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Many real applications problems can be encoded easily as quantified formulas in SMT. However, this simplicity comes at the cost of difficulty during solving by SMT solvers. Different strategies and quantifier instantiation techniques have…

Logic in Computer Science · Computer Science 2025-08-13 Mudathir Mohamed , Nick Feng , Andrew Reynolds , Cesare Tinelli , Clark Barrett , Marsha Chechik

A central goal for mechanistic interpretability has been to identify the right units of analysis in large language models (LLMs) that causally explain their outputs. While early work focused on individual neurons, evidence that neurons…

Computation and Language · Computer Science 2026-05-05 Or Shafran , Atticus Geiger , Mor Geva

Qualitative models provide crucial instruments for modelling complex biological systems. While advances in automated reasoning and symbolic encodings have enabled rigorous inference of these models from data, the process remains highly…

Molecular Networks · Quantitative Biology 2026-05-14 Ondřej Huvar , Nikola Beneš , Martin Jonáš , David Šafránek , Samuel Pastva

We investigate the domain of satisfiable formulas in satisfiability modulo theories (SMT), in particular, automatic generation of a multitude of satisfying assignments to such formulas. Despite the long and successful history of SMT in…

Logic in Computer Science · Computer Science 2022-12-14 Matan Peled , Bat-Chen Rothenberg , Shachar Itzhaky

Being able to interpret, or explain, the predictions made by a machine learning model is of fundamental importance. This is especially true when there is interest in deploying data-driven models to make high-stakes decisions, e.g. in…

Machine Learning · Computer Science 2019-10-01 An-phi Nguyen , María Rodríguez Martínez

Biological systems encode function not primarily in steady states, but in the structure of transient responses elicited by time-varying stimuli. Overshoots, biphasic dynamics, adaptation kinetics, fold-change detection, entrainment, and…

Quantitative Methods · Quantitative Biology 2026-01-05 Eduardo D. Sontag

Quantified formulas with Uninterpreted Functions (UFs) over non-linear real arithmetic pose fundamental challenges for Satisfiability Modulo Theories (SMT) solving. Traditional quantifier instantiation methods struggle because they lack…

Artificial Intelligence · Computer Science 2026-01-09 Kunhang Lv , Yuhang Dong , Rui Han , Fuqi Jia , Feifei Ma , Jian Zhang

Biological systems are often modeled as a system of ordinary differential equations (ODEs) with time-invariant parameters. However, cell signaling events or pharmacological interventions may alter the cellular state and induce multi-mode…

Quantitative Methods · Quantitative Biology 2020-04-28 Bing Liu

Speech foundation models (SFMs) are increasingly hailed as powerful computational models of human speech perception. However, since their representations are inherently black-box, it remains unclear what drives their alignment with brain…

Neurons and Cognition · Quantitative Biology 2025-09-26 Riki Shimizu , Richard J. Antonello , Chandan Singh , Nima Mesgarani

State-space models (SSMs) are a popular tool for modeling animal abundances. Inference difficulties for simple linear SSMs are well known, particularly in relation to simultaneous estimation of process and observation variances. Several…

Populations and Evolution · Quantitative Biology 2019-09-20 Leo Polansky , Ken B. Newman , Lara Mitchell

Universal quantifiers occur frequently in proof obligations produced by program verifiers, for instance, to axiomatize uninterpreted functions and to express properties of arrays. SMT-based verifiers typically reason about them via…

Programming Languages · Computer Science 2021-12-15 Alexandra Bugariu , Arshavir Ter-Gabrielyan , Peter Müller

Computational models of biological processes provide one of the most powerful methods for a detailed analysis of the mechanisms that drive the behavior of complex systems. Logic-based modeling has enhanced our understanding and…

Molecular Networks · Quantitative Biology 2022-02-08 John Zobolas , Pedro T. Monteiro , Martin Kuiper , Åsmund Flobak

Non-linear polynomial systems over finite fields are used to model functional behavior of cryptosystems, with applications in system security, computer cryptography, and post-quantum cryptography. Solving polynomial systems is also one of…

Logic in Computer Science · Computer Science 2023-10-20 Thomas Hader , Daniela Kaufmann , Laura Kovács

Time series anomaly detection forms a very crucial area in several domains but poses substantial challenges. Due to time series data possessing seasonality, trends, noise, and evolving patterns (concept drift), it becomes very difficult to…

Machine Learning · Computer Science 2025-10-07 Yadav Mahesh Lorik , Kaushik Sarveswaran , Nagaraj Sundaramahalingam , Aravindakumar Venugopalan

Without real bilingual corpus available, unsupervised Neural Machine Translation (NMT) typically requires pseudo parallel data generated with the back-translation method for the model training. However, due to weak supervision, the pseudo…

Computation and Language · Computer Science 2019-01-15 Shuo Ren , Zhirui Zhang , Shujie Liu , Ming Zhou , Shuai Ma

SMT solvers have been used successfully as reasoning engines for automated verification and other applications based on automated reasoning. Current techniques for dealing with quantified formulas in SMT are generally incomplete, forcing…

Logic in Computer Science · Computer Science 2017-06-02 Andrew Reynolds , Cesare Tinelli , Clark Barrett

This paper addresses the problem of checking invariant properties for a large class of symbolic transition systems, defined by a combination of SMT theories and quantifiers. State variables can be functions from an uninterpreted sort…

Logic in Computer Science · Computer Science 2024-03-01 Gianluca Redondi , Alessandro Cimatti , Alberto Griggio , Kenneth McMillan

Non-coding RNA structure and function are essential to understanding various biological processes, such as cell signaling, gene expression, and post-transcriptional regulations. These are all among the core problems in the RNA field. With…

Quantitative Methods · Quantitative Biology 2022-08-09 Jiayang Chen , Zhihang Hu , Siqi Sun , Qingxiong Tan , Yixuan Wang , Qinze Yu , Licheng Zong , Liang Hong , Jin Xiao , Tao Shen , Irwin King , Yu Li

This short paper proposes to learn models of satisfiability modulo theories (SMT) formulas during solving. Specifically, we focus on infinite models for problems in the logic of linear arithmetic with uninterpreted functions (UFLIA). The…

Logic in Computer Science · Computer Science 2025-03-24 Mikoláš Janota , Bartosz Piotrowski , Karel Chvalovský

This paper proposes a novel method to inject custom terminology into neural machine translation at run time. Previous works have mainly proposed modifications to the decoding algorithm in order to constrain the output to include…

Computation and Language · Computer Science 2019-06-26 Georgiana Dinu , Prashant Mathur , Marcello Federico , Yaser Al-Onaizan
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