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Noise-assisted transport phenomena highlight the nontrivial interplay between environmental effects and quantum coherence in achieving maximal efficiency. Due to the complexity of biochemical systems and their environments, effective open…

The objective of this proposal is to bridge the gap between Deep Learning (DL) and System Dynamics (SD) by developing an interpretable neural system dynamics framework. While DL excels at learning complex models and making accurate…

Machine Learning · Computer Science 2025-05-21 Riccardo D'Elia

Training Large Language Models (LLMs) typically involves a two-stage pipeline at the output layer: hidden states are projected into vocabulary logits via a linear transformation (lm_head), followed by cross-entropy loss computation against…

Machine Learning · Computer Science 2025-11-25 Jianbing Dong , Jianbin Chang

Data-driven, model-free analytics are natural choices for discovery and forecasting of complex, nonlinear systems. Methods that operate in the system state-space require either an explicit multidimensional state-space, or, one approximated…

Machine Learning · Statistics 2021-03-15 Joseph Park , Gerald M Pao , Erik Stabenau , George Sugihara , Thomas Lorimer

The integration of Large Language Models (LLMs) into scientific discovery is currently hindered by the Implicit Context problem, where governing equations extracted from literature contain invisible thermodynamic assumptions (e.g.,…

Databases · Computer Science 2026-03-11 Yue Wua , Tianhao Su , Rui Hu , Mingchuan Zhao , Shunbo Hu , Deng Pan , Jizhong Huang

Gaussian state space models have been used for decades as generative models of sequential data. They admit an intuitive probabilistic interpretation, have a simple functional form, and enjoy widespread adoption. We introduce a unified…

Machine Learning · Statistics 2016-12-06 Rahul G. Krishnan , Uri Shalit , David Sontag

State Space Models (SSMs) have recently emerged as efficient alternatives to Transformer-Based Models (TBMs) for long-sequence processing with linear scaling, yet how contextual information flows across layers in these architectures remains…

Computation and Language · Computer Science 2026-01-08 Nhat M. Hoang , Do Xuan Long , Cong-Duy Nguyen , Min-Yen Kan , Luu Anh Tuan

State Space Models (SSMs) and Hidden Markov Models (HMMs) are foundational frameworks for modeling sequential data with latent variables and are widely used in signal processing, control theory, and machine learning. Despite their shared…

Machine Learning · Computer Science 2026-01-21 Aydin Ghojogh , M. Hadi Sepanj , Benyamin Ghojogh

Many probabilistic inference problems such as stochastic filtering or the computation of rare event probabilities require model analysis under initial and terminal constraints. We propose a solution to this bridging problem for the widely…

Systems and Control · Electrical Eng. & Systems 2021-05-28 Michael Backenköhler , Luca Bortolussi , Gerrit Großmann , Verena Wolf

In text mining, topic models are a type of probabilistic generative models for inferring latent semantic topics from text corpus. One of the most popular inference approaches to topic models is perhaps collapsed Gibbs sampling (CGS), which…

Computation and Language · Computer Science 2023-01-31 Daniel Rugeles , Zhen Hai , Juan Felipe Carmona , Manoranjan Dash , Gao Cong

The transition density of a stochastic, logistic population growth model with multiplicative intrinsic noise is analytically intractable. Inferring model parameter values by fitting such stochastic differential equation (SDE) models to data…

Applications · Statistics 2015-08-17 Jonathan Heydari , Conor Lawless , David A. Lydall , Darren J. Wilkinson

State-space models (SSMs) are a highly expressive model class for learning patterns in time series data and for system identification. Deterministic versions of SSMs (e.g. LSTMs) proved extremely successful in modeling complex time series…

When examining dynamics occurring at non-zero temperatures, both energy and entropy must be taken into account while describing activated barrier crossing events. Furthermore, good reaction coordinates need to be constructed to describe…

Chemical Physics · Physics 2022-03-16 E. R. Beyerle , Shams Mehdi , Pratyush Tiwary

Stochastic embedding transitions introduce a probabilistic mechanism for adjusting token representations dynamically during inference, mitigating the constraints imposed through static or deterministic embeddings. A transition framework was…

Computation and Language · Computer Science 2025-08-11 Stefan Whitaker , Colin Sisate , Marcel Windsor , Nikolai Fairweather , Tarquin Goldborough , Oskar Lindenfeld

Conventional imitation learning assumes access to the actions of demonstrators, but these motor signals are often non-observable in naturalistic settings. Additionally, sequential decision-making behaviors in these settings can deviate from…

Machine Learning · Computer Science 2023-10-31 Aoyang Qin , Feng Gao , Qing Li , Song-Chun Zhu , Sirui Xie

Large language models (LLMs) solve complex problems by generating multi-step reasoning traces. Yet these traces are typically analyzed from only one of two perspectives: the sequence of tokens across different reasoning steps in the…

Computation and Language · Computer Science 2026-03-25 Ruidi Chang , Jiawei Zhou , Hanjie Chen

We propose a latent topic model with a Markovian transition for process data, which consist of time-stamped events recorded in a log file. Such data are becoming more widely available in computer-based educational assessment with complex…

Methodology · Statistics 2019-11-06 Haochen Xu , Guanhua Fang , Zhiliang Ying

Classical models of computation traditionally resort to halting schemes in order to enquire about the state of a computation. In such schemes, a computational process is responsible for signalling an end of a calculation by setting a halt…

Quantum Physics · Physics 2015-02-10 Luís Tarrataca , Andreas Wichert

State-space language models such as Mamba match Transformer quality while permitting linear complexity inference, yet still comprise billions of parameters that hinder deployment. Existing one-shot pruning methods are tailored to attention…

Machine Learning · Computer Science 2025-06-12 Kaiwen Tuo , Huan Wang

We tackle the question of whether Large Language Models (LLMs), viewed as dynamical systems with state evolving in the embedding space of symbolic tokens, are observable. That is, whether there exist multiple 'mental' state trajectories…

Artificial Intelligence · Computer Science 2024-05-24 Tian Yu Liu , Stefano Soatto , Matteo Marchi , Pratik Chaudhari , Paulo Tabuada
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