22 papers · ranked by Valyu relevance
Xu Yang, Masahiro Kasahara
Background Delivering tools for genome analysis to users is often difficult given the complex dependencies and conflicts of such tools. Container virtualization systems (such as Singularity) isolate environments, thereby helping developers package tools. However, these systems lack mutual composability, i.e., an easy…
Benjamin Lion, Farhad Arbab, Carolyn Talcott
We propose a component-based semantic model for Cyber-Physical Systems (CPSs) wherein the notion of a component abstracts the internal details of both cyber and physical processes, to expose a uniform semantic model of their externally observable behaviors expressed as sets of sequences of observations. We introduce…
Zijian Zhang, Sara Aronowitz, Alán Aspuru‐Guzik
catalysts, and learning Authors: ['Zijian Zhang' 'Sara Aronowitz' 'Alán Aspuru‐Guzik'] Understanding is a crucial yet elusive concept in artificial intelligence (AI). This work proposes a framework for analyzing understanding based on the notion of composability. Given any subject (e.g., a person or an AI), we suggest…
Joshua Horowitz, Jeffrey Heer
Efforts to push programming beyond static textual code have sought to imbue programming with multiple distinct qualities. One long-acknowledged quality is liveness: providing programmers with in-depth feedback about a program's dynamic behavior as the program is edited. A second quality, long-explored but lacking a…
Dipankar Sarkar
In the rapidly evolving domain of distributed ledger technology, scalability and interoperability have become paramount challenges for both academic and industry sectors. In this paper, we introduce a comprehensive formal model to address atomic composability across multiple rollups on Ethereum. The proposed model…
Massimo Bartoletti, Riccardo Marchesin, Roberto Zunino
Complex DeFi services are usually constructed by composing a variety of simpler smart contracts. The permissionless nature of the blockchains where these smart contracts are executed makes DeFi services exposed to security risks, since adversaries can target any of the underlying contracts to economically damage the…
Mariusz P. Da̧browski, Stephen Hsu, Xavier Calmet, Roberto Casadio
We present a comparative analysis of the plethora of nonextensive and/or nonadditive entropies which go beyond the standard Boltzmann-Gibbs formulation. After defining the basic notions of additivity, extensivity, and composability, we discuss the properties of these entropies and their mutual relations, if they exist.…
N. Firoz Basha, Gopinath Ganapathy, Moulana Mohammed
Component-based software development (CBD) is a methodology that has been embraced by the software industry to accelerate development, save costs and timelines, minimize testing requirements, and boost quality and output. Compared to the conventional software development approach, this led to the system's development…
Aditi T. Merchant, Daniel Guo, Ben Viggiano, Lucas Brennan-Almaraz + 6 more
Programmable composition of complex systems is a longstanding goal of biological research. Generative modeling has improved the reliability of computational design, but existing methods are highly specialized and are difficult to extend or compose. Here, we introduce Proto, a high-level programming language for…
Steven Phillips
Category theorists and cognitive scientists study the structural (analogical) relations between domains of interest albeit in different contexts, that is, formal and psychological systems, respectively. Despite this basic commonality, very few cognitive scientists take a category theory approach toward understanding…
Xiaochen Y. Zheng, Mona M. Garvert, Hanneke E. M. den Ouden, Lisa I. Horstman + 2 more
The ability to generalize previously learned knowledge to novel situations is crucial for adaptive behavior, representing a form of cognitive flexibility that is particularly relevant in language. Humans excel at combining linguistic building blocks to infer the meanings of novel compositional words, such as…
Authors not listed
Self-driving laboratories (SDLs) promise accelerated scientific discovery and product development by closing the loop between robotic execution and AI/ML-driven decision making. In practice, however, SDL orchestration remains fragmented; workflows are typically encoded as laboratory-specific scripts or bespoke…
Ivan Vegner, Sydelle de Souza, Valentin Forch, Martha Lewis + 1 more
A core aspect of compositionality, systematicity is a desirable property in ML models as it enables strong generalization to novel contexts. This has led to numerous studies proposing benchmarks to assess systematic generalization, as well as models and training regimes designed to enhance it. Many of these efforts are…
Ayush Pandey, Inigo Incer, Alberto Sangiovanni-Vincentelli, Richard M. Murray
We provide a new perspective on using formal methods to model specifications and synthesize implementations for the design of biological circuits. In synthetic biology, design objectives are rarely described formally. We present an assume-guarantee contract framework to describe biological circuit design objectives as…
Tlholohelo Sylvia Sikhosana, Ntsoaki Joyce Malebo, Tladi Gideon Mofokeng, Mpho Phillip Motloung + 2 more
'Tladi Gideon Mofokeng' 'Mpho Phillip Motloung' 'Mokgaotsa Jonas Mochane' 'Francisco Javier Espinach Orús'] There is a sizeable amount of sawdust produced from wood industries such as timber and furniture. In the past, sawdust has been utilized as a fuel source and in the manufacturing of furniture. Based on the…
Chengting Yu, Yujie Wu, Aili Wang, Wolfgang Maass
Hyperdimensional computing (HDC) addresses massively parallel implementations of symbolic computations that are both more transparent than ANNs and LLMs and more suitable for in-memory computing on highly energy-efficient analog hardware. It captures an essential aspects of brain computations: objects, concepts, and…
Stephen A. Allegri, Kevin McCoy, Cassie S. Mitchell
Large networks are quintessential to bioinformatics, knowledge graphs, social network analysis, and graph-based learning. CompositeView is a Python-based open-source application that improves interactive complex network visualization and extraction of actionable insight. CompositeView utilizes specifically formatted…
Authors not listed
Curried functions provide a systematic way of transforming multi-argument functions into nested singleargument functions. This transformation allows partial application and supports many central principles of functional programming. Their extension, called curried 𝑘-ary functions, naturally generalizes the familiar…
Mai Thi Nguyen, Daniela Solueva, Evgenia Spyridonos, Hanaa Dahy + 3 more
'Andrew Adamatzky' 'Han A.B. Wösten' 'Phil Ayres'] There is an essential need for a change in the way we build our physical environment. To prevent our ecosystems from collapsing, raising awareness of already available bio-based materials is vital. Mycelium, a living fungal organism, has the potential to replace…
Claus Kadelka, Matthew Wheeler, Alan Veliz-Cuba, David Murrugarra + 1 more
This paper addresses two topics in systems biology, the hypothesis that biological systems are modular and the problem of relating structure and function of biological systems. The focus here is on gene regulatory networks, represented by Boolean network models, a commonly used tool. Most of the research on gene…
Megan Stanley, Marwin Segler
Computational techniques, including virtual screening, de novo design, and generative models, play an increasing role in expediting DMTA cycles for modern molecular discovery. However, computationally proposed molecules must be synthetically feasible for laboratory testing. In this perspective, we offer a succinct…
Eric Smith, Harrison B. Smith, Jakob Lykke Andersen
We consider problems in the functional analysis and evolution of combinatorial chemical reaction networks as rule-based, or three-level systems. The first level consists of rules, realized here as graph-grammar representations of reaction mechanisms. The second level consists of stoichiometric networks of molecules and…