Current statistical methods in differential proteomics analysis generally leave aside several challenges, such as missing values, correlations between peptide intensities and uncertainty quantification. Moreover, they provide point estimates, such as the mean intensity for a given peptide or protein in a given condition. The decision of whether an analyte should be considered as differential is then based on comparing the p-value to a significance threshold, usually 5%. In the state-of-the-art limma approach, a hierarchical model is used to deduce the posterior distribution of the variance estimator for each analyte. The expectation of this distribution is then used as a moderated estimation of variance and is injected directly into the expression of the t-statistic. However, instead of merely relying on the moderated estimates, we could provide more powerful and intuitive results by leveraging a fully Bayesian approach and hence allow the quantification of uncertainty. The present work introduces this idea by taking advantage of standard results from Bayesian inference with conjugate priors in hierarchical models to derive a methodology tailored to handle multiple imputation contexts. Furthermore, we aim to tackle a more general problem of multivariate differential analysis, to account for possible inter-peptide correlations. By defining a hierarchical model with prior distributions on both mean and variance parameters, we achieve a global quantification of uncertainty for differential analysis. The inference is thus performed by computing the posterior distribution for the difference in mean peptide intensities between two experimental conditions. In contrast to more flexible models that can be achieved with hierarchical structures, our choice of conjugate priors maintains analytical expressions for direct sampling from posterior distributions without requiring expensive MCMC methods.
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Mixture priors provide an intuitive way to incorporate historical data while accounting for potential prior-data conflict by combining an informative prior with a non-informative prior. However, pre-specifying the mixing weight for each component remains a crucial challenge. Ideally, the mixing weight should reflect the degree of prior-data conflict, which is often unknown beforehand, posing a significant obstacle to the application and acceptance of mixture priors. To address this challenge, we introduce self-adapting mixture (SAM) priors that determine the mixing weight using likelihood ratio test statistics or Bayes factor. SAM priors are data-driven and self-adapting, favoring the informative (non-informative) prior component when there is little (substantial) evidence of prior-data conflict. Consequently, SAM priors achieve dynamic information borrowing. We demonstrate that SAM priors exhibit desirable properties in both finite and large samples and achieve information-borrowing consistency. Moreover, SAM priors are easy to compute, data-driven, and calibration-free, mitigating the risk of data dredging. Numerical studies show that SAM priors outperform existing methods in adopting prior-data conflicts effectively. We developed an R package and web application that are freely available to facilitate the use of SAM priors.
Overlapped arithmetic codes, featured by overlapped intervals, are a variant of arithmetic codes that can be used to implement Slepian-Wolf coding. To analyze overlapped arithmetic codes, we have proposed two theoretical tools: Coset Cardinality Spectrum (CCS) and Hamming Distance Spectrum (HDS). The former describes how source space is partitioned into cosets (equally or unequally), and the latter describes how codewords are structured within each coset (densely or sparsely). However, until now, these two tools are almost parallel to each other, and it seems that there is no intersection between them. The main contribution of this paper is bridging HDS with CCS through a rigorous mathematical proof. Specifically, HDS can be quickly and accurately calculated with CCS in some cases. All theoretical analyses are perfectly verified by simulation results.
Data silos, mainly caused by privacy and interoperability, significantly constrain collaborations among different organizations with similar data for the same purpose. Distributed learning based on divide-and-conquer provides a promising way to settle the data silos, but it suffers from several challenges, including autonomy, privacy guarantees, and the necessity of collaborations. This paper focuses on developing an adaptive distributed kernel ridge regression (AdaDKRR) by taking autonomy in parameter selection, privacy in communicating non-sensitive information, and the necessity of collaborations in performance improvement into account. We provide both solid theoretical verification and comprehensive experiments for AdaDKRR to demonstrate its feasibility and effectiveness. Theoretically, we prove that under some mild conditions, AdaDKRR performs similarly to running the optimal learning algorithms on the whole data, verifying the necessity of collaborations and showing that no other distributed learning scheme can essentially beat AdaDKRR under the same conditions. Numerically, we test AdaDKRR on both toy simulations and two real-world applications to show that AdaDKRR is superior to other existing distributed learning schemes. All these results show that AdaDKRR is a feasible scheme to defend against data silos, which are highly desired in numerous application regions such as intelligent decision-making, pricing forecasting, and performance prediction for products.
With the advent of powerful quantum computers, the quest for more efficient quantum algorithms becomes crucial in attaining quantum supremacy over classical counterparts in the noisy intermediate-scale quantum era. While Grover's search algorithm and its generalization, quantum amplitude amplification, offer quadratic speedup in solving various important scientific problems, their exponential time complexity limits scalability as the quantum circuit depths grow exponentially with the number of qubits. To overcome this challenge, we propose Variational Quantum Search (VQS), a novel algorithm based on variational quantum algorithms and parameterized quantum circuits. We show that a depth-10 Ansatz can amplify the total probability of $k$ ($k \geq 1$) good elements, out of $2^n$ elements represented by $n$+1 qubits, from $k/2^n$ to nearly 1, as verified for $n$ up to 26, and that the maximum depth of quantum circuits in the VQS increases linearly with the number of qubits. Our experimental results have validated the efficacy of VQS and its exponential advantage over Grover's algorithm in circuit depth for up to 26 qubits. We demonstrate that a depth-56 circuit in VQS can replace a depth-270,989 circuit in Grover's algorithm. Envisioning its potential, VQS holds promise to accelerate solutions to critical problems.
We propose a general algorithm of constructing an extended formulation for any given set of linear constraints with integer coefficients. Our algorithm consists of two phases: first construct a decision diagram $(V,E)$ that somehow represents a given $m \times n$ constraint matrix, and then build an equivalent set of $|E|$ linear constraints over $n+|V|$ variables. That is, the size of the resultant extended formulation depends not explicitly on the number $m$ of the original constraints, but on its decision diagram representation. Therefore, we may significantly reduce the computation time for optimization problems with integer constraint matrices by solving them under the extended formulations, especially when we obtain concise decision diagram representations for the matrices. We can apply our method to $1$-norm regularized hard margin optimization over the binary instance space $\{0,1\}^n$, which can be formulated as a linear programming problem with $m$ constraints with $\{-1,0,1\}$-valued coefficients over $n$ variables, where $m$ is the size of the given sample. Furthermore, introducing slack variables over the edges of the decision diagram, we establish a variant formulation of soft margin optimization. We demonstrate the effectiveness of our extended formulations for integer programming and the $1$-norm regularized soft margin optimization tasks over synthetic and real datasets.
We investigate the equational theory of Kleene algebra terms with variable complements -- (language) complement where it applies only to variables -- w.r.t. languages. While the equational theory w.r.t. languages coincides with the language equivalence (under the standard language valuation) for Kleene algebra terms, this coincidence is broken if we extend the terms with complements. In this paper, we prove the decidability of some fragments of the equational theory: the universality problem is coNP-complete, and the inequational theory t <= s is coNP-complete when t does not contain Kleene-star. To this end, we introduce words-to-letters valuations; they are sufficient valuations for the equational theory and ease us in investigating the equational theory w.r.t. languages. Additionally, we prove that for words with variable complements, the equational theory coincides with the word equivalence.
The existence of representative datasets is a prerequisite of many successful artificial intelligence and machine learning models. However, the subsequent application of these models often involves scenarios that are inadequately represented in the data used for training. The reasons for this are manifold and range from time and cost constraints to ethical considerations. As a consequence, the reliable use of these models, especially in safety-critical applications, is a huge challenge. Leveraging additional, already existing sources of knowledge is key to overcome the limitations of purely data-driven approaches, and eventually to increase the generalization capability of these models. Furthermore, predictions that conform with knowledge are crucial for making trustworthy and safe decisions even in underrepresented scenarios. This work provides an overview of existing techniques and methods in the literature that combine data-based models with existing knowledge. The identified approaches are structured according to the categories integration, extraction and conformity. Special attention is given to applications in the field of autonomous driving.
Recent contrastive representation learning methods rely on estimating mutual information (MI) between multiple views of an underlying context. E.g., we can derive multiple views of a given image by applying data augmentation, or we can split a sequence into views comprising the past and future of some step in the sequence. Contrastive lower bounds on MI are easy to optimize, but have a strong underestimation bias when estimating large amounts of MI. We propose decomposing the full MI estimation problem into a sum of smaller estimation problems by splitting one of the views into progressively more informed subviews and by applying the chain rule on MI between the decomposed views. This expression contains a sum of unconditional and conditional MI terms, each measuring modest chunks of the total MI, which facilitates approximation via contrastive bounds. To maximize the sum, we formulate a contrastive lower bound on the conditional MI which can be approximated efficiently. We refer to our general approach as Decomposed Estimation of Mutual Information (DEMI). We show that DEMI can capture a larger amount of MI than standard non-decomposed contrastive bounds in a synthetic setting, and learns better representations in a vision domain and for dialogue generation.
As soon as abstract mathematical computations were adapted to computation on digital computers, the problem of efficient representation, manipulation, and communication of the numerical values in those computations arose. Strongly related to the problem of numerical representation is the problem of quantization: in what manner should a set of continuous real-valued numbers be distributed over a fixed discrete set of numbers to minimize the number of bits required and also to maximize the accuracy of the attendant computations? This perennial problem of quantization is particularly relevant whenever memory and/or computational resources are severely restricted, and it has come to the forefront in recent years due to the remarkable performance of Neural Network models in computer vision, natural language processing, and related areas. Moving from floating-point representations to low-precision fixed integer values represented in four bits or less holds the potential to reduce the memory footprint and latency by a factor of 16x; and, in fact, reductions of 4x to 8x are often realized in practice in these applications. Thus, it is not surprising that quantization has emerged recently as an important and very active sub-area of research in the efficient implementation of computations associated with Neural Networks. In this article, we survey approaches to the problem of quantizing the numerical values in deep Neural Network computations, covering the advantages/disadvantages of current methods. With this survey and its organization, we hope to have presented a useful snapshot of the current research in quantization for Neural Networks and to have given an intelligent organization to ease the evaluation of future research in this area.
Object detection typically assumes that training and test data are drawn from an identical distribution, which, however, does not always hold in practice. Such a distribution mismatch will lead to a significant performance drop. In this work, we aim to improve the cross-domain robustness of object detection. We tackle the domain shift on two levels: 1) the image-level shift, such as image style, illumination, etc, and 2) the instance-level shift, such as object appearance, size, etc. We build our approach based on the recent state-of-the-art Faster R-CNN model, and design two domain adaptation components, on image level and instance level, to reduce the domain discrepancy. The two domain adaptation components are based on H-divergence theory, and are implemented by learning a domain classifier in adversarial training manner. The domain classifiers on different levels are further reinforced with a consistency regularization to learn a domain-invariant region proposal network (RPN) in the Faster R-CNN model. We evaluate our newly proposed approach using multiple datasets including Cityscapes, KITTI, SIM10K, etc. The results demonstrate the effectiveness of our proposed approach for robust object detection in various domain shift scenarios.
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