Mixed-Integer Linear Programming (MILP) plays an important role across a range of scientific disciplines and within areas of strategic importance to society. The MILP problems, however, suffer from combinatorial complexity. Because of integer decision variables, as the problem size increases, the number of possible solutions increases super-linearly thereby leading to a drastic increase in the computational effort. To efficiently solve MILP problems, a "price-based" decomposition and coordination approach is developed to exploit 1. the super-linear reduction of complexity upon the decomposition and 2. the geometric convergence potential inherent to Polyak's stepsizing formula for the fastest coordination possible to obtain near-optimal solutions in a computationally efficient manner. Unlike all previous methods to set stepsizes heuristically by adjusting hyperparameters, the key novel way to obtain stepsizes is purely decision-based: a novel "auxiliary" constraint satisfaction problem is solved, from which the appropriate stepsizes are inferred. Testing results for large-scale Generalized Assignment Problems (GAP) demonstrate that for the majority of instances, certifiably optimal solutions are obtained. For stochastic job-shop scheduling as well as for pharmaceutical scheduling, computational results demonstrate the two orders of magnitude speedup as compared to Branch-and-Cut (B&C). The new method has a major impact on the efficient resolution of complex Mixed-Integer Programming (MIP) problems arising within a variety of scientific fields.
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Explainable AI offers insights into what factors drive a certain prediction of a black-box AI system. One popular interpreting approach is through counterfactual explanations, which go beyond why a system arrives at a certain decision to further provide suggestions on what a user can do to alter the original outcome. A counterfactual example must possess plenty of desiderata. These constraints exist at trade-offs between one and another presenting radical challenges to existing works. We here propose a stochastic learning-based framework that effectively balances the counterfactual trade-offs. The framework consists of a generation and a feature selection module with complementary roles: the former aims to model the distribution of valid counterfactuals whereas the latter serves to enforce additional constraints in a way that allows for differentiable training and amortized optimization. We demonstrate the effectiveness of our method in generating actionable and plausible counterfactuals that are more diverse than the existing methods and particularly more efficient than closest baselines.
In the dominant paradigm for designing equitable machine learning systems, one works to ensure that model predictions satisfy various fairness criteria, such as parity in error rates across race, gender, and other legally protected traits. That approach, however, typically ignores the downstream decisions and outcomes that predictions affect, and, as a result, can induce unexpected harms. Here we present an alternative framework for fairness that directly anticipates the consequences of decisions. Stakeholders first specify preferences over the possible outcomes of an algorithmically informed decision-making process. For example, lenders may prefer extending credit to those most likely to repay a loan, while also preferring similar lending rates across neighborhoods. One then searches the space of decision policies to maximize the specified utility. We develop and describe a method for efficiently learning these optimal policies from data for a large family of expressive utility functions, facilitating a more holistic approach to equitable decision-making.
This thesis focuses on the advancement of probabilistic logic programming (PLP), which combines probability theory for uncertainty and logic programming for relations. The thesis aims to extend PLP to support both discrete and continuous random variables, which is necessary for applications with numeric data. The first contribution is the introduction of context-specific likelihood weighting (CS-LW), a new sampling algorithm that exploits context-specific independencies for computational gains. Next, a new hybrid PLP, DC#, is introduced, which integrates the syntax of Distributional Clauses with Bayesian logic programs and represents three types of independencies: i) conditional independencies (CIs) modeled in Bayesian networks; ii) context-specific independencies (CSIs) represented by logical rules, and iii) independencies amongst attributes of related objects in relational models expressed by combining rules. The scalable inference algorithm FO-CS-LW is introduced for DC#. Finally, the thesis addresses the lack of approaches for learning hybrid PLP from relational data and background knowledge with the introduction of DiceML, which learns the structure and parameters of hybrid PLP and tackles the relational autocompletion problem. The conclusion discusses future directions and open challenges for hybrid PLP.
We study mean-field variational Bayesian inference using the TAP approach, for Z2-synchronization as a prototypical example of a high-dimensional Bayesian model. We show that for any signal strength $\lambda > 1$ (the weak-recovery threshold), there exists a unique local minimizer of the TAP free energy functional near the mean of the Bayes posterior law. Furthermore, the TAP free energy in a local neighborhood of this minimizer is strongly convex. Consequently, a natural-gradient/mirror-descent algorithm achieves linear convergence to this minimizer from a local initialization, which may be obtained by a constant number of iterates of Approximate Message Passing (AMP). This provides a rigorous foundation for variational inference in high dimensions via minimization of the TAP free energy. We also analyze the finite-sample convergence of AMP, showing that AMP is asymptotically stable at the TAP minimizer for any $\lambda > 1$, and is linearly convergent to this minimizer from a spectral initialization for sufficiently large $\lambda$. Such a guarantee is stronger than results obtainable by state evolution analyses, which only describe a fixed number of AMP iterations in the infinite-sample limit. Our proofs combine the Kac-Rice formula and Sudakov-Fernique Gaussian comparison inequality to analyze the complexity of critical points that satisfy strong convexity and stability conditions within their local neighborhoods.
The computation of the distance of two time series is time-consuming for any elastic distance function that accounts for misalignments. Among those functions, DTW is the most prominent. However, a recent extensive evaluation has shown that the move-split merge (MSM) metric is superior to DTW regarding the analytical accuracy of the 1-NN classifier. Unfortunately, the running time of the standard dynamic programming algorithm for MSM distance computation is $\Omega(n^2)$, where $n$ is the length of the longest time series. In this paper, we provide approaches to reducing the cost of MSM distance computations by using lower and upper bounds for early pruning paths in the underlying dynamic programming table. For the case of one time series being a constant, we present a linear-time algorithm. In addition, we propose new linear-time heuristics and adapt heuristics known from DTW to computing the MSM distance. One heuristic employs the metric property of MSM and the previously introduced linear-time algorithm. Our experimental studies demonstrate substantial speed-ups in our approaches compared to previous MSM algorithms. In particular, the running time for MSM is faster than a state-of-the-art DTW distance computation for a majority of the popular UCR data sets.
Evolutionary Reinforcement Learning (ERL) that applying Evolutionary Algorithms (EAs) to optimize the weight parameters of Deep Neural Network (DNN) based policies has been widely regarded as an alternative to traditional reinforcement learning methods. However, the evaluation of the iteratively generated population usually requires a large amount of computational time and can be prohibitively expensive, which may potentially restrict the applicability of ERL. Surrogate is often used to reduce the computational burden of evaluation in EAs. Unfortunately, in ERL, each individual of policy usually represents millions of weights parameters of DNN. This high-dimensional representation of policy has introduced a great challenge to the application of surrogates into ERL to speed up training. This paper proposes a PE-SAERL Framework to at the first time enable surrogate-assisted evolutionary reinforcement learning via policy embedding (PE). Empirical results on 5 Atari games show that the proposed method can perform more efficiently than the four state-of-the-art algorithms. The training process is accelerated up to 7x on tested games, comparing to its counterpart without the surrogate and PE.
Many important problems in Bioinformatics (e.g., assembly or multi-assembly) admit multiple solutions, while the final objective is to report only one. A common approach to deal with this uncertainty is finding safe partial solutions (e.g., contigs) which are common to all solutions. Previous research on safety has focused on polynomially-time solvable problems, whereas many successful and natural models are NP-hard to solve, leaving a lack of "safety tools" for such problems. We propose the first method for computing all safe solutions for an NP-hard problem, minimum flow decomposition. We obtain our results by developing a "safety test" for paths based on a general Integer Linear Programming (ILP) formulation. Moreover, we provide implementations with practical optimizations aimed to reduce the total ILP time, the most efficient of these being based on a recursive group-testing procedure. Results: Experimental results on the transcriptome datasets of Shao and Kingsford (TCBB, 2017) show that all safe paths for minimum flow decompositions correctly recover up to 90% of the full RNA transcripts, which is at least 25% more than previously known safe paths, such as (Caceres et al. TCBB, 2021), (Zheng et al., RECOMB 2021), (Khan et al., RECOMB 2022, ESA 2022). Moreover, despite the NP-hardness of the problem, we can report all safe paths for 99.8% of the over 27,000 non-trivial graphs of this dataset in only 1.5 hours. Our results suggest that, on perfect data, there is less ambiguity than thought in the notoriously hard RNA assembly problem. Availability: //github.com/algbio/mfd-safety
Graph Neural Networks (GNNs) have received considerable attention on graph-structured data learning for a wide variety of tasks. The well-designed propagation mechanism which has been demonstrated effective is the most fundamental part of GNNs. Although most of GNNs basically follow a message passing manner, litter effort has been made to discover and analyze their essential relations. In this paper, we establish a surprising connection between different propagation mechanisms with a unified optimization problem, showing that despite the proliferation of various GNNs, in fact, their proposed propagation mechanisms are the optimal solution optimizing a feature fitting function over a wide class of graph kernels with a graph regularization term. Our proposed unified optimization framework, summarizing the commonalities between several of the most representative GNNs, not only provides a macroscopic view on surveying the relations between different GNNs, but also further opens up new opportunities for flexibly designing new GNNs. With the proposed framework, we discover that existing works usually utilize naive graph convolutional kernels for feature fitting function, and we further develop two novel objective functions considering adjustable graph kernels showing low-pass or high-pass filtering capabilities respectively. Moreover, we provide the convergence proofs and expressive power comparisons for the proposed models. Extensive experiments on benchmark datasets clearly show that the proposed GNNs not only outperform the state-of-the-art methods but also have good ability to alleviate over-smoothing, and further verify the feasibility for designing GNNs with our unified optimization framework.
Knowledge is a formal way of understanding the world, providing a human-level cognition and intelligence for the next-generation artificial intelligence (AI). One of the representations of knowledge is the structural relations between entities. An effective way to automatically acquire this important knowledge, called Relation Extraction (RE), a sub-task of information extraction, plays a vital role in Natural Language Processing (NLP). Its purpose is to identify semantic relations between entities from natural language text. To date, there are several studies for RE in previous works, which have documented these techniques based on Deep Neural Networks (DNNs) become a prevailing technique in this research. Especially, the supervised and distant supervision methods based on DNNs are the most popular and reliable solutions for RE. This article 1)introduces some general concepts, and further 2)gives a comprehensive overview of DNNs in RE from two points of view: supervised RE, which attempts to improve the standard RE systems, and distant supervision RE, which adopts DNNs to design the sentence encoder and the de-noise method. We further 3)cover some novel methods and describe some recent trends and discuss possible future research directions for this task.
With the rapid increase of large-scale, real-world datasets, it becomes critical to address the problem of long-tailed data distribution (i.e., a few classes account for most of the data, while most classes are under-represented). Existing solutions typically adopt class re-balancing strategies such as re-sampling and re-weighting based on the number of observations for each class. In this work, we argue that as the number of samples increases, the additional benefit of a newly added data point will diminish. We introduce a novel theoretical framework to measure data overlap by associating with each sample a small neighboring region rather than a single point. The effective number of samples is defined as the volume of samples and can be calculated by a simple formula $(1-\beta^{n})/(1-\beta)$, where $n$ is the number of samples and $\beta \in [0,1)$ is a hyperparameter. We design a re-weighting scheme that uses the effective number of samples for each class to re-balance the loss, thereby yielding a class-balanced loss. Comprehensive experiments are conducted on artificially induced long-tailed CIFAR datasets and large-scale datasets including ImageNet and iNaturalist. Our results show that when trained with the proposed class-balanced loss, the network is able to achieve significant performance gains on long-tailed datasets.
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