Cell Painting is a microscopy-based, high-content imaging assay that produces rich morphological profiles of cells and can support drug discovery by quantifying cellular responses to chemical perturbations. At scale, however, Cell Painting data is strongly affected by batch effects arising from differences in laboratories, instruments, and protocols, which can obscure biological signal. We present BALANS (Batch Alignment via Local Affinities and Subsampling), a scalable batch-correction method that aligns samples across batches by constructing a smoothed affinity matrix from pairwise distances. Given $n$ data points, BALANS builds a sparse affinity matrix $A \in \mathbb{R}^{n \times n}$ using two ideas. (i) For points $i$ and $j$, it sets a local scale using the distance from $i$ to its $k$-th nearest neighbor within the batch of $j$, then computes $A_{ij}$ via a Gaussian kernel calibrated by these batch-aware local scales. (ii) Rather than forming all $n^2$ entries, BALANS uses an adaptive sampling procedure that prioritizes rows with low cumulative neighbor coverage and retains only the strongest affinities per row, yielding a sparse but informative approximation of $A$. We prove that this sampling strategy is order-optimal in sample complexity and provides an approximation guarantee, and we show that BALANS runs in nearly linear time in $n$. Experiments on diverse real-world Cell Painting datasets and controlled large-scale synthetic benchmarks demonstrate that BALANS scales to large collections while improving runtime over native implementations of widely used batch-correction methods, without sacrificing correction quality.
We present K-Means Batch Bayesian Optimization (KMBBO), a novel batch sampling algorithm for Bayesian Optimization (BO). KMBBO uses unsupervised learning to efficiently estimate peaks of the model acquisition function. We show in empirical experiments that our method outperforms the current state-of-the-art batch allocation algorithms on a variety of test problems including tuning of algorithm hyper-parameters and a challenging drug discovery problem. In order to accommodate the real-world problem of high dimensional data, we propose a modification to KMBBO by combining it with compressed sens…
Mitsubishi Electric Research Laboratories（三菱电机研究实验室）
Physics-informed dynamical system models form critical components of digital twins of the built environment. These digital twins enable the design of energy-efficient infrastructure, but must be properly calibrated to accurately reflect system behavior for downstream prediction and analysis. Dynamical system models of modern buildings are typically described by a large number of parameters and incur significant computational expenditure during simulations. To handle large-scale calibration of digital twins without exorbitant simulations, we propose ANP-BBO: a scalable and parallelizable batch-…
It has been experimentally observed that distributed implementations of mini-batch stochastic gradient descent (SGD) algorithms exhibit speedup saturation and decaying generalization ability beyond a particular batch-size. In this work, we present an analysis hinting that high similarity between concurrently processed gradients may be a cause of this performance degradation. We introduce the notion of gradient diversity that measures the dissimilarity between concurrent gradient updates, and show its key role in the performance of mini-batch SGD. We prove that on problems with high gradient di…
It has been experimentally observed that the efficiency of distributed training with stochastic gradient (SGD) depends decisively on the batch size and -- in asynchronous implementations -- on the gradient staleness. Especially, it has been observed that the speedup saturates beyond a certain batch size and/or when the delays grow too large. We identify a data-dependent parameter that explains the speedup saturation in both these settings. Our comprehensive theoretical analysis, for strongly convex, convex and non-convex settings, unifies and generalized prior work directions that often focuse…
Tokyo Institute of Technology（东京工业大学）；AIST-Tokyo Tech RWBC-OIL, AIST（产业技术综合研究所-东京工业大学计算生物学与复杂系统研究中心，产业技术综合研究所）；Institute for Infocomm Research, A*STAR（新加坡科技研究局资讯通信研究院）；NVIDIA（英伟达）
Large-scale distributed training of deep neural networks results in models with worse generalization performance as a result of the increase in the effective mini-batch size. Previous approaches attempt to address this problem by varying the learning rate and batch size over epochs and layers, or ad hoc modifications of batch normalization. We propose Scalable and Practical Natural Gradient Descent (SP-NGD), a principled approach for training models that allows them to attain similar generalization performance to models trained with first-order optimization methods, but with accelerated conver…
Stochastic alternating direction method of multipliers (ADMM), which visits only one sample or a mini-batch of samples each time, has recently been proved to achieve better performance than batch ADMM. However, most stochastic methods can only achieve a convergence rate $O(1/\sqrt T)$ on general convex problems,where T is the number of iterations. Hence, these methods are not scalable with respect to convergence rate (computation cost). There exists only one stochastic method, called SA-ADMM, which can achieve convergence rate $O(1/T)$ on general convex problems. However, an extra memory is ne…
Generative Multi-Objective Bayesian Optimization with Scalable Batch Evaluations for Sample-Efficient De Novo Molecular Design
Department of Chemical and Biological Engineering, University of Wisconsin--Madison, Madison, Wisconsin 53706, United States（化学与生物工程系，威斯康星大学麦迪逊分校）；Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, Ohio 43210, United States（化学与生物分子工程系，俄亥俄州立大学）
Many machine learning models, such as logistic regression~(LR) and support vector machine~(SVM), can be formulated as composite optimization problems. Recently, many distributed stochastic optimization~(DSO) methods have been proposed to solve the large-scale composite optimization problems, which have shown better performance than traditional batch methods. However, most of these DSO methods are not scalable enough. In this paper, we propose a novel DSO method, called \underline{s}calable \underline{c}omposite \underline{op}timization for l\underline{e}arning~({SCOPE}), and implement it on th…
National University of Singapore（新加坡国立大学）；University of California, Los Angeles（加利福尼亚大学洛杉矶分校）
Recently, Sharpness-Aware Minimization (SAM), which connects the geometry of the loss landscape and generalization, has demonstrated significant performance boosts on training large-scale models such as vision transformers. However, the update rule of SAM requires two sequential (non-parallelizable) gradient computations at each step, which can double the computational overhead. In this paper, we propose a novel algorithm LookSAM - that only periodically calculates the inner gradient ascent, to significantly reduce the additional training cost of SAM. The empirical results illustrate that Look…
University of California Merced（加州大学默塞德分校）；Lawrence Berkeley National Laboratory（劳伦斯伯克利国家实验室）
Motivated by extreme multi-label classification applications, we consider training deep learning models over sparse data in multi-GPU servers. The variance in the number of non-zero features across training batches and the intrinsic GPU heterogeneity combine to limit accuracy and increase the time to convergence. We address these challenges with Adaptive SGD, an adaptive elastic model averaging stochastic gradient descent algorithm for heterogeneous multi-GPUs that is characterized by dynamic scheduling, adaptive batch size scaling, and normalized model merging. Instead of statically partition…
Same Encoder, Different Winner: A Paired-View Framework for Cell Painting Encoder Evaluation
Institute of Computational Biology, Helmholtz Munich（亥姆霍兹慕尼黑计算生物学研究所）；School of Computation, Information and Technology, Technical University of Munich（慕尼黑工业大学计算、信息与技术学院）；Broad Institute of MIT and Harvard（麻省理工学院和哈佛大学布罗德研究所）
Feature selection with large-scale high-dimensional data is important yet very challenging in machine learning and data mining. Online feature selection is a promising new paradigm that is more efficient and scalable than batch feature section methods, but the existing online approaches usually fall short in their inferior efficacy as compared with batch approaches. In this paper, we present a novel second-order online feature selection scheme that is simple yet effective, very fast and extremely scalable to deal with large-scale ultra-high dimensional sparse data streams. The basic idea is to…
Deep Neural Networks (DNNs) have revolutionized numerous applications, but the demand for ever more performance remains unabated. Scaling DNN computations to larger clusters is generally done by distributing tasks in batch mode using methods such as distributed synchronous SGD. Among the issues with this approach is that to make the distributed cluster work with high utilization, the workload distributed to each node must be large, which implies nontrivial growth in the SGD mini-batch size. In this paper, we propose a framework called FPDeep, which uses a hybrid of model and layer parallelism …
Fudan University（复旦大学）；University of Texas at Dallas（德克萨斯大学达拉斯分校）
A large body of literature has proved that the Bayesian optimization framework is especially efficient and effective in analog circuit synthesis. However, most of the previous research works only focus on designing informative surrogate models or efficient acquisition functions. Even if searching for the global optimum over the acquisition function surface is itself a difficult task, it has been largely ignored. In this paper, we propose a fast and robust Bayesian optimization approach via one-dimensional subspaces for analog circuit synthesis. By solely focusing on optimizing one-dimension su…
The University of Chicago（芝加哥大学）；Peking University（北京大学）
Along with developing of Peaceman-Rachford Splittling Method (PRSM), many batch algorithms based on it have been studied very deeply. But almost no algorithm focused on the performance of stochastic version of PRSM. In this paper, we propose a new stochastic algorithm based on PRSM, prove its convergence rate in ergodic sense, and test its performance on both artificial and real data. We show that our proposed algorithm, Stochastic Scalable PRSM (SS-PRSM), enjoys the $O(1/K)$ convergence rate, which is the same as those newest stochastic algorithms that based on ADMM but faster than general St…
Bayesian optimization is a technique for optimizing black-box target functions. At the core of Bayesian optimization is a surrogate model that predicts the output of the target function at previously unseen inputs to facilitate the selection of promising input values. Gaussian processes (GPs) are commonly used as surrogate models but are known to scale poorly with the number of observations. We adapt the Vecchia approximation, a popular GP approximation from spatial statistics, to enable scalable high-dimensional Bayesian optimization. We develop several improvements and extensions, including …
In this paper we introduce Feature Gradients, a gradient-based search algorithm for feature selection. Our approach extends a recent result on the estimation of learnability in the sublinear data regime by showing that the calculation can be performed iteratively (i.e., in mini-batches) and in linear time and space with respect to both the number of features D and the sample size N . This, along with a discrete-to-continuous relaxation of the search domain, allows for an efficient, gradient-based search algorithm among feature subsets for very large datasets. Crucially, our algorithm is capabl…
Tencent Inc.（腾讯公司）；Hong Kong Baptist University（香港浸会大学）
Synchronized stochastic gradient descent (SGD) optimizers with data parallelism are widely used in training large-scale deep neural networks. Although using larger mini-batch sizes can improve the system scalability by reducing the communication-to-computation ratio, it may hurt the generalization ability of the models. To this end, we build a highly scalable deep learning training system for dense GPU clusters with three main contributions: (1) We propose a mixed-precision training method that significantly improves the training throughput of a single GPU without losing accuracy. (2) We propo…
United States Naval Academy（美国海军学院）；University of Maryland, College Park（马里兰大学帕克分校）；Rice University（莱斯大学）
With the growing importance of large network models and enormous training datasets, GPUs have become increasingly necessary to train neural networks. This is largely because conventional optimization algorithms rely on stochastic gradient methods that don't scale well to large numbers of cores in a cluster setting. Furthermore, the convergence of all gradient methods, including batch methods, suffers from common problems like saturation effects, poor conditioning, and saddle points. This paper explores an unconventional training method that uses alternating direction methods and Bregman iterat…
Stanford University（斯坦福大学）；University of Toronto（多伦多大学）
In this technical report, we consider an approach that combines the PPO objective and K-FAC natural gradient optimization, for which we call PPOKFAC. We perform a range of empirical analysis on various aspects of the algorithm, such as sample complexity, training speed, and sensitivity to batch size and training epochs. We observe that PPOKFAC is able to outperform PPO in terms of sample complexity and speed in a range of MuJoCo environments, while being scalable in terms of batch size. In spite of this, it seems that adding more epochs is not necessarily helpful for sample efficiency, and PPO…
Active learning has demonstrated data efficiency in many fields. Existing active learning algorithms, especially in the context of batch-mode deep Bayesian active models, rely heavily on the quality of uncertainty estimations of the model, and are often challenging to scale to large batches. In this paper, we propose Batch-BALanCe, a scalable batch-mode active learning algorithm, which combines insights from decision-theoretic active learning, combinatorial information measure, and diversity sampling. At its core, Batch-BALanCe relies on a novel decision-theoretic acquisition function that fac…
Information Sciences Institute University of Southern California（南加州大学信息科学研究所）
We propose a new learning to rank algorithm, named Weighted Margin-Rank Batch loss (WMRB), to extend the popular Weighted Approximate-Rank Pairwise loss (WARP). WMRB uses a new rank estimator and an efficient batch training algorithm. The approach allows more accurate item rank approximation and explicit utilization of parallel computation to accelerate training. In three item recommendation tasks, WMRB consistently outperforms WARP and other baselines. Moreover, WMRB shows clear time efficiency advantages as data scale increases.
Most existing set encoding algorithms operate under the implicit assumption that all the set elements are accessible, and that there are ample computational and memory resources to load the set into memory during training and inference. However, both assumptions fail when the set is excessively large such that it is impossible to load all set elements into memory, or when data arrives in a stream. To tackle such practical challenges in large-scale set encoding, the general set-function constraints of permutation invariance and equivariance are not sufficient. We introduce a new property termed…
Skolkovo Institute of Science and Technology（斯科尔科沃科学技术研究院）；Technology Innovation Institute（技术创新研究院）
In deep active learning, it is especially important to choose multiple examples to markup at each step to work efficiently, especially on large datasets. At the same time, existing solutions to this problem in the Bayesian setup, such as BatchBALD, have significant limitations in selecting a large number of examples, associated with the exponential complexity of computing mutual information for joint random variables. We, therefore, present the Large BatchBALD algorithm, which gives a well-grounded approximation to the BatchBALD method that aims to achieve comparable quality while being more c…
Scalable Graph Attention-based Instance Selection via Mini-Batch Sampling and Hierarchical Hashing
College of Information Technology, United Arab Emirates University（阿联酋大学信息科技学院）；Department of Computer Science, KU Leuven（比利时库尔勒大学计算机科学系）；College of Science, United Arab Emirates University（阿联酋大学科学学院）
Information Sciences Institute（信息科学研究所）；University of Southern California（南加州大学）
In designing personalized ranking algorithms, it is desirable to encourage a high precision at the top of the ranked list. Existing methods either seek a smooth convex surrogate for a non-smooth ranking metric or directly modify updating procedures to encourage top accuracy. In this work we point out that these methods do not scale well to a large-scale setting, and this is partly due to the inaccurate pointwise or pairwise rank estimation. We propose a new framework for personalized ranking. It uses batch-based rank estimators and smooth rank-sensitive loss functions. This new batch learning …
Entity alignment (EA) aims at finding equivalent entities in different knowledge graphs (KGs). Embedding-based approaches have dominated the EA task in recent years. Those methods face problems that come from the geometric properties of embedding vectors, including hubness and isolation. To solve these geometric problems, many normalization approaches have been adopted for EA. However, the increasing scale of KGs renders it hard for EA models to adopt the normalization processes, thus limiting their usage in real-world applications. To tackle this challenge, we present ClusterEA, a general fra…
Intel - Artificial Intelligence Products Group (AIPG)（英特尔人工智能产品事业部）；Technion - Israel Institute of Technology（以色列理工学院）
Quantized Neural Networks (QNNs) are often used to improve network efficiency during the inference phase, i.e. after the network has been trained. Extensive research in the field suggests many different quantization schemes. Still, the number of bits required, as well as the best quantization scheme, are yet unknown. Our theoretical analysis suggests that most of the training process is robust to substantial precision reduction, and points to only a few specific operations that require higher precision. Armed with this knowledge, we quantize the model parameters, activations and layer gradient…
Apt-Serve: Adaptive Request Scheduling on Hybrid Cache for Scalable LLM Inference Serving
The Hong Kong University of Science and Technology（香港科技大学）；Shanghai Jiao Tong University（上海交通大学）；The Hong Kong University of Science and Technology (Guangzhou)（香港科技大学（广州））
Variational inference has had great success in scaling approximate Bayesian inference to big data by exploiting mini-batch training. To date, however, this strategy has been most applicable to models of independent data. We propose an extension to state space models of time series data based on a novel generative model for latent temporal states: the neural moving average model. This permits a subsequence to be sampled without drawing from the entire distribution, enabling training iterations to use mini-batches of the time series at low computational cost. We illustrate our method on autoregr…
Learning from diverse offline datasets is a promising path towards learning general purpose robotic agents. However, a core challenge in this paradigm lies in collecting large amounts of meaningful data, while not depending on a human in the loop for data collection. One way to address this challenge is through task-agnostic exploration, where an agent attempts to explore without a task-specific reward function, and collect data that can be useful for any downstream task. While these approaches have shown some promise in simple domains, they often struggle to explore the relevant regions of th…
We present a Bayesian non-negative tensor factorization model for count-valued tensor data, and develop scalable inference algorithms (both batch and online) for dealing with massive tensors. Our generative model can handle overdispersed counts as well as infer the rank of the decomposition. Moreover, leveraging a reparameterization of the Poisson distribution as a multinomial facilitates conjugacy in the model and enables simple and efficient Gibbs sampling and variational Bayes (VB) inference updates, with a computational cost that only depends on the number of nonzeros in the tensor. The mo…
Full-batch training on Graph Neural Networks (GNN) to learn the structure of large graphs is a critical problem that needs to scale to hundreds of compute nodes to be feasible. It is challenging due to large memory capacity and bandwidth requirements on a single compute node and high communication volumes across multiple nodes. In this paper, we present DistGNN that optimizes the well-known Deep Graph Library (DGL) for full-batch training on CPU clusters via an efficient shared memory implementation, communication reduction using a minimum vertex-cut graph partitioning algorithm and communicat…
Missing data imputation (MDI) is crucial when dealing with tabular datasets across various domains. Autoencoders can be trained to reconstruct missing values, and graph autoencoders (GAE) can additionally consider similar patterns in the dataset when imputing new values for a given instance. However, previously proposed GAEs suffer from scalability issues, requiring the user to define a similarity metric among patterns to build the graph connectivity beforehand. In this paper, we leverage recent progress in latent graph imputation to propose a novel EdGe Generation Graph AutoEncoder (EGG-GAE) …
