Shan Shan

Rosa Aghdam, Xudong Tang, Shan Shan et al.

The preservation of soil health is a critical challenge in the 21st century due to its significant impact on agriculture, human health, and biodiversity. We provide the first deep investigation of the predictive potential of machine learning models to understand the connections between soil and biological phenotypes. We investigate an integrative framework performing accurate machine learning-based prediction of plant phenotypes from biological, chemical, and physical properties of the soil via two models: random forest and Bayesian neural network. We show that prediction is improved when incorporating environmental features like soil physicochemical properties and microbial population density into the models, in addition to the microbiome information. Exploring various data preprocessing strategies confirms the significant impact of human decisions on predictive performance. We show that the naive total sum scaling normalization that is commonly used in microbiome research is not the optimal strategy to maximize predictive power. Also, we find that accurately defined labels are more important than normalization, taxonomic level or model characteristics. In cases where humans are unable to classify samples accurately, machine learning model performance is limited. Lastly, we provide domain scientists via a full model selection decision tree to identify the human choices that optimize model prediction power. Our work is accompanied by open source reproducible scripts (https://github.com/solislemuslab/soil-microbiome-nn) for maximum outreach among the microbiome research community.

Shan Shan, Ingrid Daubechies

Diffusion maps (DM) constitute a classic dimension reduction technique, for data lying on or close to a (relatively) low-dimensional manifold embedded in a much larger dimensional space. The DM procedure consists in constructing a spectral parametrization for the manifold from simulated random walks or diffusion paths on the data set. However, DM is hard to tune in practice. In particular, the task to set a diffusion time t when constructing the diffusion kernel matrix is critical. We address this problem by using the semigroup property of the diffusion operator. We propose a semigroup criterion for picking t. Experiments show that this principled approach is effective and robust.

Shan Shan

The complex interaction between social behaviors and climate change requires more than traditional data-driven prediction; it demands interpretable and adaptive analytical frameworks capable of integrating heterogeneous sources of knowledge. This study introduces ClimateAgents, a multi-agent research assistant designed to support social-climate analysis through coordinated AI agents. Rather than focusing solely on predictive modeling, the framework assists researchers in exploring socio-environmental dynamics by integrating multimodal data retrieval, statistical modeling, textual analysis, and automated reasoning. Traditional approaches to climate analysis often address narrowly defined indicators and lack the flexibility to incorporate cross-domain socio-economic knowledge or adapt to evolving research questions. To address these limitations, ClimateAgents employs a set of collaborative, domain-specialized agents that collectively perform key stages of the research workflow, including hypothesis generation, data analysis, evidence retrieval, and structured reporting. The framework supports exploratory analysis and scenario investigation using datasets from sources such as the United Nations and the World Bank. By combining agent-based reasoning with quantitative analysis of socio-economic behavioral dynamics, ClimateAgents enables adaptive and interpretable exploration of relationships between climate indicators, social variables, and environmental outcomes. The results illustrate how multi-agent AI systems can augment analytical reasoning and facilitate interdisciplinary, data-driven investigation of complex socio-environmental systems.

Shan Shan

This research presents a three-step causal inference framework that integrates correlation analysis, machine learning-based causality discovery, and LLM-driven interpretations to identify socioeconomic factors influencing carbon emissions and contributing to climate change. The approach begins with identifying correlations, progresses to causal analysis, and enhances decision making through LLM-generated inquiries about the context of climate change. The proposed framework offers adaptable solutions that support data-driven policy-making and strategic decision-making in climate-related contexts, uncovering causal relationships within the climate change domain.

Shan Shan

The quantification of social science remains a longstanding challenge, largely due to the philosophical nature of its foundational theories. Although quantum computing has advanced rapidly in recent years, its relevance to social theory remains underexplored. Most existing research focuses on micro-cognitive models or philosophical analogies, leaving a gap in system-level applications of quantum principles to the analysis of social systems. This study addresses that gap by proposing a theoretical and computational framework that combines quantum mechanics with Generative AI to simulate the emergence and evolution of social norms. Drawing on core quantum concepts--such as superposition, entanglement, and probabilistic measurement--this research models society as a dynamic, uncertain system and sets up five ideal-type experiments. These scenarios are simulated using 25 generative agents, each assigned evolving roles as compliers, resistors, or enforcers. Within a simulated environment monitored by a central observer (the Watcher), agents interact, respond to surveillance, and adapt to periodic normative disruptions. These interactions allow the system to self-organize under external stress and reveal emergent patterns. Key findings show that quantum principles, when integrated with generative AI, enable the modeling of uncertainty, emergence, and interdependence in complex social systems. Simulations reveal patterns including convergence toward normative order, the spread of resistance, and the spontaneous emergence of new equilibria in social rules. In conclusion, this study introduces a novel computational lens that lays the groundwork for a quantum-informed social theory. It offers interdisciplinary insights into how society can be understood not just as a structure to observe but as a dynamic system to simulate and redesign through quantum technologies.

Shan Shan

Achieving Sustainable Development Goal 7 (Affordable and Clean Energy) requires not only technological innovation but also a deeper understanding of the socioeconomic factors influencing energy access and carbon emissions. While these factors are gaining attention, critical questions remain, particularly regarding how to quantify their impacts on energy systems, model their cross-domain interactions, and capture feedback dynamics in the broader context of energy transitions. To address these gaps, this study introduces ClimateAgents, an AI-based framework that combines large language models with domain-specialized agents to support hypothesis generation and scenario exploration. Leveraging 20 years of socioeconomic and emissions data from 265 economies, countries and regions, and 98 indicators drawn from the World Bank database, the framework applies a machine learning based causal inference approach to identify key determinants of carbon emissions in an evidence-based, data driven manner. The analysis highlights three primary drivers: access to clean cooking fuels in rural areas, access to clean cooking fuels in urban areas, and the percentage of population living in urban areas. These findings underscore the critical role of clean cooking technologies and urbanization patterns in shaping emission outcomes. In line with growing calls for evidence-based AI policy, ClimateAgents offers a modular and reflexive learning system that supports the generation of credible and actionable insights for policy. By integrating heterogeneous data modalities, including structured indicators, policy documents, and semantic reasoning, the framework contributes to adaptive policymaking infrastructures that can evolve with complex socio-technical challenges. This approach aims to support a shift from siloed modeling to reflexive, modular systems designed for dynamic, context-aware climate action.