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This Thesis presents research at the boundary between Statistical Physics and Biology. First, we have devised a class of Boolean constraint satisfaction problems (CSP) whose solutions describe the feasible operational states of a chemical…

Molecular Networks · Quantitative Biology 2019-08-15 Alessandro Seganti

Identifying governing equations for a dynamical system is a topic of critical interest across an array of disciplines, from mathematics to engineering to biology. Machine learning -- specifically deep learning -- techniques have shown their…

Dynamical Systems · Mathematics 2026-05-07 Nibodh Boddupalli , Timothy Matchen , Jeff Moehlis

We determine stability and attractor properties of random Boolean genetic network models with canalyzing rules for a variety of architectures. For all power law, exponential, and flat in-degree distributions, we find that the networks are…

Molecular Networks · Quantitative Biology 2007-05-23 Stuart Kauffman , Carsten Peterson , Björn Samuelsson , Carl Troein

This paper presents Merlin, a new framework for managing resources in software-defined networks. With Merlin, administrators express high-level policies using programs in a declarative language. The language includes logical predicates to…

Networking and Internet Architecture · Computer Science 2014-07-07 Robert Soulé , Shrutarshi Basu , Parisa Jalili Marandi , Fernando Pedone , Robert Kleinberg , Emin Gün Sirer , Nate Foster

Automated interpretability research aims to identify concepts encoded in neural network features to enhance human understanding of model behavior. Within the context of large language models (LLMs) for natural language processing (NLP),…

Machine Learning · Computer Science 2025-11-13 Laura Kopf , Nils Feldhus , Kirill Bykov , Philine Lou Bommer , Anna Hedström , Marina M. -C. Höhne , Oliver Eberle

Large Language Models (LLMs) achieve strong linguistic performance, yet their internal mechanisms for producing these predictions remain unclear. We investigate the hypothesis that LLMs encode representations of linguistic constraint…

Computation and Language · Computer Science 2026-05-15 Hardy , Sebastian Padó

We propose a method to teach multiple large language models (LLM) to collaborate by interleaving their generations at the token level. We model the decision of which LLM generates the next token as a latent variable. By optimizing the…

Computation and Language · Computer Science 2024-08-28 Shannon Zejiang Shen , Hunter Lang , Bailin Wang , Yoon Kim , David Sontag

In this paper, we address the scenario where nodes with sensor data are connected in a tree network, and every node wants to compute a given symmetric Boolean function of the sensor data. We first consider the problem of computing a…

Information Theory · Computer Science 2010-05-03 Hemant Kowshik , P. R. Kumar

Neural population activity often exhibits regime-dependent non-stationarity in the form of switching dynamics. Learning accurate switching dynamical system models can reveal how behavior is encoded in neural activity. Existing switching…

Machine Learning · Computer Science 2025-12-16 DongKyu Kim , Han-Lin Hsieh , Maryam M. Shanechi

Hierarchical Bayesian models are increasingly used in large, inhomogeneous complex network dynamical systems by modeling parameters as draws from a hyperparameter-governed distribution. However, theoretical guarantees for these estimates as…

Statistics Theory · Mathematics 2026-01-23 Yi Yu , Yubo Hou , Yinchong Wang , Nan Zhang , Jianfeng Feng , Wenlian Lu

We consider classical and entanglement-assisted versions of a distributed computation scheme that computes nonlinear Boolean functions of a set of input bits supplied by separated parties. Communication between the parties is restricted to…

Quantum Physics · Physics 2020-02-04 Adam Henry Marblestone , Michel Devoret

Large Language Models (LLMs) have demonstrated strong capabilities in various natural language processing tasks; however, their application to graph-related problems remains limited, primarily due to scalability constraints and the absence…

Machine Learning · Computer Science 2025-05-08 Hyun Lee , Chris Yi , Maminur Islam , B. D. S. Aritra

Carefully engineered system prompts play a critical role in guiding the behavior of LLM agents, but their considerable length introduces significant drawbacks, including increased inference latency, higher computational cost, and reduced…

Computation and Language · Computer Science 2025-12-01 Jiancheng Dong , Pengyue Jia , Jingyu Peng , Maolin Wang , Yuhao Wang , Lixin Su , Xin Sun , Shuaiqiang Wang , Dawei Yin , Xiangyu Zhao

Bilevel optimization refers to scenarios whereby the optimal solution of a lower-level energy function serves as input features to an upper-level objective of interest. These optimal features typically depend on tunable parameters of the…

Machine Learning · Computer Science 2024-03-08 Amber Yijia Zheng , Tong He , Yixuan Qiu , Minjie Wang , David Wipf

Semantic communication (SemCom) with learned encoder-decoder architectures enables end-to-end learning of compact task-oriented representations optimized for the wireless channel, reducing channel resources needed to convey task-relevant…

Information Theory · Computer Science 2026-05-08 Yalin E. Sagduyu , Tugba Erpek

A probabilistic Boolean network (PBN) is a discrete-time system composed of a collection of Boolean networks between which the PBN switches in a stochastic manner. This paper focuses on the study of quotients of PBNs. Given a PBN and an…

Optimization and Control · Mathematics 2021-08-02 Rui Li , Qi Zhang , Tianguang Chu

This paper shows that a classic metalogical framework, including all Boolean operators, can be used to support the development of a metric behavioural theory for Markov processes. Previously, only intuitionistic frameworks or frameworks…

Logic in Computer Science · Computer Science 2012-12-18 Kim G. Larsen , Radu Mardare , Claus Thrane

Recently, the ever-increasing demand for bandwidth in multi-modal communication systems requires a paradigm shift. Powered by deep learning, semantic communications are applied to multi-modal scenarios to boost communication efficiency and…

Signal Processing · Electrical Eng. & Systems 2023-05-19 Yangshuo He , Guanding Yu , Yunlong Cai

We propose a generative model for single-channel EEG that incorporates the constraints experts actively enforce during visual scoring. The framework takes the form of a dynamic Bayesian network with depth in both the latent variables and…

Machine Learning · Computer Science 2021-03-04 Carlos A. Loza , Laura L. Colgin

We computationally implement and experimentally test the behavioral predictions of a dynamic neural model of lexical meaning in the framework of Dynamic Field Theory. We demonstrate the architecture and behavior of the model using as a test…

Computation and Language · Computer Science 2025-09-18 Michael C. Stern , Maria M. Piñango
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