Author: cxdig

Rapid Computation of the Assembly Index of Molecular Graphs

Ian Seet, Keith Y. Patarroyo, Gage Siebert, Sara I. Walker, Leroy Cronin

Determining the assembly index of a molecule, which aims to find the least number of steps required to make its molecular graph by recursively using previously made structures, is a novel problem seeking to quantify the minimum number of constraints required to build a given molecular graph which has wide applications from biosignature detection to cheminformatics including drug discovery. In this article, we consider this problem from an algorithmic perspective and propose an exact algorithm to efficiently find assembly indexes of large molecules including some natural products. To achieve this, we start by identifying the largest possible duplicate sub-graphs during the sub-graph enumeration process and subsequently implement a dynamic programming strategy with a branch and bound heuristic to exploit already used duplicates and reject impossible states in the enumeration. To do so efficiently, we introduce the assembly state data-structure as an array of edge-lists that keeps track of the graph fragmentation, by keeping the last fragmented sub-graph as its first element. By a precise manipulation of this data-structure we can efficiently perform each fragmentation step and reconstruct an exact minimal pathway construction for the molecular graph. These techniques are shown to compute assembly indices of many large molecules with speed and memory efficiency. Finally, we demonstrate the strength of our approach with different benchmarks, including calculating assembly indices of hundreds of thousands molecules from the COCONUT natural product database.

Read the full article at: arxiv.org

COMPLEX CONTAGION IN SOCIAL SYSTEMS WITH DISTRUST

JEAN-FRANÇOIS DE KEMMETER, LUCA GALLO, FABRIZIO BONCORAGLIO, VITO LATORA, and TIMOTEO CARLETTI

Advances in Complex Systems Vol. 27, No. 04n05, 2440001 (2024)

Social systems are characterized by the presence of group interactions and by the existence of both trust and distrust relations. Although there is a wide literature on signed social networks, where positive signs associated to the links indicate trust, friendship, agreement, while negative signs represent distrust, antagonism, and disagreement, very little is known about the effect that signed interactions can have on the spreading of social behaviors when, not only pairwise, but also higher-order interactions are taken into account. In this paper, we introduce a model of complex contagion on signed simplicial complexes, and we investigate the role played by trust and distrust on the dynamics of a social contagion process, where exposure to multiple sources is needed for the contagion to occur. The presence of higher-order signed structures in our model naturally induces new infection and recovery mechanisms, thus increasing the richness of the contagion dynamics. Through numerical simulations and analytical results in the mean-field approximation, we show how distrust determines the way the system moves from a state where no individuals adopt the social behavior, to a state where a finite fraction of the population actively spreads it. Interestingly, we observe that the fraction of spreading individuals displays a non-monotonic dependence with respect to the average number of connections between individuals. We then investigate how social balance affects social contagion, finding that balanced triads have an ambivalent impact on the spreading process, either promoting or impeding contagion based on the relative abundance of fully trusted relations. Our results shed light on the nontrivial effect of trust on the spreading of social behaviors in systems with group interactions, paving the way to further investigations of spreading phenomena in structured populations.

Read the full article at: www.worldscientific.com

Quantifying the use and potential benefits of artificial intelligence in scientific research

Jian Gao & Dashun Wang

Nature Human Behaviour (2024)

The rapid advancement of artificial intelligence (AI) is poised to reshape almost every line of work. Despite enormous efforts devoted to understanding AI’s economic impacts, we lack a systematic understanding of the benefits to scientific research associated with the use of AI. Here we develop a measurement framework to estimate the direct use of AI and associated benefits in science. We find that the use and benefits of AI appear widespread throughout the sciences, growing especially rapidly since 2015. However, there is a substantial gap between AI education and its application in research, highlighting a misalignment between AI expertise supply and demand. Our analysis also reveals demographic disparities, with disciplines with higher proportions of women or Black scientists reaping fewer benefits from AI, potentially exacerbating existing inequalities in science. These findings have implications for the equity and sustainability of the research enterprise, especially as the integration of AI with science continues to deepen.

Read the full article at: www.nature.com

MPIDR – Postdocs/Research Scientists in Digital and Computational Demography

The Max Planck Institute for Demographic Research (MPIDR) is recruiting highly qualified Post-Docs or Research Scientists to join the Department of Digital and Computational Demography, headed by MPIDR Director Emilio Zagheni. The positions will be filled in the Lab of Migration and Mobility and/or in the Lab of Population Dynamics and Sustainable Well-Being.

Digital and computational demography is a growing interdisciplinary field that tackles fundamental questions across all domains of demographic research by combining the methods and perspectives of computational sciences, social and behavioral sciences, and statistics. The field has emerged in parallel with rapid technological improvements in computing, the spread of Internet and mobile technologies, and the increased digitalization of people’s lives. Our group brings together methodologists (from areas like statistics, computer science or formal demography) with experts in various areas of the social sciences in order to foster cross-pollination of ideas, to advance methods and theories of population research, and to address pressing scientific and societal questions.

Candidates who can enrich or complement projects in any Research Area of the Lab of Migration and Mobility or of the Lab of Population Dynamics and Sustainable Well-Being will be considered. Across all profiles, ability and willingness to work in interdisciplinary teams in order to conduct cutting-edge research that advances our understanding of population processes is key.

More at: www.demogr.mpg.de

The Prize in Economic Sciences 2024

When Europeans colonised large parts of the globe, the institutions in those societies changed. This was sometimes dramatic, but did not occur in the same way everywhere. In some places the aim was to exploit the indigenous population and extract resources for the colonisers’ benefit. In others, the colonisers formed inclusive political and economic systems for the long-term benefit of European migrants.

The laureates have shown that one explanation for differences in countries’ prosperity is the societal institutions that were introduced during colonisation. Inclusive institutions were often introduced in countries that were poor when they were colonised, over time resulting in a generally prosperous population. This is an important reason for why former colonies that were once rich are now poor, and vice versa.

Some countries become trapped in a situation with extractive institutions and low economic growth. The introduction of inclusive institutions would create long-term benefits for everyone, but extractive institutions provide short-term gains for the people in power. As long as the political system guarantees they will remain in control, no one will trust their promises of future economic reforms. According to the laureates, this is why no improvement occurs.

However, this inability to make credible promises of positive change can also explain why democratisation sometimes occurs. When there is a threat of revolution, the people in power face a dilemma. They would prefer to remain in power and try to placate the masses by promising economic reforms, but the population are unlikely to believe that they will not return to the old system as soon as the situation settles down. In the end, the only option may be to transfer power and establish democracy.

“Reducing the vast differences in income between countries is one of our time’s greatest challenges. The laureates have demonstrated the importance of societal institutions for achieving this,” says Jakob Svensson, Chair of the Committee for the Prize in Economic Sciences.

Read the full article at: www.nobelprize.org