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In the past decade, advances in deep learning have resulted in breakthroughs in a variety of areas, including computer vision, natural language understanding, speech recognition, and reinforcement learning. Specialized, high-performing neural architectures are crucial to the success of deep learning in these areas. Neural architecture search (NAS), the process of automating the design of neural architectures for a given task, is an inevitable next step in automating machine learning and has already outpaced the best human-designed architectures on many tasks. In the past few years, research in NAS has been progressing rapidly, with over 1000 papers released since 2020 (Deng and Lindauer, 2021). In this survey, we provide an organized and comprehensive guide to neural architecture search. We give a taxonomy of search spaces, algorithms, and speedup techniques, and we discuss resources such as benchmarks, best practices, other surveys, and open-source libraries.

This is a collection of (mostly) pen-and-paper exercises in machine learning. The exercises are on the following topics: linear algebra, optimisation, directed graphical models, undirected graphical models, expressive power of graphical models, factor graphs and message passing, inference for hidden Markov models, model-based learning (including ICA and unnormalised models), sampling and Monte-Carlo integration, and variational inference., The associated github page is https://github.com/michaelgutmann/ml-pen-and-paper-exercises

In this paper, we study the sum rate maximization for successive zero-forcing dirty-paper coding (SZFDPC) with per-antenna power constraint (PAPC). Although SZFDPC is a low-complexity alternative to the optimal dirty paper coding (DPC), efficient algorithms to compute its sum rate are still open problems especially under practical PAPC. The existing solution to the considered problem is computationally inefficient due to employing high-complexity interior-point method. In this study, we propose two new low-complexity approaches to this important problem. More specifically, the first algorithm achieves the optimal solution by transforming the original problem in the broadcast channel into an equivalent problem in the multiple access channel, then the resulting problem is solved by alternating optimization together with successive convex approximation. We also derive a suboptimal solution based on machine learning to which simple linear regressions are applicable. The approaches are analyzed and validated extensively to demonstrate their superiors over the existing approach., Comment: 5 pages, 4 figures

Machine learning has been applied to several problems in particle physics research, beginning with applications to high-level physics analysis in the 1990s and 2000s, followed by an explosion of applications in particle and event identification and reconstruction in the 2010s. In this document we discuss promising future research and development areas for machine learning in particle physics. We detail a roadmap for their implementation, software and hardware resource requirements, collaborative initiatives with the data science community, academia and industry, and training the particle physics community in data science. The main objective of the document is to connect and motivate these areas of research and development with the physics drivers of the High-Luminosity Large Hadron Collider and future neutrino experiments and identify the resource needs for their implementation. Additionally we identify areas where collaboration with external communities will be of great benefit., Comment: Editors: Sergei Gleyzer, Paul Seyfert and Steven Schramm

Current daily paper releases are becoming increasingly large and areas of research are growing in diversity. This makes it harder for scientists to keep up to date with current state of the art and identify relevant work within their lines of interest. The goal of this article is to address this problem using Machine Learning techniques. We model a scientific paper to be built as a combination of different scientific knowledge from diverse topics into a new problem. In light of this, we implement the unsupervised Machine Learning technique of Latent Dirichlet Allocation (LDA) on the corpus of papers in a given field to: i) define and extract underlying topics in the corpus; ii) get the topics weight vector for each paper in the corpus; and iii) get the topics weight vector for new papers. By registering papers preferred by a user, we build a user vector of weights using the information of the vectors of the selected papers. Hence, by performing an inner product between the user vector and each paper in the daily Arxiv release, we can sort the papers according to the user preference on the underlying topics. We have created the website IArxiv.org where users can read sorted daily Arxiv releases (and more) while the algorithm learns each users preference, yielding a more accurate sorting every day. Current IArxiv.org version runs on Arxiv categories astro-ph, gr-qc, hep-ph and hep-th and we plan to extend to others. We propose several new useful and relevant implementations to be additionally developed as well as new Machine Learning techniques beyond LDA to further improve the accuracy of this new tool., We are open to new ideas and to scientists and institutions wishing to collaborate and/or partner in further improvements for this service. With this tool the time a paper is sent is irrelevant for its order of appearance

This note corrects a mistake in the paper "consistent cross-validatory model-selection for dependent data: $hv$-block cross-validation" by Racine (2000). In his paper, he implied that the therein proposed $hv$-block cross-validation is consistent in the sense of Shao (1993). To get this intuition, he relied on the speculation that $hv$-block is a balanced incomplete block design (BIBD). This note demonstrates that this is not the case, and thus the theoretical consistency of $hv$-block remains an open question. In addition, I also provide a Python program counting the number of occurrences of each sample and each pair of samples., Technique report. 5 pages, 1 figure

A fundamental component of neural network verification is the computation of bounds on the values their outputs can take. Previous methods have either used off-the-shelf solvers, discarding the problem structure, or relaxed the problem even further, making the bounds unnecessarily loose. We propose a novel approach based on Lagrangian Decomposition. Our formulation admits an efficient supergradient ascent algorithm, as well as an improved proximal algorithm. Both the algorithms offer three advantages: (i) they yield bounds that are provably at least as tight as previous dual algorithms relying on Lagrangian relaxations; (ii) they are based on operations analogous to forward/backward pass of neural networks layers and are therefore easily parallelizable, amenable to GPU implementation and able to take advantage of the convolutional structure of problems; and (iii) they allow for anytime stopping while still providing valid bounds. Empirically, we show that we obtain bounds comparable with off-the-shelf solvers in a fraction of their running time, and obtain tighter bounds in the same time as previous dual algorithms. This results in an overall speed-up when employing the bounds for formal verification. Code for our algorithms is available at https://github.com/oval-group/decomposition-plnn-bounds., UAI 2020 conference paper

Widely-used public benchmarks are of huge importance to computer vision and machine learning research, especially with the computational resources required to reproduce state of the art results quickly becoming untenable. In medical image computing, the wide variety of image modalities and problem formulations yields a huge task-space for benchmarks to cover, and thus the widespread adoption of standard benchmarks has been slow, and barriers to releasing medical data exacerbate this issue. In this paper, we examine the role that publicly available data has played in MICCAI papers from the past five years. We find that more than half of these papers are based on private data alone, although this proportion seems to be decreasing over time. Additionally, we observed that after controlling for open access publication and the release of code, papers based on public data were cited over 60% more per year than their private-data counterparts. Further, we found that more than 20% of papers using public data did not provide a citation to the dataset or associated manuscript, highlighting the "second-rate" status that data contributions often take compared to theoretical ones. We conclude by making recommendations for MICCAI policies which could help to better incentivise data sharing and move the field toward more efficient and reproducible science., 8 pages, 2 figures

Systematic reviews, which summarize and synthesize all the current research in a specific topic, are a crucial component to academia. They are especially important in the biomedical and health sciences, where they synthesize the state of medical evidence and conclude the best course of action for various diseases, pathologies, and treatments. Due to the immense amount of literature that exists, as well as the output rate of research, reviewing abstracts can be a laborious process. Automation may be able to significantly reduce this workload. Of course, such classifications are not easily automated due to the peculiar nature of written language. Machine learning may be able to help. This paper explored the viability and effectiveness of using machine learning modelling to classify abstracts according to specific exclusion/inclusion criteria, as would be done in the first stage of a systematic review. The specific task was performing the classification of deciding whether an abstract is a randomized control trial (RCT) or not, a very common classification made in systematic reviews in the healthcare field. Random training/testing splits of an n=2042 dataset of labelled abstracts were repeatedly created (1000 times in total), with a model trained and tested on each of these instances. A Bayes classifier as well as an SVM classifier were used, and compared to non-machine learning, simplistic approaches to textual classification. An SVM classifier was seen to be highly effective, yielding a 90% accuracy, as well as an F1 score of 0.84, and yielded a potential workload reduction of 70%. This shows that machine learning has the potential to significantly revolutionize the abstract screening process in healthcare systematic reviews., 10 pages, 2 figures, 6 tables

International audience; In recent years, the number of papers on Alzheimer's disease classification has increased dramatically, generating interesting methodological ideas on the use machine learning and feature extraction methods. However, practical impact is much more limited and, eventually, one could not tell which of these approaches are the most efficient. While over 90% of these works make use of ADNI an objective comparison between approaches is impossible due to variations in the subjects included, image pre-processing, performance metrics and cross-validation procedures. In this paper, we propose a framework for reproducible classification experiments using multimodal MRI and PET data from ADNI. The core components are: 1) code to automatically convert the full ADNI database into BIDS format; 2) a modular architecture based on Nipype in order to easily plug-in different classification and feature extraction tools; 3) feature extraction pipelines for MRI and PET data; 4) baseline classification approaches for unimodal and multimodal features. This provides a flexible framework for benchmarking different feature extraction and classification tools in a reproducible manner. Data management tools for obtaining the lists of subjects in AD, MCI converter, MCI non-converters, CN classes are also provided. We demonstrate its use on all (1519) baseline T1 MR images and all (1102) baseline FDG PET images from ADNI 1, GO and 2 with SPM-based feature extraction pipelines and three different classification techniques (linear SVM, anatomically regularized SVM and multiple kernel learning SVM). The highest accuracies achieved were: 91% for AD vs CN, 83% for MCIc vs CN, 75% for MCIc vs MCInc, 94% for AD-ABeta+ vs CN-ABeta- and 72% for MCIc-ABeta+ vs MCInc-ABeta+. The code is publicly available at : https://github.com/aramis-lab/AD-ML.

Quantitative metrics in lung computed tomography (CT) images have been widely used, often without a clear connection with physiology. This work proposes a patient-independent model for the estimation of well-aerated volume of lungs in CT images (WAVE). A Gaussian fit, with mean (Mu.f) and width (Sigma.f) values, was applied to the lower CT histogram data points of the lung to provide the estimation of the well-aerated lung volume (WAVE.f). Independence from CT reconstruction parameters and respiratory cycle was analysed using healthy lung CT images and 4DCT acquisitions. The Gaussian metrics and first order radiomic features calculated for a third cohort of COVID-19 patients were compared with those relative to healthy lungs. Each lung was further segmented in 24 subregions and a new biomarker derived from Gaussian fit parameter Mu.f was proposed to represent the local density changes. WAVE.f resulted independent from the respiratory motion in 80% of the cases. Differences of 1%, 2% and up to 14% resulted comparing a moderate iterative strength and FBP algorithm, 1 and 3 mm of slice thickness and different reconstruction kernel. Healthy subjects were significantly different from COVID-19 patients for all the metrics calculated. Graphical representation of the local biomarker provides spatial and quantitative information in a single 2D picture. Unlike other metrics based on fixed histogram thresholds, this model is able to consider the inter-and intra-subject variability. In addition, it defines a local biomarker to quantify the severity of the disease, independently of the observer., 31 pages, 7 figures, accepted in EJMP

Background The COVID-19 outbreak has left many people isolated within their homes; these people are turning to social media for news and social connection, which leaves them vulnerable to believing and sharing misinformation. Health-related misinformation threatens adherence to public health messaging, and monitoring its spread on social media is critical to understanding the evolution of ideas that have potentially negative public health impacts. Objective The aim of this study is to use Twitter data to explore methods to characterize and classify four COVID-19 conspiracy theories and to provide context for each of these conspiracy theories through the first 5 months of the pandemic. Methods We began with a corpus of COVID-19 tweets (approximately 120 million) spanning late January to early May 2020. We first filtered tweets using regular expressions (n=1.8 million) and used random forest classification models to identify tweets related to four conspiracy theories. Our classified data sets were then used in downstream sentiment analysis and dynamic topic modeling to characterize the linguistic features of COVID-19 conspiracy theories as they evolve over time. Results Analysis using model-labeled data was beneficial for increasing the proportion of data matching misinformation indicators. Random forest classifier metrics varied across the four conspiracy theories considered (F1 scores between 0.347 and 0.857); this performance increased as the given conspiracy theory was more narrowly defined. We showed that misinformation tweets demonstrate more negative sentiment when compared to nonmisinformation tweets and that theories evolve over time, incorporating details from unrelated conspiracy theories as well as real-world events. Conclusions Although we focus here on health-related misinformation, this combination of approaches is not specific to public health and is valuable for characterizing misinformation in general, which is an important first step in creating targeted messaging to counteract its spread. Initial messaging should aim to preempt generalized misinformation before it becomes widespread, while later messaging will need to target evolving conspiracy theories and the new facets of each as they become incorporated.

Graphical Abstract The prediction model of oral disintegrating tablets formulations with direct compression process by artificial neural network (ANN) and deep neural network (DNN) techniques were established. 145 formulation data were extracted from Web of Science. All datasets were divided into three parts: training set (105 data), validation set (20) and testing set (20) to build prediction model.Image, graphical abstract, Oral disintegrating tablets (ODTs) are a novel dosage form that can be dissolved on the tongue within 3 min or less especially for geriatric and pediatric patients. Current ODT formulation studies usually rely on the personal experience of pharmaceutical experts and trial-and-error in the laboratory, which is inefficient and time-consuming. The aim of current research was to establish the prediction model of ODT formulations with direct compression process by artificial neural network (ANN) and deep neural network (DNN) techniques. 145 formulation data were extracted from Web of Science. All datasets were divided into three parts: training set (105 data), validation set (20) and testing set (20). ANN and DNN were compared for the prediction of the disintegrating time. The accuracy of the ANN model have reached 85.60%, 80.00% and 75.00% on the training set, validation set and testing set respectively, whereas that of the DNN model were 85.60%, 85.00% and 80.00%, respectively. Compared with the ANN, DNN showed the better prediction for ODT formulations. It is the first time that deep neural network with the improved dataset selection algorithm is applied to formulation prediction on small data. The proposed predictive approach could evaluate the critical parameters about quality control of formulation, and guide research and process development. The implementation of this prediction model could effectively reduce drug product development timeline and material usage, and proactively facilitate the development of a robust drug product.

Motivation: Analysis of relationships of drug structure to biological response is key to understanding off-target and unexpected drug effects, and for developing hypotheses on how to tailor drug thera-pies. New methods are required for integrated analyses of a large number of chemical features of drugs against the corresponding genome-wide responses of multiple cell models. Results: In this paper, we present the first comprehensive multi-set analysis on how the chemical structure of drugs impacts on ge-nome-wide gene expression across several cancer cell lines (CMap database). The task is formulated as searching for drug response components across multiple cancers to reveal shared effects of drugs and the chemical features that may be responsible. The com-ponents can be computed with an extension of a very recent ap-proach called Group Factor Analysis (GFA). We identify 11 compo-nents that link the structural descriptors of drugs with specific gene expression responses observed in the three cell lines, and identify structural groups that may be responsible for the responses. Our method quantitatively outperforms the limited earlier studies on CMap and identifies both the previously reported associations and several interesting novel findings, by taking into account multiple cell lines and advanced 3D structural descriptors. The novel observations include: previously unknown similarities in the effects induced by 15-delta prostaglandin J2 and HSP90 inhibitors, which are linked to the 3D descriptors of the drugs; and the induction by simvastatin of leukemia-specific anti-inflammatory response, resem-bling the effects of corticosteroids., Comment: 7 pages, 6 figures

Motivation: Drug discovery demands rapid quantification of compound-protein interaction (CPI). However, there is a lack of methods that can predict compound-protein affinity from sequences alone with high applicability, accuracy, and interpretability. Results: We present a seamless integration of domain knowledges and learning-based approaches. Under novel representations of structurally-annotated protein sequences, a semi-supervised deep learning model that unifies recurrent and convolutional neural networks has been proposed to exploit both unlabeled and labeled data, for jointly encoding molecular representations and predicting affinities. Our representations and models outperform conventional options in achieving relative error in IC$_{50}$ within 5-fold for test cases and 20-fold for protein classes not included for training. Performances for new protein classes with few labeled data are further improved by transfer learning. Furthermore, separate and joint attention mechanisms are developed and embedded to our model to add to its interpretability, as illustrated in case studies for predicting and explaining selective drug-target interactions. Lastly, alternative representations using protein sequences or compound graphs and a unified RNN/GCNN-CNN model using graph CNN (GCNN) are also explored to reveal algorithmic challenges ahead. Availability: Data and source codes are available at https://github.com/Shen-Lab/DeepAffinity Supplementary Information: Supplementary data are available at http://shen-lab.github.io/deep-affinity-bioinf18-supp-rev.pdf, https://github.com/Shen-Lab/DeepAffinity

Components of biological systems interact with each other in order to carry out vital cell functions. Such information can be used to improve estimation and inference, and to obtain better insights into the underlying cellular mechanisms. Discovering regulatory interactions among genes is therefore an important problem in systems biology. Whole-genome expression data over time provides an opportunity to determine how the expression levels of genes are affected by changes in transcription levels of other genes, and can therefore be used to discover regulatory interactions among genes. In this paper, we propose a novel penalization method, called truncating lasso, for estimation of causal relationships from time-course gene expression data. The proposed penalty can correctly determine the order of the underlying time series, and improves the performance of the lasso-type estimators. Moreover, the resulting estimate provides information on the time lag between activation of transcription factors and their effects on regulated genes. We provide an efficient algorithm for estimation of model parameters, and show that the proposed method can consistently discover causal relationships in the large $p$, small $n$ setting. The performance of the proposed model is evaluated favorably in simulated, as well as real, data examples. The proposed truncating lasso method is implemented in the R-package grangerTlasso and is available at http://www.stat.lsa.umich.edu/~shojaie., Comment: 12 pages, 4 figures, 1 table

Approaches for testing sets of variants, such as a set of rare or common variants within a gene or pathway, for association with complex traits are important. In particular, set tests allow for aggregation of weak signal within a set, can capture interplay among variants, and reduce the burden of multiple hypothesis testing. Until now, these approaches did not address confounding by family relatedness and population structure, a problem that is becoming more important as larger data sets are used to increase power. Results: We introduce a new approach for set tests that handles confounders. Our model is based on the linear mixed model and uses two random effects-one to capture the set association signal and one to capture confounders. We also introduce a computational speedup for two-random-effects models that makes this approach feasible even for extremely large cohorts. Using this model with both the likelihood ratio test and score test, we find that the former yields more power while controlling type I error. Application of our approach to richly structured GAW14 data demonstrates that our method successfully corrects for population structure and family relatedness, while application of our method to a 15,000 individual Crohn's disease case-control cohort demonstrates that it additionally recovers genes not recoverable by univariate analysis. Availability: A Python-based library implementing our approach is available at http://mscompbio.codeplex.com, * denotes equal contributions

Motivation Recent advances in technology for brain imaging and high-throughput genotyping have motivated studies examining the influence of genetic variation on brain structure. Wang et al. have developed an approach for the analysis of imaging genomic studies using penalized multi-task regression with regularization based on a novel group l2,1-norm penalty which encourages structured sparsity at both the gene level and SNP level. While incorporating a number of useful features, the proposed method only furnishes a point estimate of the regression coefficients; techniques for conducting statistical inference are not provided. A new Bayesian method is proposed here to overcome this limitation. Results We develop a Bayesian hierarchical modeling formulation where the posterior mode corresponds to the estimator proposed by Wang et al. and an approach that allows for full posterior inference including the construction of interval estimates for the regression parameters. We show that the proposed hierarchical model can be expressed as a three-level Gaussian scale mixture and this representation facilitates the use of a Gibbs sampling algorithm for posterior simulation. Simulation studies demonstrate that the interval estimates obtained using our approach achieve adequate coverage probabilities that outperform those obtained from the nonparametric bootstrap. Our proposed methodology is applied to the analysis of neuroimaging and genetic data collected as part of the Alzheimer’s Disease Neuroimaging Initiative (ADNI), and this analysis of the ADNI cohort demonstrates clearly the value added of incorporating interval estimation beyond only point estimation when relating SNPs to brain imaging endophenotypes. Availability and Implementation Software and sample data is available as an R package ‘bgsmtr’ that can be downloaded from The Comprehensive R Archive Network (CRAN). Supplementary information Supplementary data are available at Bioinformatics online.

Motivation: Metagenomics characterizes the taxonomic diversity of microbial communities by sequencing DNA directly from an environmental sample. One of the main challenges in metagenomics data analysis is the binning step, where each sequenced read is assigned to a taxonomic clade. Because of the large volume of metagenomics datasets, binning methods need fast and accurate algorithms that can operate with reasonable computing requirements. While standard alignment-based methods provide state-of-the-art performance, compositional approaches that assign a taxonomic class to a DNA read based on the k-mers it contains have the potential to provide faster solutions. Results: We propose a new rank-flexible machine learning-based compositional approach for taxonomic assignment of metagenomics reads and show that it benefits from increasing the number of fragments sampled from reference genome to tune its parameters, up to a coverage of about 10, and from increasing the k-mer size to about 12. Tuning the method involves training machine learning models on about 108 samples in 107 dimensions, which is out of reach of standard softwares but can be done efficiently with modern implementations for large-scale machine learning. The resulting method is competitive in terms of accuracy with well-established alignment and composition-based tools for problems involving a small to moderate number of candidate species and for reasonable amounts of sequencing errors. We show, however, that machine learning-based compositional approaches are still limited in their ability to deal with problems involving a greater number of species and more sensitive to sequencing errors. We finally show that the new method outperforms the state-of-the-art in its ability to classify reads from species of lineage absent from the reference database and confirm that compositional approaches achieve faster prediction times, with a gain of 2–17 times with respect to the BWA-MEM short read mapper, depending on the number of candidate species and the level of sequencing noise. Availability and implementation: Data and codes are available at http://cbio.ensmp.fr/largescalemetagenomics. Contact: pierre.mahe@biomerieux.com Supplementary information: Supplementary data are available at Bioinformatics online.

Motivation: As an increasing number of genome-wide association studies reveal the limitations of the attempt to explain phenotypic heritability by single genetic loci, there is a recent focus on associating complex phenotypes with sets of genetic loci. Although several methods for multi-locus mapping have been proposed, it is often unclear how to relate the detected loci to the growing knowledge about gene pathways and networks. The few methods that take biological pathways or networks into account are either restricted to investigating a limited number of predetermined sets of loci or do not scale to genome-wide settings. Results: We present SConES, a new efficient method to discover sets of genetic loci that are maximally associated with a phenotype while being connected in an underlying network. Our approach is based on a minimum cut reformulation of the problem of selecting features under sparsity and connectivity constraints, which can be solved exactly and rapidly. SConES outperforms state-of-the-art competitors in terms of runtime, scales to hundreds of thousands of genetic loci and exhibits higher power in detecting causal SNPs in simulation studies than other methods. On flowering time phenotypes and genotypes from Arabidopsis thaliana, SConES detects loci that enable accurate phenotype prediction and that are supported by the literature., Bioinformatics, 29 (13), ISSN:1367-4803, ISSN:1460-2059

The task of clustering a set of objects based on multiple sources of data arises in several modern applications. We propose an integrative statistical model that permits a separate clustering of the objects for each data source. These separate clusterings adhere loosely to an overall consensus clustering, and hence they are not independent. We describe a computationally scalable Bayesian framework for simultaneous estimation of both the consensus clustering and the source-specific clusterings. We demonstrate that this flexible approach is more robust than joint clustering of all data sources, and is more powerful than clustering each data source separately. This work is motivated by the integrated analysis of heterogeneous biomedical data, and we present an application to subtype identification of breast cancer tumor samples using publicly available data from The Cancer Genome Atlas. Software is available at http://people.duke.edu/~el113/software.html., 32 pages, 13 figures

Inference of gene regulatory network from expression data is a challenging task. Many methods have been developed to this purpose but a comprehensive evaluation that covers unsupervised, semi-supervised and supervised methods, and provides guidelines for their practical application, is lacking. We performed an extensive evaluation of inference methods on simulated and experimental expression data. The results reveal low prediction accuracies for unsupervised techniques with the notable exception of the Z-SCORE method on knockout data. In all other cases, the supervised approach achieved the highest accuracies and even in a semi-supervised setting with small numbers of only positive samples, outperformed the unsupervised techniques.

Driven by a large number of potential applications in areas like bioinformatics, information retrieval and social network analysis, the problem setting of inferring relations between pairs of data objects has recently been investigated quite intensively in the machine learning community. To this end, current approaches typically consider datasets containing crisp relations, so that standard classification methods can be adopted. However, relations between objects like similarities and preferences are often expressed in a graded manner in real-world applications. A general kernel-based framework for learning relations from data is introduced here. It extends existing approaches because both crisp and graded relations are considered, and it unifies existing approaches because different types of graded relations can be modeled, including symmetric and reciprocal relations. This framework establishes important links between recent developments in fuzzy set theory and machine learning. Its usefulness is demonstrated through various experiments on synthetic and real-world data., This work has been submitted to the IEEE for possible publication. Copyright may be transferred without notice, after which this version may no longer be accessible

Diverse applications - particularly in tumour subtyping - have demonstrated the importance of integrative clustering techniques for combining information from multiple data sources. Cluster-Of-Clusters Analysis (COCA) is one such approach that has been widely applied in the context of tumour subtyping. However, the properties of COCA have never been systematically explored, and its robustness to the inclusion of noisy datasets, or datasets that define conflicting clustering structures, is unclear. We rigorously benchmark COCA, and present Kernel Learning Integrative Clustering (KLIC) as an alternative strategy. KLIC frames the challenge of combining clustering structures as a multiple kernel learning problem, in which different datasets each provide a weighted contribution to the final clustering. This allows the contribution of noisy datasets to be down-weighted relative to more informative datasets. We compare the performances of KLIC and COCA in a variety of situations through simulation studies. We also present the output of KLIC and COCA in real data applications to cancer subtyping and transcriptional module discovery. R packages "klic" and "coca" are available on the Comprehensive R Archive Network., Comment: Manuscript: 18 pages, 6 figures. Supplement: 29 pages, 19 figures. This version contains additional simulation studies and comparisons to other methods. For associated R code, see https://CRAN.R-project.org/package=klic and https://github.com/acabassi/klic-pancancer-analysis

In this paper, we introduce and analyze a variant of the Thompson sampling (TS) algorithm for contextual bandits. At each round, traditional TS requires samples from the current posterior distribution, which is usually intractable. To circumvent this issue, approximate inference techniques can be used and provide samples with distribution close to the posteriors. However, current approximate techniques yield to either poor estimation (Laplace approximation) or can be computationally expensive (MCMC methods, Ensemble sampling...). In this paper, we propose a new algorithm, Varational Inference Thompson sampling VITS, based on Gaussian Variational Inference. This scheme provides powerful posterior approximations which are easy to sample from, and is computationally efficient, making it an ideal choice for TS. In addition, we show that VITS achieves a sub-linear regret bound of the same order in the dimension and number of round as traditional TS for linear contextual bandit. Finally, we demonstrate experimentally the effectiveness of VITS on both synthetic and real world datasets.

Low-rank tensor analysis has received widespread attention with many practical applications. However, the tensor data are often contaminated by outliers or sample-specific corruptions. How to recover the tensor data that are corrupted by outliers and perform data clustering remains a challenging problem. This paper develops an outlier-robust tensor low-rank representation (OR-TLRR) method for simultaneous outlier detection and tensor data clustering based on the tensor singular value decomposition (t-SVD) algebraic framework. It is motivated by the recently proposed tensor-tensor product induced by invertible linear transforms that satisfy certain conditions. For tensor observations with arbitrary outlier corruptions, OR-TLRR has provable performance guarantee for exactly recovering the row space of clean data and detecting outliers under mild conditions. Moreover, an extension of OR-TLRR is also proposed to handle the case when parts of the data are missing. Finally, extensive experimental results on both synthetic and real data demonstrate the effectiveness of the proposed algorithms., 12 pages, 1 figure; preprint of a journal paper

The field of text-conditioned image generation has made unparalleled progress with the recent advent of latent diffusion models. While remarkable, as the complexity of given text input increases, the state-of-the-art diffusion models may still fail in generating images which accurately convey the semantics of the given prompt. Furthermore, it has been observed that such misalignments are often left undetected by pretrained multi-modal models such as CLIP. To address these problems, in this paper we explore a simple yet effective decompositional approach towards both evaluation and improvement of text-to-image alignment. In particular, we first introduce a Decompositional-Alignment-Score which given a complex prompt decomposes it into a set of disjoint assertions. The alignment of each assertion with generated images is then measured using a VQA model. Finally, alignment scores for different assertions are combined aposteriori to give the final text-to-image alignment score. Experimental analysis reveals that the proposed alignment metric shows significantly higher correlation with human ratings as opposed to traditional CLIP, BLIP scores. Furthermore, we also find that the assertion level alignment scores provide a useful feedback which can then be used in a simple iterative procedure to gradually increase the expression of different assertions in the final image outputs. Human user studies indicate that the proposed approach surpasses previous state-of-the-art by 8.7% in overall text-to-image alignment accuracy. Project page for our paper is available at https://1jsingh.github.io/divide-evaluate-and-refine

Linear latent variable models such as principal component analysis (PCA), independent component analysis (ICA), canonical correlation analysis (CCA), and factor analysis (FA) identify latent directions (or loadings) either ordered or unordered. The data is then projected onto the latent directions to obtain their projected representations (or scores). For example, PCA solvers usually rank the principal directions by explaining the most to least variance, while ICA solvers usually return independent directions unordered and often with single sources spread across multiple directions as multiple sub-sources, which is of severe detriment to their usability and interpretability. This paper proposes a general framework to enhance latent space representations for improving the interpretability of linear latent spaces. Although the concepts in this paper are language agnostic, the framework is written in Python. This framework automates the clustering and ranking of latent vectors to enhance the latent information per latent vector, as well as, the interpretation of latent vectors. Several innovative enhancements are incorporated including latent ranking (LR), latent scaling (LS), latent clustering (LC), and latent condensing (LCON). For a specified linear latent variable model, LR ranks latent directions according to a specified metric, LS scales latent directions according to a specified metric, LC automatically clusters latent directions into a specified number of clusters, while, LCON automatically determines an appropriate number of clusters into which to condense the latent directions for a given metric. Additional functionality of the framework includes single-channel and multi-channel data sources, data preprocessing strategies such as Hankelisation to seamlessly expand the applicability of linear latent variable models (LLVMs) to a wider variety of data. The effectiveness of LR, LS, and LCON are showcased on two crafted foundational problems with two applied latent variable models, namely, PCA and ICA., 15 pages, 5 figures, to be submitted SoftwareX

This paper revisits an adaptation of the random forest algorithm for Fr\'echet regression, addressing the challenge of regression in the context of random objects in metric spaces. Recognizing the limitations of previous approaches, we introduce a new splitting rule that circumvents the computationally expensive operation of Fr\'echet means by substituting with a medoid-based approach. We validate this approach by demonstrating its asymptotic equivalence to Fr\'echet mean-based procedures and establish the consistency of the associated regression estimator. The paper provides a sound theoretical framework and a more efficient computational approach to Fr\'echet regression, broadening its application to non-standard data types and complex use cases.

Twin revolutions in wearable technologies and smartphone-delivered digital health interventions have significantly expanded the accessibility and uptake of mobile health (mHealth) interventions across various health science domains. Sequentially randomized experiments called micro-randomized trials (MRTs) have grown in popularity to empirically evaluate the effectiveness of these mHealth intervention components. MRTs have given rise to a new class of causal estimands known as "causal excursion effects", which enable health scientists to assess how intervention effectiveness changes over time or is moderated by individual characteristics, context, or responses in the past. However, current data analysis methods for estimating causal excursion effects require pre-specified features of the observed high-dimensional history to construct a working model of an important nuisance parameter. While machine learning algorithms are ideal for automatic feature construction, their naive application to causal excursion estimation can lead to bias under model misspecification, potentially yielding incorrect conclusions about intervention effectiveness. To address this issue, this paper revisits the estimation of causal excursion effects from a meta-learner perspective, where the analyst remains agnostic to the choices of supervised learning algorithms used to estimate nuisance parameters. The paper presents asymptotic properties of the novel estimators and compares them theoretically and through extensive simulation experiments, demonstrating relative efficiency gains and supporting the recommendation for a doubly robust alternative to existing methods. Finally, the practical utility of the proposed methods is demonstrated by analyzing data from a multi-institution cohort of first-year medical residents in the United States (NeCamp et al., 2020).

This paper considers a single-trajectory system identification problem for linear systems under general nonlinear and/or time-varying policies with i.i.d. random excitation noises. The problem is motivated by safe learning-based control for constrained linear systems, where the safe policies during the learning process are usually nonlinear and time-varying for satisfying the state and input constraints. In this paper, we provide a non-asymptotic error bound for least square estimation when the data trajectory is generated by any nonlinear and/or time-varying policies as long as the generated state and action trajectories are bounded. This significantly generalizes the existing non-asymptotic guarantees for linear system identification, which usually consider i.i.d. random inputs or linear policies. Interestingly, our error bound is consistent with that for linear policies with respect to the dependence on the trajectory length, system dimensions, and excitation levels. Lastly, we demonstrate the applications of our results by safe learning with robust model predictive control and provide numerical analysis.

This paper contributes to the challenge of learning a function on streamed multimodal data through evaluation. The core of the result of our paper is the combination of two quite different approaches to this problem. One comes from the mathematically principled technology of signatures and log-signatures as representations for streamed data, while the other draws on the techniques of recurrent neural networks (RNN). The ability of the former to manage high sample rate streams and the latter to manage large scale nonlinear interactions allows hybrid algorithms that are easy to code, quicker to train, and of lower complexity for a given accuracy. We illustrate the approach by approximating the unknown functional as a controlled differential equation. Linear functionals on solutions of controlled differential equations are the natural universal class of functions on data streams. Following this approach, we propose a hybrid Logsig-RNN algorithm that learns functionals on streamed data. By testing on various datasets, i.e. synthetic data, NTU RGB+D 120 skeletal action data, and Chalearn2013 gesture data, our algorithm achieves the outstanding accuracy with superior efficiency and robustness.

This paper introduces the award-winning deep learning (DL) library called LibAUC for implementing state-of-the-art algorithms towards optimizing a family of risk functions named X-risks. X-risks refer to a family of compositional functions in which the loss function of each data point is defined in a way that contrasts the data point with a large number of others. They have broad applications in AI for solving classical and emerging problems, including but not limited to classification for imbalanced data (CID), learning to rank (LTR), and contrastive learning of representations (CLR). The motivation of developing LibAUC is to address the convergence issues of existing libraries for solving these problems. In particular, existing libraries may not converge or require very large mini-batch sizes in order to attain good performance for these problems, due to the usage of the standard mini-batch technique in the empirical risk minimization (ERM) framework. Our library is for deep X-risk optimization (DXO) that has achieved great success in solving a variety of tasks for CID, LTR and CLR. The contributions of this paper include: (1) It introduces a new mini-batch based pipeline for implementing DXO algorithms, which differs from existing DL pipeline in the design of controlled data samplers and dynamic mini-batch losses; (2) It provides extensive benchmarking experiments for ablation studies and comparison with existing libraries. The LibAUC library features scalable performance for millions of items to be contrasted, faster and better convergence than existing libraries for optimizing X-risks, seamless PyTorch deployment and versatile APIs for various loss optimization. Our library is available to the open source community at https://github.com/Optimization-AI/LibAUC, to facilitate further academic research and industrial applications., Accepted by KDD2023

This paper proposes to learn Multi-task, Multi-modal Direct Acyclic Graphs (MM-DAGs), which are commonly observed in complex systems, e.g., traffic, manufacturing, and weather systems, whose variables are multi-modal with scalars, vectors, and functions. This paper takes the traffic congestion analysis as a concrete case, where a traffic intersection is usually regarded as a DAG. In a road network of multiple intersections, different intersections can only have some overlapping and distinct variables observed. For example, a signalized intersection has traffic light-related variables, whereas unsignalized ones do not. This encourages the multi-task design: with each DAG as a task, the MM-DAG tries to learn the multiple DAGs jointly so that their consensus and consistency are maximized. To this end, we innovatively propose a multi-modal regression for linear causal relationship description of different variables. Then we develop a novel Causality Difference (CD) measure and its differentiable approximator. Compared with existing SOTA measures, CD can penalize the causal structural difference among DAGs with distinct nodes and can better consider the uncertainty of causal orders. We rigidly prove our design's topological interpretation and consistency properties. We conduct thorough simulations and one case study to show the effectiveness of our MM-DAG. The code is available under https://github.com/Lantian72/MM-DAG, Accepted in SIGKDD 2023

When machine learning models are trained continually on a sequence of tasks, they are liable to forget what they learned on previous tasks -- a phenomenon known as catastrophic forgetting. Proposed solutions to catastrophic forgetting tend to involve storing information about past tasks, meaning that memory usage is a chief consideration in determining their practicality. This paper proposes a memory-efficient solution to catastrophic forgetting, improving upon an established algorithm known as orthogonal gradient descent (OGD). OGD utilizes prior model gradients to find weight updates that preserve performance on prior datapoints. However, since the memory cost of storing prior model gradients grows with the runtime of the algorithm, OGD is ill-suited to continual learning over arbitrarily long time horizons. To address this problem, this paper proposes SketchOGD. SketchOGD employs an online sketching algorithm to compress model gradients as they are encountered into a matrix of a fixed, user-determined size. In contrast to existing memory-efficient variants of OGD, SketchOGD runs online without the need for advance knowledge of the total number of tasks, is simple to implement, and is more amenable to analysis. We provide theoretical guarantees on the approximation error of the relevant sketches under a novel metric suited to the downstream task of OGD. Experimentally, we find that SketchOGD tends to outperform current state-of-the-art variants of OGD given a fixed memory budget.

In the early days of machine learning (ML), the emphasis was on developing complex algorithms to achieve best predictive performance. To understand and explain the model results, one had to rely on post hoc explainability techniques, which are known to have limitations. Recently, with the recognition that interpretability is just as important, researchers are compromising on small increases in predictive performance to develop algorithms that are inherently interpretable. While doing so, the ML community has rediscovered the use of low-order functional ANOVA (fANOVA) models that have been known in the statistical literature for some time. This paper starts with a description of challenges with post hoc explainability and reviews the fANOVA framework with a focus on main effects and second-order interactions. This is followed by an overview of two recently developed techniques: Explainable Boosting Machines or EBM (Lou et al., 2013) and GAMI-Net (Yang et al., 2021b). The paper proposes a new algorithm, called GAMI-Lin-T, that also uses trees like EBM, but it does linear fits instead of piecewise constants within the partitions. There are many other differences, including the development of a new interaction filtering algorithm. Finally, the paper uses simulated and real datasets to compare selected ML algorithms. The results show that GAMI-Lin-T and GAMI-Net have comparable performances, and both are generally better than EBM., 24 pages, 15 figures. arXiv admin note: substantial text overlap with arXiv:2207.06950

Deep kernel processes are a recently introduced class of deep Bayesian models that have the flexibility of neural networks, but work entirely with Gram matrices. They operate by alternately sampling a Gram matrix from a distribution over positive semi-definite matrices, and applying a deterministic transformation. When the distribution is chosen to be Wishart, the model is called a deep Wishart process (DWP). This particular model is of interest because its prior is equivalent to a deep Gaussian process (DGP) prior, but at the same time it is invariant to rotational symmetries, leading to a simpler posterior distribution. Practical inference in the DWP was made possible in recent work ("A variational approximate posterior for the deep Wishart process" Ober and Aitchison 2021a) where the authors used a generalisation of the Bartlett decomposition of the Wishart distribution as the variational approximate posterior. However, predictive performance in that paper was less impressive than one might expect, with the DWP only beating a DGP on a few of the UCI datasets used for comparison. In this paper, we show that further generalising their distribution to allow linear combinations of rows and columns in the Bartlett decomposition results in better predictive performance, while incurring negligible additional computation cost.

We introduce Multi-Objective Counterfactuals for Design (MCD), a novel method for counterfactual optimization in design problems. Counterfactuals are hypothetical situations that can lead to a different decision or choice. In this paper, the authors frame the counterfactual search problem as a design recommendation tool that can help identify modifications to a design, leading to better functional performance. MCD improves upon existing counterfactual search methods by supporting multi-objective queries, which are crucial in design problems, and by decoupling the counterfactual search and sampling processes, thus enhancing efficiency and facilitating objective tradeoff visualization. The paper demonstrates MCD's core functionality using a two-dimensional test case, followed by three case studies of bicycle design that showcase MCD's effectiveness in real-world design problems. In the first case study, MCD excels at recommending modifications to query designs that can significantly enhance functional performance, such as weight savings and improvements to the structural safety factor. The second case study demonstrates that MCD can work with a pre-trained language model to suggest design changes based on a subjective text prompt effectively. Lastly, the authors task MCD with increasing a query design's similarity to a target image and text prompt while simultaneously reducing weight and improving structural performance, demonstrating MCD's performance on a complex multimodal query. Overall, MCD has the potential to provide valuable recommendations for practitioners and design automation researchers looking for answers to their ``What if'' questions by exploring hypothetical design modifications and their impact on multiple design objectives. The code, test problems, and datasets used in the paper are available to the public at decode.mit.edu/projects/counterfactuals/.

The Pearson-Matthews correlation coefficient (usually abbreviated MCC) is considered to be one of the most useful metrics for the performance of a binary classification or hypothesis testing method (for the sake of conciseness we will use the classification terminology throughout, but the concepts and methods discussed in the paper apply verbatim to hypothesis testing as well). For multinary classification tasks (with more than two classes) the existing extension of MCC, commonly called the $\text{R}_{\text{K}}$ metric, has also been successfully used in many applications. The present paper begins with an introductory discussion on certain aspects of MCC. Then we go on to discuss the topic of multinary classification that is the main focus of this paper and which, despite its practical and theoretical importance, appears to be less developed than the topic of binary classification. Our discussion of the $\text{R}_{\text{K}}$ is followed by the introduction of two other metrics for multinary classification derived from the multivariate Pearson correlation (MPC) coefficients. We show that both $\text{R}_{\text{K}}$ and the MPC metrics suffer from the problem of not decisively indicating poor classification results when they should, and introduce three new enhanced metrics that do not suffer from this problem. We also present an additional new metric for multinary classification which can be viewed as a direct extension of MCC.

This paper investigates Gaussian copula mixture models (GCMM), which are an extension of Gaussian mixture models (GMM) that incorporate copula concepts. The paper presents the mathematical definition of GCMM and explores the properties of its likelihood function. Additionally, the paper proposes extended Expectation Maximum algorithms to estimate parameters for the mixture of copulas. The marginal distributions corresponding to each component are estimated separately using nonparametric statistical methods. In the experiment, GCMM demonstrates improved goodness-of-fitting compared to GMM when using the same number of clusters. Furthermore, GCMM has the ability to leverage un-synchronized data across dimensions for more comprehensive data analysis., 11 pages paper for theoretical properties and new algorithms for GCMM

In this paper, we provide a rigorous proof of convergence of the Adaptive Moment Estimate (Adam) algorithm for a wide class of optimization objectives. Despite the popularity and efficiency of the Adam algorithm in training deep neural networks, its theoretical properties are not yet fully understood, and existing convergence proofs require unrealistically strong assumptions, such as globally bounded gradients, to show the convergence to stationary points. In this paper, we show that Adam provably converges to $\epsilon$-stationary points with $\mathcal{O}(\epsilon^{-4})$ gradient complexity under far more realistic conditions. The key to our analysis is a new proof of boundedness of gradients along the optimization trajectory of Adam, under a generalized smoothness assumption according to which the local smoothness (i.e., Hessian norm when it exists) is bounded by a sub-quadratic function of the gradient norm. Moreover, we propose a variance-reduced version of Adam with an accelerated gradient complexity of $\mathcal{O}(\epsilon^{-3})$., Comment: 33 pages

Many techniques in machine learning attempt explicitly or implicitly to infer a low-dimensional manifold structure of an underlying physical phenomenon from measurements without an explicit model of the phenomenon or the measurement apparatus. This paper presents a cautionary tale regarding the discrepancy between the geometry of measurements and the geometry of the underlying phenomenon in a benign setting. The deformation in the metric illustrated in this paper is mathematically straightforward and unavoidable in the general case, and it is only one of several similar effects. While this is not always problematic, we provide an example of an arguably standard and harmless data processing procedure where this effect leads to an incorrect answer to a seemingly simple question. Although we focus on manifold learning, these issues apply broadly to dimensionality reduction and unsupervised learning., 7 pages, 9 figures

Anchors (Ribeiro et al., 2018) is a post-hoc, rule-based interpretability method. For text data, it proposes to explain a decision by highlighting a small set of words (an anchor) such that the model to explain has similar outputs when they are present in a document. In this paper, we present the first theoretical analysis of Anchors, considering that the search for the best anchor is exhaustive. After formalizing the algorithm for text classification, we present explicit results on different classes of models when the vectorization step is TF-IDF, and words are replaced by a fixed out-of-dictionary token when removed. Our inquiry covers models such as elementary if-then rules and linear classifiers. We then leverage this analysis to gain insights on the behavior of Anchors for any differentiable classifiers. For neural networks, we empirically show that the words corresponding to the highest partial derivatives of the model with respect to the input, reweighted by the inverse document frequencies, are selected by Anchors., Accepted to AISTATS 2023. 9+2 page paper, 21-page appendix

We study the generalization error of statistical learning models in a Federated Learning (FL) setting. Specifically, there are $K$ devices or clients, each holding an independent own dataset of size $n$. Individual models, learned locally via Stochastic Gradient Descent, are aggregated (averaged) by a central server into a global model and then sent back to the devices. We consider multiple (say $R \in \mathbb N^*$) rounds of model aggregation and study the effect of $R$ on the generalization error of the final aggregated model. We establish an upper bound on the generalization error that accounts explicitly for the effect of $R$ (in addition to the number of participating devices $K$ and dataset size $n$). It is observed that, for fixed $(n, K)$, the bound increases with $R$, suggesting that the generalization of such learning algorithms is negatively affected by more frequent communication with the parameter server. Combined with the fact that the empirical risk, however, generally decreases for larger values of $R$, this indicates that $R$ might be a parameter to optimize to reduce the population risk of FL algorithms. The results of this paper, which extend straightforwardly to the heterogeneous data setting, are also illustrated through numerical examples., Extended version of paper accepted at ISIT 2023

This paper introduces a stochastic plug-and-play (PnP) sampling algorithm that leverages variable splitting to efficiently sample from a posterior distribution. The algorithm based on split Gibbs sampling (SGS) draws inspiration from the alternating direction method of multipliers (ADMM). It divides the challenging task of posterior sampling into two simpler sampling problems. The first problem depends on the likelihood function, while the second is interpreted as a Bayesian denoising problem that can be readily carried out by a deep generative model. Specifically, for an illustrative purpose, the proposed method is implemented in this paper using state-of-the-art diffusion-based generative models. Akin to its deterministic PnP-based counterparts, the proposed method exhibits the great advantage of not requiring an explicit choice of the prior distribution, which is rather encoded into a pre-trained generative model. However, unlike optimization methods (e.g., PnP-ADMM) which generally provide only point estimates, the proposed approach allows conventional Bayesian estimators to be accompanied by confidence intervals at a reasonable additional computational cost. Experiments on commonly studied image processing problems illustrate the efficiency of the proposed sampling strategy. Its performance is compared to recent state-of-the-art optimization and sampling methods.

Manufacturing advanced materials and products with a specific property or combination of properties is often warranted. To achieve that it is crucial to find out the optimum recipe or processing conditions that can generate the ideal combination of these properties. Most of the time, a sufficient number of experiments are needed to generate a Pareto front. However, manufacturing experiments are usually costly and even conducting a single experiment can be a time-consuming process. So, it's critical to determine the optimal location for data collection to gain the most comprehensive understanding of the process. Sequential learning is a promising approach to actively learn from the ongoing experiments, iteratively update the underlying optimization routine, and adapt the data collection process on the go. This paper presents a novel data-driven Bayesian optimization framework that utilizes sequential learning to efficiently optimize complex systems with multiple conflicting objectives. Additionally, this paper proposes a novel metric for evaluating multi-objective data-driven optimization approaches. This metric considers both the quality of the Pareto front and the amount of data used to generate it. The proposed framework is particularly beneficial in practical applications where acquiring data can be expensive and resource intensive. To demonstrate the effectiveness of the proposed algorithm and metric, the algorithm is evaluated on a manufacturing dataset. The results indicate that the proposed algorithm can achieve the actual Pareto front while processing significantly less data. It implies that the proposed data-driven framework can lead to similar manufacturing decisions with reduced costs and time.

In this paper, we propose a randomly projected convex clustering model for clustering a collection of $n$ high dimensional data points in $\mathbb{R}^d$ with $K$ hidden clusters. Compared to the convex clustering model for clustering original data with dimension $d$, we prove that, under some mild conditions, the perfect recovery of the cluster membership assignments of the convex clustering model, if exists, can be preserved by the randomly projected convex clustering model with embedding dimension $m = O(\epsilon^{-2}\log(n))$, where $0 < \epsilon < 1$ is some given parameter. We further prove that the embedding dimension can be improved to be $O(\epsilon^{-2}\log(K))$, which is independent of the number of data points. Extensive numerical experiment results will be presented in this paper to demonstrate the robustness and superior performance of the randomly projected convex clustering model. The numerical results presented in this paper also demonstrate that the randomly projected convex clustering model can outperform the randomly projected K-means model in practice.

In this paper, we study the well-known "Heavy Ball" method for convex and nonconvex optimization introduced by Polyak in 1964, and establish its convergence under a variety of situations. Traditionally, most algorithms use "full-coordinate update," that is, at each step, every component of the argument is updated. However, when the dimension of the argument is very high, it is more efficient to update some but not all components of the argument at each iteration. We refer to this as "batch updating" in this paper. When gradient-based algorithms are used together with batch updating, in principle it is sufficient to compute only those components of the gradient for which the argument is to be updated. However, if a method such as backpropagation is used to compute these components, computing only some components of gradient does not offer much savings over computing the entire gradient. Therefore, to achieve a noticeable reduction in CPU usage at each step, one can use first-order differences to approximate the gradient. The resulting estimates are biased, and also have unbounded variance. Thus some delicate analysis is required to ensure that the HB algorithm converge when batch updating is used instead of full-coordinate updating, and/or approximate gradients are used instead of true gradients. In this paper, we establish the almost sure convergence of the iterations to the stationary point(s) of the objective function under suitable conditions; in addition, we also derive upper bounds on the rate of convergence. To the best of our knowledge, there is no other paper that combines all of these features. This paper is dedicated to the memory of Boris Teodorovich Polyak, 33 pages, 6 figures