Related papers: A Categorical Model for Retrosynthetic Reaction An…

A flexible treatment for gas- and aerosol-phase chemical processes has been developed for models of diverse scale, from box models up to global models. At the core of this novel framework is an "abstracted aerosol representation" that…

The theory of biochemical processes needs simple but realistic models of phenomena underlying microscopic dynamics of proteins. Many experiments performed in the 1980s have demonstrated that within the protein native state, apart from usual…

Representing molecular structures effectively in chemistry remains a challenging task. Language models and graph-based models are extensively utilized within this domain, consistently achieving state-of-the-art results across an array of…

We provide a category theoretical framework capturing two approaches to graph-based models of chemistry: formal reactions and disconnection rules. We model a translation from the latter to the former as a functor, which is faithful, and…

We present a general framework for classifying partially observed dynamical systems based on the idea of learning in the model space. In contrast to the existing approaches using model point estimates to represent individual data items, we…

We propose an approach for learning the causal structure in stochastic dynamical systems with a $1$-step functional dependency in the presence of latent variables. We propose an information-theoretic approach that allows us to recover the…

Retrosynthesis is the process of determining the set of reactant molecules that can react to form a desired product. Semi-template-based retrosynthesis methods, which imitate the reverse logic of synthesis reactions, first predict the…

The trace regression model, a direct extension of the well-studied linear regression model, allows one to map matrices to real-valued outputs. We here introduce an even more general model, namely the partial-trace regression model, a family…

We present a method of parameter estimation for large class of nonlinear systems, namely those in which the state consists of output derivatives and the flow is linear in the parameter. The method, which solves for the unknown parameter by…

Implicit sentiment analysis aims to uncover emotions that are subtly expressed, often obscured by ambiguity and figurative language. To accomplish this task, large language models and multi-step reasoning are needed to identify those…

Graph-based reaction systems were recently introduced as a generalization of the intensely studied set-based reaction systems. They deal with simple edge-labeled directed graphs, and dynamic semantics of graph-based reaction systems is…

Prototypal analysis is introduced to overcome two shortcomings of archetypal analysis: its sensitivity to outliers and its non-locality, which reduces its applicability as a learning tool. Same as archetypal analysis, prototypal analysis…

An isospin and spin dependent form of the equation of state for nuclear matter is presented. This form is used for the description of nucleon interaction in a new dynamic model. Preliminary calculations show that the new approach makes…

This two-part paper presents a new approach to predictive analysis for social processes. In Part I, we begin by identifying a class of social processes which are simultaneously important in applications and difficult to predict using…

Many biological systems dynamically rearrange their components through a sequence of configurations in order to perform their functions. Such dynamic processes have been studied using network models that sequentially retrieve a set of…

Subdiffusion has been proposed as an explanation of various kinetic phenomena inside living cells. In order to fascilitate large-scale computational studies of subdiffusive chemical processes, we extend a recently suggested mesoscopic model…

A novel information-theoretic method for reconstruction of interaction networks is introduced. We prove that the method is exact for some class of networks. Performance tests on large synthetic transcriptional regulatory networks produce…

Parsing chemical reaction diagrams from scientific literature is challenging due to heterogeneous layouts, intertwined visual elements, and the difficulty of integrating recognition and reasoning. Existing vision-language models advance…

The primary emphasis of this work on kinetics is to illustrate the a posteriori approach to applications, where focus on data leads to novel outcomes, rather than the a priori tendencies of applied analysis which imposes constructs on the…

A new categorical setting is defined in order to characterize the subrecursive classes belonging to complexity hierarchies. This is achieved by means of coercion functors over a symmetric monoidal category endowed with certain recursion…