batch selection
Generative Multi-Objective Bayesian Optimization with Scalable Batch Evaluations for Sample-Efficient De Novo Molecular Design
Muthyala, Madhav R., Sorourifar, Farshud, Tan, Tianhong, Peng, You, Paulson, Joel A.
Designing molecules that must satisfy multiple, often conflicting objectives is a central challenge in molecular discovery. The enormous size of chemical space and the cost of high-fidelity simulations have driven the development of machine learning-guided strategies for accelerating design with limited data. Among these, Bayesian optimization (BO) offers a principled framework for sample-efficient search, while generative models provide a mechanism to propose novel, diverse candidates beyond fixed libraries. However, existing methods that couple the two often rely on continuous latent spaces, which introduces both architectural entanglement and scalability challenges. This work introduces an alternative, modular "generate-then-optimize" framework for de novo multi-objective molecular design/discovery. At each iteration, a generative model is used to construct a large, diverse pool of candidate molecules, after which a novel acquisition function, qPMHI (multi-point Probability of Maximum Hypervolume Improvement), is used to optimally select a batch of candidates most likely to induce the largest Pareto front expansion. The key insight is that qPMHI decomposes additively, enabling exact, scalable batch selection via only simple ranking of probabilities that can be easily estimated with Monte Carlo sampling. We benchmark the framework against state-of-the-art latent-space and discrete molecular optimization methods, demonstrating significant improvements across synthetic benchmarks and application-driven tasks. Specifically, in a case study related to sustainable energy storage, we show that our approach quickly uncovers novel, diverse, and high-performing organic (quinone-based) cathode materials for aqueous redox flow battery applications.
Instance-wise Supervision-level Optimization in Active Learning
Matsuo, Shinnosuke, Togashi, Riku, Bise, Ryoma, Uchida, Seiichi, Nomura, Masahiro
For classification tasks, a weak supervision approach is often designed to just attach rough Active learning (AL) is a label-efficient machine learning class labels to individual instances. For example, instead paradigm that focuses on selectively annotating high-value of attaching the exact class label "song sparrow" or "house instances to maximize learning efficiency. Its effectiveness sparrow" to an image instance, annotators can attach a can be further enhanced by incorporating weak supervision, rough class label "sparrows." This approach drastically reduces which uses rough yet cost-effective annotations instead annotation costs (budgets) because the fee paid to a of exact (i.e., full) but expensive annotations. We introduce non-expert annotator, who can only assign rough class labels a novel AL framework, Instance-wise Supervision-rather than exact ones via a crowdsourcing service, is Level Optimization (ISO), which not only selects the instances lower than that of an expert annotator. Hereafter, we call to annotate but also determines their optimal annotation rough classes as superclasses; therefore, "sparrows" is a superclass level within a fixed annotation budget.
Multi-Label Adaptive Batch Selection by Highlighting Hard and Imbalanced Samples
Zhou, Ao, Liu, Bin, Wang, Jin, Tsoumakas, Grigorios
Deep neural network models have demonstrated their effectiveness in classifying multi-label data from various domains. Typically, they employ a training mode that combines mini-batches with optimizers, where each sample is randomly selected with equal probability when constructing mini-batches. However, the intrinsic class imbalance in multi-label data may bias the model towards majority labels, since samples relevant to minority labels may be underrepresented in each mini-batch. Meanwhile, during the training process, we observe that instances associated with minority labels tend to induce greater losses. Existing heuristic batch selection methods, such as priority selection of samples with high contribution to the objective function, i.e., samples with high loss, have been proven to accelerate convergence while reducing the loss and test error in single-label data. However, batch selection methods have not yet been applied and validated in multi-label data. In this study, we introduce a simple yet effective adaptive batch selection algorithm tailored to multi-label deep learning models. It adaptively selects each batch by prioritizing hard samples related to minority labels. A variant of our method also takes informative label correlations into consideration. Comprehensive experiments combining five multi-label deep learning models on thirteen benchmark datasets show that our method converges faster and performs better than random batch selection.
Surprising Instabilities in Training Deep Networks and a Theoretical Analysis
Sun, Yuxin, Lao, Dong, Sundaramoorthi, Ganesh, Yezzi, Anthony
We discover restrained numerical instabilities in current training practices of deep networks with stochastic gradient descent (SGD). We show numerical error (on the order of the smallest floating point bit) induced from floating point arithmetic in training deep nets can be amplified significantly and result in significant test accuracy variance, comparable to the test accuracy variance due to stochasticity in SGD. We show how this is likely traced to instabilities of the optimization dynamics that are restrained, i.e., localized over iterations and regions of the weight tensor space. We do this by presenting a theoretical framework using numerical analysis of partial differential equations (PDE), and analyzing the gradient descent PDE of convolutional neural networks (CNNs). We show that it is stable only under certain conditions on the learning rate and weight decay. We show that rather than blowing up when the conditions are violated, the instability can be restrained. We show this is a consequence of the non-linear PDE associated with the gradient descent of the CNN, whose local linearization changes when over-driving the step size of the discretization, resulting in a stabilizing effect. We link restrained instabilities to the recently discovered Edge of Stability (EoS) phenomena, in which the stable step size predicted by classical theory is exceeded while continuing to optimize the loss and still converging. Because restrained instabilities occur at the EoS, our theory provides new predictions about the EoS, in particular, the role of regularization and the dependence on the network complexity.
FairBatch: Batch Selection for Model Fairness
Roh, Yuji, Lee, Kangwook, Whang, Steven Euijong, Suh, Changho
Training a fair machine learning model is essential to prevent demographic disparity. Existing techniques for improving model fairness require broad changes in either data preprocessing or model training, rendering themselves difficult-to-adopt for potentially already complex machine learning systems. We address this problem via the lens of bilevel optimization. While keeping the standard training algorithm as an inner optimizer, we incorporate an outer optimizer so as to equip the inner problem with an additional functionality: Adaptively selecting minibatch sizes for the purpose of improving model fairness. Our batch selection algorithm, which we call FairBatch, implements this optimization and supports prominent fairness measures: equal opportunity, equalized odds, and demographic parity. FairBatch comes with a significant implementation benefit -- it does not require any modification to data preprocessing or model training. For instance, a single-line change of PyTorch code for replacing batch selection part of model training suffices to employ FairBatch. Our experiments conducted both on synthetic and benchmark real data demonstrate that FairBatch can provide such functionalities while achieving comparable (or even greater) performances against the state of the arts. Furthermore, FairBatch can readily improve fairness of any pre-trained model simply via fine-tuning. It is also compatible with existing batch selection techniques intended for different purposes, such as faster convergence, thus gracefully achieving multiple purposes.
Not Your Grandfathers Test Set: Reducing Labeling Effort for Testing
Taskazan, Begum, Navratil, Jiri, Arnold, Matthew, Murthi, Anupama, Venkataraman, Ganesh, Elder, Benjamin
Building and maintaining high-quality test sets remains a laborious and expensive task. As a result, test sets in the real world are often not properly kept up to date and drift from the production traffic they are supposed to represent. The frequency and severity of this drift raises serious concerns over the value of manually labeled test sets in the QA process. This paper proposes a simple but effective technique that drastically reduces the effort needed to construct and maintain a high-quality test set (reducing labeling effort by 80-100% across a range of practical scenarios). This result encourages a fundamental rethinking of the testing process by both practitioners, who can use these techniques immediately to improve their testing, and researchers who can help address many of the open questions raised by this new approach.
Committee-Based Sample Selection for Probabilistic Classifiers
Argamon-Engelson, S., Dagan, I.
In many real-world learning tasks, it is expensive to acquire a sufficient number of labeled examples for training. This paper investigates methods for reducing annotation cost by `sample selection'. In this approach, during training the learning program examines many unlabeled examples and selects for labeling only those that are most informative at each stage. This avoids redundantly labeling examples that contribute little new information. Our work follows on previous research on Query By Committee, extending the committee-based paradigm to the context of probabilistic classification. We describe a family of empirical methods for committee-based sample selection in probabilistic classification models, which evaluate the informativeness of an example by measuring the degree of disagreement between several model variants. These variants (the committee) are drawn randomly from a probability distribution conditioned by the training set labeled so far. The method was applied to the real-world natural language processing task of stochastic part-of-speech tagging. We find that all variants of the method achieve a significant reduction in annotation cost, although their computational efficiency differs. In particular, the simplest variant, a two member committee with no parameters to tune, gives excellent results. We also show that sample selection yields a significant reduction in the size of the model used by the tagger.