Advanced Persistent Threats (APTs) pose a significant challenge in cybersecurity due to their stealthy and long-term nature. Modern supervised learning methods require extensive labeled data, which is often scarce in real-world cybersecurity environments. In this paper, we propose an innovative approach that leverages AutoEncoders for unsupervised anomaly detection, augmented by active learning to iteratively improve the detection of APT anomalies. By selectively querying an oracle for labels on uncertain or ambiguous samples, we minimize labeling costs while improving detection rates, enabling the model to improve its detection accuracy with minimal data while reducing the need for extensive manual labeling. We provide a detailed formulation of the proposed Attention Adversarial Dual AutoEncoder-based anomaly detection framework and show how the active learning loop iteratively enhances the model. The framework is evaluated on real-world imbalanced provenance trace databases produced by the DARPA Transparent Computing program, where APT-like attacks constitute as little as 0.004\% of the data. The datasets span multiple operating systems, including Android, Linux, BSD, and Windows, and cover two attack scenarios. The results have shown significant improvements in detection rates during active learning and better performance compared to other existing approaches.

Machine-learned coarse-grained (CG) potentials are fast, but degrade over time when simulations reach under-sampled bio-molecular conformations, and generating widespread all-atom (AA) data to combat this is computationally infeasible. We propose a novel active learning (AL) framework for CG neural network potentials in molecular dynamics (MD). Building on the CGSchNet model, our method employs root mean squared deviation (RMSD)-based frame selection from MD simulations in order to generate data on-the-fly by querying an oracle during the training of a neural network potential. This framework preserves CG-level efficiency while correcting the model at precise, RMSD-identified coverage gaps. By training CGSchNet, a coarse-grained neural network potential, we empirically show that our framework explores previously unseen configurations and trains the model on unexplored regions of conformational space. Our active learning framework enables a CGSchNet model trained on the Chignolin protein to achieve a 33.05\% improvement in the Wasserstein-1 (W1) metric in Time-lagged Independent Component Analysis (TICA) space on an in-house benchmark suite.

In this paper we present active learning algorithms in the context of structured prediction problems. To reduce the amount of labeling necessary to learn good models, our algorithms operate with weakly labeled data and we query additional examples based on entropies of local marginals, which are a good surrogate for uncertainty. We demonstrate the effectiveness of our approach in the task of 3D layout prediction from single images, and show that good models are learned when labeling only a handful of random variables. In particular, the same performance as using the full training set can be obtained while only labeling 10% of the random variables.

Fine-tuning the pre-trained model with active learning holds promise for reducing annotation costs. However, this combination introduces significant computational costs, particularly with the growing scale of pre-trained models. Recent research has proposed proxy-based active learning, which pre-computes features to reduce computational costs. Yet, this approach often incurs a significant loss in active learning performance, which may even outweigh the computational cost savings. In this paper, we argue the performance drop stems not only from pre-computed features' inability to distinguish between categories of labeled samples, resulting in the selection of redundant samples but also from the tendency to compromise valuable pre-trained information when fine-tuning with samples selected through the proxy model. To address this issue, we propose a novel method called aligned selection via proxy to update pre-computed features while selecting a proper training method to inherit valuable pre-training information. Extensive experiments validate that our method significantly improves the total cost of efficient active learning while maintaining computational efficiency.

Generating a data set that is representative of the accessible configuration space of a molecular system is crucial for the robustness of machine learned interatomic potentials (MLIP). However, the complexity of molecular systems, characterized by intricate potential energy surfaces (PESs) with numerous local minima and energy barriers, presents a significant challenge. Traditional methods of data generation, such as random sampling or exhaustive exploration, are either intractable or may not capture rare, but highly informative configurations. In this study, we propose a method that leverages uncertainty as the collective variable (CV) to guide the acquisition of chemically-relevant data points, focusing on regions of the configuration space where ML model predictions are most uncertain. This approach employs a Gaussian Mixture Model-based uncertainty metric from a single model as the CV for biased molecular dynamics simulations. The effectiveness of our approach in overcoming energy barriers and exploring unseen energy minima, thereby enhancing the data set in an active learning framework, is demonstrated on the alanine dipeptide benchmark system.

Entity matching, a core data integration problem, is the task of deciding whether two data tuples refer to the same real-world entity. Recent advances in deep learning methods, using pre-trained language models, were proposed for resolving entity matching. Although demonstrating unprecedented results, these solutions suffer from a major drawback as they require large amounts of labeled data for training, and, as such, are inadequate to be applied to low resource entity matching problems. To overcome the challenge of obtaining sufficient labeled data we offer a new active learning approach, focusing on a selection mechanism that exploits unique properties of entity matching. We argue that a distributed representation of a tuple pair indicates its informativeness when considered among other pairs. This is used consequently in our approach that iteratively utilizes space-aware considerations. Bringing it all together, we treat the low resource entity matching problem as a Battleship game, hunting indicative samples, focusing on positive ones, through awareness of the latent space along with careful planning of next sampling iterations. An extensive experimental analysis shows that the proposed algorithm outperforms state-of-the-art active learning solutions to low resource entity matching, and although using less samples, can be as successful as state-of-the-art fully trained known algorithms.

Bayesian optimization offers a sample-efficient framework for navigating the exploration-exploitation trade-off in the vast design space of biological sequences. Whereas it is possible to optimize the various properties of interest jointly using a multi-objective acquisition function, such as the expected hypervolume improvement (EHVI), this approach does not account for objectives with a hierarchical dependency structure. We consider a common use case where some regions of the Pareto frontier are prioritized over others according to a specified $\textit{partial ordering}$ in the objectives. For instance, when designing antibodies, we would like to maximize the binding affinity to a target antigen only if it can be expressed in live cell culture -- modeling the experimental dependency in which affinity can only be measured for antibodies that can be expressed and thus produced in viable quantities. In general, we may want to confer a partial ordering to the properties such that each property is optimized conditioned on its parent properties satisfying some feasibility condition. To this end, we present PropertyDAG, a framework that operates on top of the traditional multi-objective BO to impose this desired ordering on the objectives, e.g. expression $\rightarrow$ affinity. We demonstrate its performance over multiple simulated active learning iterations on a penicillin production task, toy numerical problem, and a real-world antibody design task.

Semantic segmentation neural networks require pixel-level annotations in large quantities to achieve a good performance. In the medical domain, such annotations are expensive, because they are time-consuming and require expert knowledge. Active learning optimizes the annotation effort by devising strategies to select cases for labeling that are most informative to the model. In this work, we propose an uncertainty slice sampling (USS) strategy for semantic segmentation of 3D medical volumes that selects 2D image slices for annotation and compare it with various other strategies. We demonstrate the efficiency of USS on a CT liver segmentation task using multi-site data. After five iterations, the training data resulting from USS consisted of 2410 slices (4% of all slices in the data pool) compared to 8121 (13%), 8641 (14%), and 3730 (6%) for uncertainty volume (UVS), random volume (RVS), and random slice (RSS) sampling, respectively. Despite being trained on the smallest amount of data, the model based on the USS strategy evaluated on 234 test volumes significantly outperformed models trained according to other strategies and achieved a mean Dice index of 0.964, a relative volume error of 4.2%, a mean surface distance of 1.35 mm, and a Hausdorff distance of 23.4 mm. This was only slightly inferior to 0.967, 3.8%, 1.18 mm, and 22.9 mm achieved by a model trained on all available data, but the robustness analysis using the 5th percentile of Dice and the 95th percentile of the remaining metrics demonstrated that USS resulted not only in the most robust model compared to other sampling schemes, but also outperformed the model trained on all data according to Dice (0.946 vs. 0.945) and mean surface distance (1.92 mm vs. 2.03 mm).

This paper introduces supervised contrastive active learning (SCAL) by leveraging the contrastive loss for active learning in a supervised setting. We propose efficient query strategies in active learning to select unbiased and informative data samples of diverse feature representations. We demonstrate our proposed method reduces sampling bias, achieves state-of-the-art accuracy and model calibration in an active learning setup with the query computation 11x faster than CoreSet and 26x faster than Bayesian active learning by disagreement. Our method yields well-calibrated models even with imbalanced datasets. We also evaluate robustness to dataset shift and out-of-distribution in active learning setup and demonstrate our proposed SCAL method outperforms high performing compute-intensive methods by a bigger margin (average 8.9% higher AUROC for out-of-distribution detection and average 7.2% lower ECE under dataset shift).

The availability of labelled data is one of the main limitations in machine learning. We can alleviate this using weak supervision: a framework that uses expert-defined rules $\boldsymbol{\lambda}$ to estimate probabilistic labels $p(y|\boldsymbol{\lambda})$ for the entire data set. These rules, however, are dependent on what experts know about the problem, and hence may be inaccurate or may fail to capture important parts of the problem-space. To mitigate this, we propose Active WeaSuL: an approach that incorporates active learning into weak supervision. In Active WeaSuL, experts do not only define rules, but they also iteratively provide the true label for a small set of points where the weak supervision model is most likely to be mistaken, which are then used to better estimate the probabilistic labels. In this way, the weak labels provide a warm start, which active learning then improves upon. We make two contributions: 1) a modification of the weak supervision loss function, such that the expert-labelled data inform and improve the combination of weak labels; and 2) the maxKL divergence sampling strategy, which determines for which data points expert labelling is most beneficial. Our experiments show that when the budget for labelling data is limited (e.g. $\leq 60$ data points), Active WeaSuL outperforms weak supervision, active learning, and competing strategies, with only a handful of labelled data points. This makes Active WeaSuL ideal for situations where obtaining labelled data is difficult.