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Weighted model integration (WMI) is a relatively recent formalism that has received significant interest as a technique for solving probabilistic inference tasks with complicated weight functions. Existing methods and tools are mostly focused on linear and polynomial functions and provide limited support for WMI of rational or radical functions, which naturally arise in several applications. In this work, we present a novel method for approximate WMI, which provides more effective support for the wide class of semi-algebraic functions that includes rational and radical functions, with literals defined over non-linear real arithmetic. Our algorithm leverages Farkas’ lemma and Handelman's theorem from real algebraic geometry to reduce WMI to solving a number of linear programming (LP) instances. The algorithm provides formal guarantees on the error bound of the obtained approximation and can reduce it to any user-defined value epsilon. Furthermore, our approach is perfectly parallelizable. Finally, we present extensive experimental results, demonstrating the superior performance of our method on a range of WMI tasks for rational and radical functions when compared to state-of-the-art tools for WMI, in terms of both applicability and tightness.
Most Probable Explanation (MPE) is a fundamental problem in statistical relational artificial intelligence. In the context of Probabilistic Answer Set Programming (PASP), solving MPE is still an open research problem. In this paper, we present three novel approaches for solving the MPE task in PASP that are based on: i) Algebraic Model Counting, ii) Answer Set Programming (ASP), and iii) ASP with quantifiers (ASP(Q)). These approaches are implemented and evaluated against existing solvers across different datasets and configurations. Empirical results demonstrate that the novel solutions consistently outperform existing alternatives for non-stratified programs.
Reasoning under uncertainty is a fundamental challenge in Artificial Intelligence. As with most of these challenges, there is a harsh dilemma between the expressive power of the language used, and the tractability of the computational problem posed by reasoning. Inspired by human reasoning, we introduce a method of first-order relational probabilistic inference that satisfies both criteria, and can handle hybrid (discrete and continuous) variables. Specifically, we extend sum-of-squares logic of expectation to relational settings, demonstrating that lifted reasoning in the bounded-degree fragment for knowledge bases of bounded quantifier rank can be performed in polynomial time, even with an a priori unknown and/or countably infinite set of objects. Crucially, our notion of tractability is framed in proof-theoretic terms, which extends beyond the syntactic properties of the language or queries. We are able to derive the tightest bounds provable by proofs of a given degree and size and establish completeness in our sum-of-squares refutations for fixed degrees.
The de novo generation of drug-like molecules capable of inducing desirable phenotypic changes is receiving increasing attention. However, previous methods predominantly rely on expression profiles to guide molecule generation, but overlook the perturbative effect of the molecules on cellular contexts. To overcome this limitation, we propose SmilesGEN, a novel generative model based on variational autoencoder (VAE) architecture to generate molecules with potential therapeutic effects. SmilesGEN integrates a pre-trained drug VAE (SmilesNet) with an expression profile VAE (ProfileNet), jointly modeling the interplay between drug perturbations and transcriptional responses in a common latent space. Specifically, ProfileNet is imposed to reconstruct pre-treatment expression profiles when eliminating drug-induced perturbations in the latent space, while SmilesNet is informed by desired expression profiles to generate drug-like molecules. Our empirical experiments demonstrate that SmilesGEN outperforms current state-of-the-art models in generating molecules with higher degree of validity, uniqueness, novelty, as well as higher Tanimoto similarity to known ligands targeting the relevant proteins. Moreover, we evaluate SmilesGEN for scaffold-based molecule optimization and generation of therapeutic agents, and confirmed its superior performance in generating molecules with higher similarity to approved drugs. SmilesGEN establishes a robust framework that leverages gene signatures to generate drug-like molecules that hold promising potential to induce desirable cellular phenotypic changes. The source code and datasets are available at: https://github.com/hliulab/SmilesGEN.
Probabilistic relational models such as parametric factor graphs enable efficient (lifted) inference by exploiting the indistinguishability of objects. In lifted inference, a representative of indistinguishable objects is used for computations. To obtain a relational (i.e., lifted) representation, the Advanced Colour Passing (ACP) algorithm is the state of the art. The ACP algorithm, however, requires underlying distributions, encoded as potential-based factorisations, to exactly match to identify and exploit indistinguishabilities. Hence, ACP is unsuitable for practical applications where potentials learned from data inevitably deviate even if associated objects are indistinguishable. To mitigate this problem, we introduce the ε-Advanced Colour Passing (ε-ACP) algorithm, which allows for a deviation of potentials depending on a hyperparameter ε. ε-ACP efficiently uncovers and exploits indistinguishabilities that are not exact. We prove that the approximation error induced by ε-ACP is strictly bounded and our experiments show that the approximation error is close to zero in practice.
Causal structure learning (CSL) plays a pivotal role in causality and is often formulated as an optimization problem within score-and-search methods. Under the assumption of an infinite dataset and a predefined distribution, several well-established and consistent score functions have been shown to be both optimal and reliable for identifying ground-truth causal graphs. However, in practice, these idealized assumptions are often infeasible, which can result in CSL algorithms learning suboptimal structures. In this paper, we introduce L-SFE, a framework designed to automatically discover effective score functions by exploring the "score function space". L-SFE addresses this task from a bi-level optimization perspective. First, it leverages a Large Language Model (LLM) to interpret the characteristics of score functions and generate the corresponding code implementations. Next, L-SFE employs evolutionary algorithms along with carefully designed operators, to search for solutions with higher fitness. Additionally, we take the BIC as example and prove the consistency of the generated score functions. Experimental evaluations, conducted on discrete, continuous, and real datasets, demonstrate the high stability, generality and effectiveness of L-SFE.
We address the identification of direct causes in time series with multiple time lags, and propose a constraint-based window causal graph discovery method. A key advantage of our method is that the number of required conditional independence (CI) tests scales quadratically with the number of sub-series. The method first uses CI tests to find the minimum trek lag between two arbitrary sub-series, followed by designing an efficient CI testing strategy to identify the direct causes between them. We show that the method is both sound and complete under some graph constraints. We compare the proposed method with typical baselines on various datasets. Experimental results show that our method outperforms all the counterparts in both accuracy and running speed.
Practical machine learning systems often operate in multiple sequential stages, as seen in ranking and recommendation systems, which typically include a retrieval phase followed by a ranking phase. Effectively assessing prediction uncertainty and ensuring effective risk control in such systems pose significant challenges due to their inherent complexity. To address these challenges, we developed two-stage risk control methods based on the recently proposed learn-then-test (LTT) and conformal risk control (CRC) frameworks. Unlike the methods in prior work that address multiple risks, our approach leverages the sequential nature of the problem, resulting in reduced computational burden. We provide theoretical guarantees for our proposed methods and design novel loss functions tailored for ranked retrieval tasks. The effectiveness of our approach is validated through experiments on two large-scale, widely-used datasets: MSLR- Web and Yahoo LTRC.
Testing conditional independence is a critical task, particularly in causal discovery and learning in Bayesian networks. However, in many real-world scenarios, variables are often measured with errors, such as those introduced by insufficient measurement accuracy, complicating the testing process. This paper focuses on testing conditional independence in the linear non-Gaussian measurement error model, under the condition that measurement error noise follows a Gaussian distribution. By leveraging high-order cumulants, we derive rank constraints on the cumulant matrix and establish their role in effectively assessing conditional independence, even in the presence of measurement errors. Based on these theoretical results, we leverage the rank constraints of the cumulant matrix as a tool for conditional independence testing and incorporate it into the PC algorithm, resulting in the PC-ME algorithm — a method designed to learn causal structures from observed data while accounting for measurement errors. Experimental results demonstrate that the proposed method outperforms existing approaches, particularly in cases other methods encounter difficulties.
Sequential Resource Allocation with situational constraints presents a significant challenge in real-world applications, where resource demands and priorities are context-dependent. This paper introduces a novel framework, SCRL, to address this problem. We formalize situational constraints as logic implications and develop a new algorithm that dynamically penalizes constraint violations. To handle situational constraints effectively, we propose a probabilistic selection mechanism to overcome limitations of traditional constraint reinforcement learning (CRL) approaches. We evaluate SCRL across two scenarios: medical resource allocation during a pandemic and pesticide distribution in agriculture. Experiments demonstrate that SCRL outperforms existing baselines in satisfying constraints while maintaining high resource efficiency, showcasing its potential for real-world, context-sensitive decision-making tasks.