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Inferring the Effects of Protein Variants on Protein-Protein Interactions with Interpretable Transformer Representations

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Research 2024年第2期2023卷 473-489页

作者： Zhe Liu Wei Qian Wenxiang Cai Weichen Song Weidi Wang Dhruba Tara Maharjan Wenhong Cheng Jue Chen Han Wang Dong Xu Guan Ning Lin Shanghai Mental Health Center Shanghai Jiao Tong University School of MedicineSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghaiChina Shanghai Key Laboratory of Psychotic Disorders ShanghaiChina School of Information Science and Technology Institute of Computational BiologyNortheast Normal UniversityChangchunChina Department of Electrical Engineering and Computer Science University of MissouriColumbiaMO 65211USA Christopher S.Bond Life Sciences Center University of MissouriColumbiaMO 65211USA

Identifying pathogenetic variants and inferring their impact on protein-protein interactions sheds light on their functional consequences on *** by the availability of experimental data on the consequences of protein interaction,most existing methods focus on building models to predict changes in protein binding ***,we introduced MIPPI,an end-to-end,interpretable transformer-based deep learning model that learns features directly from sequences by leveraging the interaction data from *** was specifically trained to determine the types of variant impact(increasing,decreasing,disrupting,and no effect)on protein-protein *** demonstrate the accuracy of MIPPI and provide interpretation through the analysis of learned attention weights,which exhibit correlations with the amino acids interacting with the ***,we showed the practicality of MIPPI in prioritizing de novo mutations associated with complex neurodevelopmental disorders and the potential to determine the pathogenic and driving ***,we experimentally validated the functional impact of several variants identified in patients with such ***,MIPPI emerges as a versatile,robust,and interpretable model,capable of effectively predicting mutation impacts on protein-protein interactions and facilitating the discovery of clinically actionable variants.

关键词： consequences weights versatile

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Efficient Optimal Control of Open Quantum Systems 19

Efficient Optimal Control of Open Quantum Systems

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19th Conference on the Theory of Quantum Computation, Communication and Cryptography, TQC 2024

作者： He, Wenhao Li, Tongyang Li, Xiantao Li, Zecheng Wang, Chunhao Wang, Ke Center for Computational Science and Engineering MIT CambridgeMA United States School of Physics Peking University Beijing China Center on Frontiers of Computing Studies School of Computer Science Peking University Beijing China Department of Mathematics Pennsylvania State University University ParkPA United States Department of Computer Science and Engineering Pennsylvania State University University ParkPA United States

ISBN: (纸本)9783959773287

The optimal control problem for open quantum systems can be formulated as a time-dependent Lindbladian that is parameterized by a number of time-dependent control variables. Given an observable and an initial state, the goal is to tune the control variables so that the expected value of some observable with respect to the final state is maximized. In this paper, we present algorithms for solving this optimal control problem efficiently, i.e., having a poly-logarithmic dependency on the system dimension, which is exponentially faster than best-known classical algorithms. Our algorithms are hybrid, consisting of both quantum and classical components. The quantum procedure simulates time-dependent Lindblad evolution that drives the initial state to the final state, and it also provides access to the gradients of the objective function via quantum gradient estimation. The classical procedure uses the gradient information to update the control variables. At the technical level, we provide the first (to the best of our knowledge) simulation algorithm for time-dependent Lindbladians with an 1-norm dependence. As an alternative, we also present a simulation algorithm in the interaction picture to improve the algorithm for the cases where the time-independent component of a Lindbladian dominates the time-dependent part. On the classical side, we heavily adapt the state-of-the-art classical optimization analysis to interface with the quantum part of our algorithms. Both the quantum simulation techniques and the classical optimization analyses might be of independent interest. © Wenhao He, Tongyang Li, Xiantao Li, Zecheng Li, Chunhao Wang, and Ke Wang.

关键词： Optimal control systems

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Meta Generative Data Augmentation Optimization

Meta Generative Data Augmentation Optimization

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2023 Congress in computer science, computer Engineering, and Applied Computing, CSCE 2023

作者： Zhang, Enzhi Dong, Bochen Wahib, Mohamed Zhong, Rui Munetomo, Masaharu Grad. School of Info. Science and Technology Hokkaido University Sapporo Japan Western University Department of Computer Science London Canada Riken Center for Computational Science Kobe Japan Hokkaido University Information Initiative Center Sapporo Japan

ISBN: (纸本)9798350327595

This paper proposes a method called Meta Gener-ative Data Augmentation Optimization (MGDAO) to overcome limitations in existing data augmentation techniques. While traditional data augmentation methods have relied on expert intuition to determine effective transformations, recent approaches have attempted to generate data augmentation strategies automatically. However, these automatic methods can still suffer from limited operation sets, high computational costs, or difficulty in training conditional generative models. To address these issues, MGDAO replaces the limited operations space in the AutoAugment series with a deep-style generator and replaces the discriminator in a generative adversarial model with the validation loss of the target model. The generator learns to transform the data from the training domain to the validation data domain. It is further used to generate data-augmented samples to train the target model and reduce the validation loss. Experiments on few-shot image classification benchmarks show that MGDAO achieves competitive results compared to existing data auto-augmentation methods. © 2023 IEEE.

关键词： data augmentation few-shot learning generative models hyper gradient meta-learning

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BAYESIAN ORACLE FOR BOUNDING INFORMATION GAIN IN NEURAL ENCODING MODELS 11

BAYESIAN ORACLE FOR BOUNDING INFORMATION GAIN IN NEURAL ENCO...

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11th International Conference on Learning Representations, ICLR 2023

作者： Lurz, Konstantin-Klemens Bashiri, Mohammad Walker, Edgar Y. Sinz, Fabian H. Institute for Bioinformatics and Medical Informatics University of Tübingen Germany Department of Physiology Computational Neuroscience Center University of Washington United States Department of Computer Science University Göttingen Germany

In recent years, deep learning models have set new standards in predicting neural population responses. Most of these models currently focus on predicting the mean response of each neuron for a given input. However, neural variability around this mean is not just noise and plays a central role in several theories on neural computation. To capture this variability, we need models that predict full response distributions for a given stimulus. However, to measure the quality of such models, commonly used correlation-based metrics are not sufficient as they mainly care about the mean of the response distribution. An interpretable alternative evaluation metric for likelihood-based models is Normalized Information Gain (NInGa) which evaluates the likelihood of a model relative to a lower and upper bound. However, while a lower bound is usually easy to obtain, constructing an upper bound turns out to be challenging for neural recordings with relatively low numbers of repeated trials, high (shared) variability, and sparse responses. In this work, we generalize the jack-knife oracle estimator for the mean-commonly used for correlation metrics-to a flexible Bayesian oracle estimator for NInGa based on posterior predictive distributions. We describe and address the challenges that arise when estimating the lower and upper bounds from small datasets. We then show that our upper bound estimate is data-efficient and robust even in the case of sparse responses and low signal-to-noise ratio. We further provide the derivation of the upper bound estimator for a variety of common distributions including the state-of-the-art zero-inflated mixture models, and relate NInGa to common mean-based metrics. Finally, we use our approach to evaluate such a mixture model resulting in 90% NInGa performance. © 2023 11th International Conference on Learning Representations, ICLR 2023. All rights reserved.

关键词： Signal to noise ratio

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Deep Learning Model for computer Vision: Sustainable Image Classification Using Machine Learning 1st

Deep Learning Model for Computer Vision: Sustainable Image C...

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1st International Conference on Sustainable Development through Machine Learning, Artificial Intelligence, and IoT, ICSD 2023

作者： Alankar, Bhavya Chauhan, Ritu Kaur, Harleen Ebadati, E. Omid Mahdi Department of Computer Science and Engineering School of Engineering Sciences and Technology Jamia Hamdard New Delhi India Artificial Intelligence and IoT Lab Center for Computational Biology and Bioinformatics Amity University UP Noida India Department of Mathematics and Computer Science Kharazmi University Tehran Iran

ISBN: (纸本)9783031470547

The core challenge within computer vision is image classification, which involves assigning an image a label and categorizing it using the features that have been extracted from it. Even though this work appears rudimentary, it requires the application involving artificial intelligence, specifically Deep Learning, a subfield of Machine Learning. In this paper, we have discussed how Convolutional Neural Networks (CNN), the most modern technique for image classification, are used in Deep Learning to classify images. We have discussed the applications of image classification and drawn the conclusion that using deep learning is preferable to using machine learning. Additionally, we have also presented a comparative study of various CNN models to observe how they could potentially be employed as pre-trained models for the image classification job. © 2023, The Author(s), under exclusive license to Springer Nature Switzerland AG.

关键词： Convolution

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Level Set Teleportation: An Optimization Perspective

arXiv

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arXiv 2024年

作者： Mishkin, Aaron Bietti, Alberto Gower, Robert M. Department of Computer Science Stanford University United States Center for Computational Mathematics Flatiron Institute

We study level set teleportation, an optimization sub-routine which seeks to accelerate gradient methods by maximizing the gradient norm on a level-set of the objective function. Since the descent lemma implies that gradient descent (GD) decreases the objective proportional to the squared norm of the gradient, level-set teleportation maximizes this one-step progress guarantee. For convex functions satisfying Hessian stability, we prove that GD with level-set teleportation obtains a combined sub-linear/linear convergence rate which is strictly faster than standard GD when the optimality gap is small. This is in sharp contrast to the standard (strongly) convex setting, where we show level-set teleportation neither improves nor worsens convergence rates. To evaluate teleportation in practice, we develop a projected-gradient-type method requiring only Hessian-vector products. We use this method to show that gradient methods with access to a teleportation oracle uniformly out-perform their standard versions on a variety of learning problems. Copyright © 2024, The Authors. All rights reserved.

关键词： Gradient methods

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Designing Adaptive Multiple Dependent State Sampling Plan for Accelerated Life Tests

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computer Systems science & Engineering 2023年第8期46卷 1631-1651页

作者： Pramote Charongrattanasakul Wimonmas Bamrungsetthapong Poom Kumam Division of Mathematics Department of Mathematics and Computer ScienceFaculty of Science and TechnologyRajamangala University of Technology KrungthepBangkok10120Thailand Division of Applied Statistics Department of Mathematics and Computer ScienceFaculty of Science and TechnologyRajamangala University of Technology ThanyaburiPathum Thani12110Thailand Center of Excellence in Theoretical and Computational Science(TaCS-CoE)&KMUTT Fixed Point Research Laboratory Room SCL 802 Fixed Point LaboratoryScience Laboratory BuildingDepartments of MathematicsFaculty of ScienceKing Mongkut’s University of Technology Thonburi(KMUTT)Bangkok10140Thailand

A novel adaptive multiple dependent state sampling plan(AMDSSP)was designed to inspect products from a continuous manufacturing process under the accelerated life test(ALT)using both double sampling plan(DSP)and multiple dependent state sampling plan(MDSSP)*** accelerated conditions,the lifetime of a product follows the Weibull distribution with a known shape parameter,while the scale parameter can be determined using the acceleration factor(AF).The Arrhenius model is used to estimate AF when the damaging process is *** economic design of the proposed sampling plan was also considered for the ALT.A genetic algorithm with nonlinear optimization was used to estimate optimal plan parameters to minimize the average sample number(ASN)and total cost of inspection(TC)under both producer’s and consumer’s *** results are presented to support the AMDSSP for the ALT,while performance comparisons between the AMDSSP,the MDSSP and a single sampling plan(SSP)for the ALT are *** indicated that the AMDSSP was more flexible and efficient for ASN and TC than the MDSSP and SSP plans under accelerated *** AMDSSP also had a higher operating characteristic(OC)curve than both the existing sampling *** real datasets of electronic devices for the ALT at high temperatures demonstrated the practicality and usefulness of the proposed sampling plan.

关键词： Accelerated life test acceleration factor adaptive of multiple dependent state sampling plan average sample number total cost of inspection weibull distribution

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Pareto smoothed importance sampling

The Journal of Machine Learning Research

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The Journal of Machine Learning Research 2024年第1期25卷 3491-3548页

作者： Aki Vehtari Daniel Simpson Andrew Gelman Yuling Yao Jonah Gabry Department of Computer Science Aalto University Normal Computing Departments of Statistics and Political Science Columbia University Center for Computational Mathematics Flatiron Institute Department of Statistics Columbia University

Importance weighting is a general way to adjust Monte Carlo integration to account for draws from the wrong distribution, but the resulting estimate can be highly variable when the importance ratios have a heavy right tail. This routinely occurs when there are aspects of the target distribution that are not well captured by the approximating distribution, in which case more stable estimates can be obtained by modifying extreme importance ratios. We present a new method for stabilizing importance weights using a generalized Pareto distribution fit to the upper tail of the distribution of the simulated importance ratios. The method, which empirically performs better than existing methods for stabilizing importance sampling estimates, includes stabilized effective sample size estimates, Monte Carlo error estimates, and convergence diagnostics. The presented Pareto $\hat{k}$ finite sample convergence rate diagnostic is useful for any Monte Carlo estimator.

关键词： importance sampling Monte Carlo Bayesian computation diagnostics

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Batch and match: black-box variational inference with a score-based divergence 24

Batch and match: black-box variational inference with a scor...

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Proceedings of the 41st International Conference on Machine Learning

作者： Diana Cai Chirag Modi Loucas Pillaud-Vivien Charles C. Margossian Robert M. Gower David M. Blei Lawrence K. Saul Center for Computational Mathematics Flatiron Institute Center for Computational Mathematics Flatiron Institute and Center for Computational Astrophysics Flatiron Institute Center for Computational Mathematics Flatiron Institute and CERMICS Laboratory Ecole des Ponts ParisTech Department of Statistics Department of Computer Science Columbia University

Most leading implementations of black-box variational inference (BBVI) are based on optimizing a stochastic evidence lower bound (ELBO). But such approaches to BBVI often converge slowly due to the high variance of their gradient estimates and their sensitivity to hyperparameters. In this work, we propose batch and match (BaM), an alternative approach to BBVI based on a score-based divergence. Notably, this score-based divergence can be optimized by a closed-form proximal update for Gaussian variational families with full covariance matrices. We analyze the convergence of BaM when the target distribution is Gaussian, and we prove that in the limit of infinite batch size the variational parameter updates converge exponentially quickly to the target mean and covariance. We also evaluate the performance of BaM on Gaussian and non-Gaussian target distributions that arise from posterior inference in hierarchical and deep generative models. In these experiments, we find that BaM typically converges in fewer (and sometimes significantly fewer) gradient evaluations than leading implementations of BBVI based on ELBO maximization.

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Trust-Region Based Stochastic Variational Inference for Distributed and Asynchronous Networks

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Journal of Systems science & Complexity 2022年第6期35卷 2062-2076页

作者： FU Weiming QIN Jiahu LING Qing KANG Yu YE Baijia Department of Automation University of Science and Technology of ChinaHefei 230027China Institute of Artificial Intelligence Hefei Comprehensive National Science CenterHefei 230088China School of Computer Science and Engineering and Guangdong Province Key Laboratory of Computational ScienceSun Yat-Sen UniversityGuangzhou 510006China Institute of Advanced Technology University of Science and Technology of ChinaHefei 230027China

Stochastic variational inference is an efficient Bayesian inference technology for massive datasets,which approximates posteriors by using noisy gradient *** stochastic variational inference can only be performed in a centralized manner,which limits its applications in a wide range of situations where data is possessed by multiple ***,this paper develops a novel trust-region based stochastic variational inference algorithm for a general class of conjugate-exponential models over distributed and asynchronous networks,where the global parameters are diffused over the network by using the Metropolis rule and the local parameters are updated by using the trust-region ***,a simple rule is introduced to balance the transmission frequencies between neighboring nodes such that the proposed distributed algorithm can be performed in an asynchronous *** utility of the proposed algorithm is tested by fitting the Bernoulli model and the Gaussian model to different datasets on a synthetic network,and experimental results demonstrate its effectiveness and advantages over existing works.

关键词： Asynchronous networks Bayesian inference distributed algorithm stochastic variational inference trust-region method

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