentation is incredibly laborious, often making labeled dataset construction prohibitively expensive. Here, we endeavor to overcome this problem with a novel algorithm that combines semi-supervised and active learning, resulting in the ability to train an effective semantic segmentation algorithm with significantly lesser labeled data. To do this, we extend the prior state-of-the-art S4AL algorithm by replacing its mean teacher approach for semi-supervised learning with a self-training approach that improves learning with noisy labels. We further boost the neural network's ability to query useful data by adding a contrastive learning head, which leads to better understanding of the objects in the scene, and hence, better queries for active learning. We evaluate our method on CamVid and CityScapes datasets, the de-facto standards for active learning for semantic segmentation. We achieve more than 95% of the network's performance on CamVid and CityScapes datasets, utilizing only 12.1% and 15.1% of the labeled data, respectively. We also benchmark our method across existing stand-alone semi-supervised learning methods on the CityScapes dataset and achieve superior performance without any bells or whistles.

Using deep learning, we now have the ability to create exceptionally good semantic segmentation systems; however, collecting the prerequisite pixel-wise annotations for training images remains expensive and time-consuming. Therefore, it would be ideal to minimize the number of human annotations needed when creating a new dataset. Here, we address this problem by proposing a novel algorithm that combines active learning and semi-supervised learning. Active learning is an approach for identifying the best unlabeled samples to annotate. While there has been work on active learning for segmentation, most methods require annotating all pixel objects in each image, rather than only the most informative regions. We argue that this is inefficient. Instead, our active learning approach aims to minimize the number of annotations per-image. Our method is enriched with semi-supervised learning, where we use pseudo labels generated with a teacher-student framework to identify image regions that help disambiguate confused classes. We also integrate mechanisms that enable better performance on imbalanced label distributions, which have not been studied previously for active learning in semantic segmentation. In experiments on the CamVid and CityScapes datasets, our method obtains over 95% of the network's performance on the full-training set using less than 17% of the training data, whereas the previous state of the art required 40% of the training data.