pwc-archive/papers-with-abstracts huggingface dataset:
Variational Bayes for high-dimensional proportional hazards models with applications within gene expression
Authors: Michael Komodromos, Eric Aboagye, Marina Evangelou, Sarah Filippi, Kolyan Ray
Date: 2021-12-19 00:00:00
Tasks: Uncertainty Quantification, Variable Selection

Few Bayesian methods for analyzing high-dimensional sparse survival data provide scalable variable selection, effect estimation and uncertainty quantification. Such methods often either sacrifice uncertainty quantification by computing maximum a posteriori estimates, or quantify the uncertainty at high (unscalable) computational expense. We bridge this gap and develop an interpretable and scalable Bayesian proportional hazards model for prediction and variable selection, referred to as SVB. Our method, based on a mean-field variational approximation, overcomes the high computational cost of MCMC whilst retaining useful features, providing a posterior distribution for the parameters and offering a natural mechanism for variable selection via posterior inclusion probabilities. The performance of our proposed method is assessed via extensive simulations and compared against other state-of-the-art Bayesian variable selection methods, demonstrating comparable or better performance. Finally, we demonstrate how the proposed method can be used for variable selection on two transcriptomic datasets with censored survival outcomes, and how the uncertainty quantification offered by our method can be used to provide an interpretable assessment of patient risk.
Mixed Precision of Quantization of Transformer Language Models for Speech Recognition
Authors: Junhao Xu, Shoukang Hu, Jianwei Yu, Xunying Liu, Helen Meng
Date: 2021-11-29 00:00:00
Tasks: Quantization, Sensitivity, speech-recognition, Speech Recognition

State-of-the-art neural language models represented by Transformers are becoming increasingly complex and expensive for practical applications. Low-bit deep neural network quantization techniques provides a powerful solution to dramatically reduce their model size. Current low-bit quantization methods are based on uniform precision and fail to account for the varying performance sensitivity at different parts of the system to quantization errors. To this end, novel mixed precision DNN quantization methods are proposed in this paper. The optimal local precision settings are automatically learned using two techniques. The first is based on a quantization sensitivity metric in the form of Hessian trace weighted quantization perturbation. The second is based on mixed precision Transformer architecture search. Alternating direction methods of multipliers (ADMM) are used to efficiently train mixed precision quantized DNN systems. Experiments conducted on Penn Treebank (PTB) and a Switchboard corpus trained LF-MMI TDNN system suggest the proposed mixed precision Transformer quantization techniques achieved model size compression ratios of up to 16 times over the full precision baseline with no recognition performance degradation. When being used to compress a larger full precision Transformer LM with more layers, overall word error rate (WER) reductions up to 1.7% absolute (18% relative) were obtained.
Stable Conformal Prediction Sets
Authors: Eugene Ndiaye
Date: 2021-12-19 00:00:00
Tasks: Conformal Prediction, Prediction

When one observes a sequence of variables $(x_1, y_1), \ldots, (x_n, y_n)$, Conformal Prediction (CP) is a methodology that allows to estimate a confidence set for $y_{n+1}$ given $x_{n+1}$ by merely assuming that the distribution of the data is exchangeable. CP sets have guaranteed coverage for any finite population size $n$. While appealing, the computation of such a set turns out to be infeasible in general, e.g. when the unknown variable $y_{n+1}$ is continuous. The bottleneck is that it is based on a procedure that readjusts a prediction model on data where we replace the unknown target by all its possible values in order to select the most probable one. This requires computing an infinite number of models, which often makes it intractable. In this paper, we combine CP techniques with classical algorithmic stability bounds to derive a prediction set computable with a single model fit. We demonstrate that our proposed confidence set does not lose any coverage guarantees while avoiding the need for data splitting as currently done in the literature. We provide some numerical experiments to illustrate the tightness of our estimation when the sample size is sufficiently large, on both synthetic and real datasets.
RELAX: Representation Learning Explainability
Authors: Kristoffer K. Wickstrøm, Daniel J. Trosten, Sigurd Løkse, Ahcène Boubekki, Karl Øyvind Mikalsen, Michael C. Kampffmeyer, Robert Jenssen
Date: 2021-12-19 00:00:00
Tasks: Representation Learning

Despite the significant improvements that representation learning via self-supervision has led to when learning from unlabeled data, no methods exist that explain what influences the learned representation. We address this need through our proposed approach, RELAX, which is the first approach for attribution-based explanations of representations. Our approach can also model the uncertainty in its explanations, which is essential to produce trustworthy explanations. RELAX explains representations by measuring similarities in the representation space between an input and masked out versions of itself, providing intuitive explanations and significantly outperforming the gradient-based baseline. We provide theoretical interpretations of RELAX and conduct a novel analysis of feature extractors trained using supervised and unsupervised learning, providing insights into different learning strategies. Finally, we illustrate the usability of RELAX in multi-view clustering and highlight that incorporating uncertainty can be essential for providing low-complexity explanations, taking a crucial step towards explaining representations.
Information Field Theory and Artificial Intelligence
Authors: Torsten Enßlin
Date: 2021-12-19 00:00:00
Tasks: Variational Inference

Information field theory (IFT), the information theory for fields, is a mathematical framework for signal reconstruction and non-parametric inverse problems. Artificial intelligence (AI) and machine learning (ML) aim at generating intelligent systems including such for perception, cognition, and learning. This overlaps with IFT, which is designed to address perception, reasoning, and inference tasks. Here, the relation between concepts and tools in IFT and those in AI and ML research are discussed. In the context of IFT, fields denote physical quantities that change continuously as a function of space (and time) and information theory refers to Bayesian probabilistic logic equipped with the associated entropic information measures. Reconstructing a signal with IFT is a computational problem similar to training a generative neural network (GNN) in ML. In this paper, the process of inference in IFT is reformulated in terms of GNN training. In contrast to classical neural networks, IFT based GNNs can operate without pre-training thanks to incorporating expert knowledge into their architecture. Furthermore, the cross-fertilization of variational inference methods used in IFT and ML are discussed. These discussions suggests that IFT is well suited to address many problems in AI and ML research and application.
Multimeasurement Generative Models
Authors: Saeed Saremi, Rupesh Kumar Srivastava
Date: 2021-12-18 00:00:00
Proceeding: ICLR 2022 4
Tasks: Denoising

We formally map the problem of sampling from an unknown distribution with a density in $\mathbb{R}^d$ to the problem of learning and sampling a smoother density in $\mathbb{R}^{Md}$ obtained by convolution with a fixed factorial kernel: the new density is referred to as M-density and the kernel as multimeasurement noise model (MNM). The M-density in $\mathbb{R}^{Md}$ is smoother than the original density in $\mathbb{R}^d$, easier to learn and sample from, yet for large $M$ the two problems are mathematically equivalent since clean data can be estimated exactly given a multimeasurement noisy observation using the Bayes estimator. To formulate the problem, we derive the Bayes estimator for Poisson and Gaussian MNMs in closed form in terms of the unnormalized M-density. This leads to a simple least-squares objective for learning parametric energy and score functions. We present various parametrization schemes of interest including one in which studying Gaussian M-densities directly leads to multidenoising autoencoders--this is the first theoretical connection made between denoising autoencoders and empirical Bayes in the literature. Samples in $\mathbb{R}^d$ are obtained by walk-jump sampling (Saremi & Hyvarinen, 2019) via underdamped Langevin MCMC (walk) to sample from M-density and the multimeasurement Bayes estimation (jump). We study permutation invariant Gaussian M-densities on MNIST, CIFAR-10, and FFHQ-256 datasets, and demonstrate the effectiveness of this framework for realizing fast-mixing stable Markov chains in high dimensions.
GPEX, A Framework For Interpreting Artificial Neural Networks
Authors: Amir Akbarnejad, Gilbert Bigras, Nilanjan Ray
Date: 2021-12-18 00:00:00
Proceeding: NeurIPS 2023 11
Tasks: Gaussian Processes, GPU

The analogy between Gaussian processes (GPs) and deep artificial neural networks (ANNs) has received a lot of interest, and has shown promise to unbox the blackbox of deep ANNs. Existing theoretical works put strict assumptions on the ANN (e.g. requiring all intermediate layers to be wide, or using specific activation functions). Accommodating those theoretical assumptions is hard in recent deep architectures, and those theoretical conditions need refinement as new deep architectures emerge. In this paper we derive an evidence lower-bound that encourages the GP's posterior to match the ANN's output without any requirement on the ANN. Using our method we find out that on 5 datasets, only a subset of those theoretical assumptions are sufficient. Indeed, in our experiments we used a normal ResNet-18 or feed-forward backbone with a single wide layer in the end. One limitation of training GPs is the lack of scalability with respect to the number of inducing points. We use novel computational techniques that allow us to train GPs with hundreds of thousands of inducing points and with GPU acceleration. As shown in our experiments, doing so has been essential to get a close match between the GPs and the ANNs on 5 datasets. We implement our method as a publicly available tool called GPEX: https://github.com/amirakbarnejad/gpex. On 5 datasets (4 image datasets, and 1 biological dataset) and ANNs with 2 types of functionality (classifier or attention-mechanism) we were able to find GPs whose outputs closely match those of the corresponding ANNs. After matching the GPs to the ANNs, we used the GPs' kernel functions to explain the ANNs' decisions. We provide more than 200 explanations (around 30 explanations in the paper and the rest in the supplementary) which are highly interpretable by humans and show the ability of the obtained GPs to unbox the ANNs' decisions.
AutoTransfer: Subject Transfer Learning with Censored Representations on Biosignals Data
Authors: Niklas Smedemark-Margulies, Ye Wang, Toshiaki Koike-Akino, Deniz Erdogmus
Date: 2021-12-17 00:00:00
Tasks: EEG, Electroencephalogram (EEG), Subject Transfer, Transfer Learning

We provide a regularization framework for subject transfer learning in which we seek to train an encoder and classifier to minimize classification loss, subject to a penalty measuring independence between the latent representation and the subject label. We introduce three notions of independence and corresponding penalty terms using mutual information or divergence as a proxy for independence. For each penalty term, we provide several concrete estimation algorithms, using analytic methods as well as neural critic functions. We provide a hands-off strategy for applying this diverse family of regularization algorithms to a new dataset, which we call "AutoTransfer". We evaluate the performance of these individual regularization strategies and our AutoTransfer method on EEG, EMG, and ECoG datasets, showing that these approaches can improve subject transfer learning for challenging real-world datasets.
Discrete Probabilistic Inverse Optimal Transport
Authors: Wei-Ting Chiu, Pei Wang, Patrick Shafto
Date: 2021-12-17 00:00:00

Optimal transport (OT) formalizes the problem of finding an optimal coupling between probability measures given a cost matrix. The inverse problem of inferring the cost given a coupling is Inverse Optimal Transport (IOT). IOT is less well understood than OT. We formalize and systematically analyze the properties of IOT using tools from the study of entropy-regularized OT. Theoretical contributions include characterization of the manifold of cross-ratio equivalent costs, the implications of model priors, and derivation of an MCMC sampler. Empirical contributions include visualizations of cross-ratio equivalent effect on basic examples and simulations validating theoretical results.
Supervised Multivariate Learning with Simultaneous Feature Auto-grouping and Dimension Reduction
Authors: Yiyuan She, Jiahui Shen, Chao Zhang
Date: 2021-12-17 00:00:00
Tasks: Dimensionality Reduction, Variable Selection

Modern high-dimensional methods often adopt the "bet on sparsity" principle, while in supervised multivariate learning statisticians may face "dense" problems with a large number of nonzero coefficients. This paper proposes a novel clustered reduced-rank learning (CRL) framework that imposes two joint matrix regularizations to automatically group the features in constructing predictive factors. CRL is more interpretable than low-rank modeling and relaxes the stringent sparsity assumption in variable selection. In this paper, new information-theoretical limits are presented to reveal the intrinsic cost of seeking for clusters, as well as the blessing from dimensionality in multivariate learning. Moreover, an efficient optimization algorithm is developed, which performs subspace learning and clustering with guaranteed convergence. The obtained fixed-point estimators, though not necessarily globally optimal, enjoy the desired statistical accuracy beyond the standard likelihood setup under some regularity conditions. Moreover, a new kind of information criterion, as well as its scale-free form, is proposed for cluster and rank selection, and has a rigorous theoretical support without assuming an infinite sample size. Extensive simulations and real-data experiments demonstrate the statistical accuracy and interpretability of the proposed method.
Envisioning Future Deep Learning Theories: Some Basic Concepts and Characteristics
Authors: Weijie J. Su
Date: 2021-12-17 00:00:00
Tasks: Deep Learning, Learning Theory

To advance deep learning methodologies in the next decade, a theoretical framework for reasoning about modern neural networks is needed. While efforts are increasing toward demystifying why deep learning is so effective, a comprehensive picture remains lacking, suggesting that a better theory is possible. We argue that a future deep learning theory should inherit three characteristics: a \textit{hierarchically} structured network architecture, parameters \textit{iteratively} optimized using stochastic gradient-based methods, and information from the data that evolves \textit{compressively}. As an instantiation, we integrate these characteristics into a graphical model called \textit{neurashed}. This model effectively explains some common empirical patterns in deep learning. In particular, neurashed enables insights into implicit regularization, information bottleneck, and local elasticity. Finally, we discuss how neurashed can guide the development of deep learning theories.
Silent Bugs in Deep Learning Frameworks: An Empirical Study of Keras and TensorFlow
Authors: Florian Tambon, Amin Nikanjam, Le An, Foutse khomh, Giuliano Antoniol
Date: 2021-12-26 00:00:00

Deep Learning (DL) frameworks are now widely used, simplifying the creation of complex models as well as their integration to various applications even to non DL experts. However, like any other programs, they are prone to bugs. This paper deals with the subcategory of bugs named silent bugs: they lead to wrong behavior but they do not cause system crashes or hangs, nor show an error message to the user. Such bugs are even more dangerous in DL applications and frameworks due to the "black-box" and stochastic nature of the systems (the end user can not understand how the model makes decisions). This paper presents the first empirical study of Keras and TensorFlow silent bugs, and their impact on users' programs. We extracted closed issues related to Keras from the TensorFlow GitHub repository. Out of the 1,168 issues that we gathered, 77 were reproducible silent bugs affecting users' programs. We categorized the bugs based on the effects on the users' programs and the components where the issues occurred, using information from the issue reports. We then derived a threat level for each of the issues, based on the impact they had on the users' programs. To assess the relevance of identified categories and the impact scale, we conducted an online survey with 103 DL developers. The participants generally agreed with the significant impact of silent bugs in DL libraries and acknowledged our findings (i.e., categories of silent bugs and the proposed impact scale). Finally, leveraging our analysis, we provide a set of guidelines to facilitate safeguarding against such bugs in DL frameworks.
End to End Software Engineering Research
Authors: Idan Amit
Date: 2021-12-22 00:00:00
Tasks: BIG-bench Machine Learning

End to end learning is machine learning starting in raw data and predicting a desired concept, with all steps done automatically. In software engineering context, we see it as starting from the source code and predicting process metrics. This framework can be used for predicting defects, code quality, productivity and more. End-to-end improves over features based machine learning by not requiring domain experts and being able to extract new knowledge. We describe a dataset of 5M files from 15k projects constructed for this goal. The dataset is constructed in a way that enables not only predicting concepts but also investigating their causes.
VELVET: a noVel Ensemble Learning approach to automatically locate VulnErable sTatements
Authors: Yangruibo Ding, Sahil Suneja, Yunhui Zheng, Jim Laredo, Alessandro Morari, Gail Kaiser, Baishakhi Ray
Date: 2021-12-20 00:00:00
Tasks: Ensemble Learning

Automatically locating vulnerable statements in source code is crucial to assure software security and alleviate developers' debugging efforts. This becomes even more important in today's software ecosystem, where vulnerable code can flow easily and unwittingly within and across software repositories like GitHub. Across such millions of lines of code, traditional static and dynamic approaches struggle to scale. Although existing machine-learning-based approaches look promising in such a setting, most work detects vulnerable code at a higher granularity -- at the method or file level. Thus, developers still need to inspect a significant amount of code to locate the vulnerable statement(s) that need to be fixed. This paper presents VELVET, a novel ensemble learning approach to locate vulnerable statements. Our model combines graph-based and sequence-based neural networks to successfully capture the local and global context of a program graph and effectively understand code semantics and vulnerable patterns. To study VELVET's effectiveness, we use an off-the-shelf synthetic dataset and a recently published real-world dataset. In the static analysis setting, where vulnerable functions are not detected in advance, VELVET achieves 4.5x better performance than the baseline static analyzers on the real-world data. For the isolated vulnerability localization task, where we assume the vulnerability of a function is known while the specific vulnerable statement is unknown, we compare VELVET with several neural networks that also attend to local and global context of code. VELVET achieves 99.6% and 43.6% top-1 accuracy over synthetic data and real-world data, respectively, outperforming the baseline deep-learning models by 5.3-29.0%.
Joint machine learning analysis of muon spectroscopy data from different materials
Authors: T. Tula, G. Möller, J. Quintanilla, S. R. Giblin, A. D. Hillier, E. E. McCabe, S. Ramos, D. S. Barker, S. Gibson
Date: 2021-12-17 00:00:00
Tasks: BIG-bench Machine Learning

Machine learning (ML) methods have proved to be a very successful tool in physical sciences, especially when applied to experimental data analysis. Artificial intelligence is particularly good at recognizing patterns in high dimensional data, where it usually outperforms humans. Here we applied a simple ML tool called principal component analysis (PCA) to study data from muon spectroscopy. The measured quantity from this experiment is an asymmetry function, which holds the information about the average intrinsic magnetic field of the sample. A change in the asymmetry function might indicate a phase transition; however, these changes can be very subtle, and existing methods of analyzing the data require knowledge about the specific physics of the material. PCA is an unsupervised ML tool, which means that no assumption about the input data is required, yet we found that it still can be successfully applied to asymmetry curves, and the indications of phase transitions can be recovered. The method was applied to a range of magnetic materials with different underlying physics. We discovered that performing PCA on all those materials simultaneously can have a positive effect on the clarity of phase transition indicators and can also improve the detection of the most important variations of asymmetry functions. For this joint PCA we introduce a simple way to track the contributions from different materials for a more meaningful analysis.
Towards Trustworthy Cross-patient Model Development
Authors: Ali El-Merhi, Helena Odenstedt Hergés, Linda Block, Mikael Elam, Richard Vithal, Jaquette Liljencrantz, Miroslaw Staron
Date: 2021-12-20 00:00:00
Tasks: model

Machine learning is used in medicine to support physicians in examination, diagnosis, and predicting outcomes. One of the most dynamic area is the usage of patient generated health data from intensive care units. The goal of this paper is to demonstrate how we advance cross-patient ML model development by combining the patient's demographics data with their physiological data. We used a population of patients undergoing Carotid Enderarterectomy (CEA), where we studied differences in model performance and explainability when trained for all patients and one patient at a time. The results show that patients' demographics has a large impact on the performance and explainability and thus trustworthiness. We conclude that we can increase trust in ML models in a cross-patient context, by careful selection of models and patients based on their demographics and the surgical procedure.