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1. Artificial Intelligence for Biology

   https://doi.org/10.1093/icb/icab188  

   Hassoun, Soha; Jefferson, Felicia; Shi, Xinghua; Stucky, Brian; Wang, Jin; Rosa, Epaminondas (August 2021, Integrative and Comparative Biology)

   null (Ed.)

   Abstract Despite efforts to integrate research across different subdisciplines of biology, the scale of integration remains limited. We hypothesize that future generations of Artificial Intelligence (AI) technologies specifically adapted for biological sciences will help enable the reintegration of biology. AI technologies will allow us not only to collect, connect and analyze data at unprecedented scales, but also to build comprehensive predictive models that span various subdisciplines. They will make possible both targeted (testing specific hypotheses) and untargeted discoveries. AI for biology will be the cross-cutting technology that will enhance our ability to do biological research at every scale. We expect AI to revolutionize biology in the 21st century much like statistics transformed biology in the 20th century. The difficulties, however, are many, including data curation and assembly, development of new science in the form of theories that connect the subdisciplines, and new predictive and interpretable AI models that are more suited to biology than existing machine learning and AI techniques. Development efforts will require strong collaborations between biological and computational scientists. This white paper provides a vision for AI for Biology and highlights some challenges. 

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2. Charting a New Frontier Integrating Mathematical Modeling in Complex Biological Systems from Molecules to Ecosystems

   https://doi.org/10.1093/icb/icab165  

   White, Katharine A; McEntire, Kira D; Buan, Nicole R; Robinson, Lecia; Barbar, Elisar (July 2021, Integrative and Comparative Biology)

   Abstract Advances in quantitative biology data collection and analysis across scales (molecular, cellular, organismal, and ecological) have transformed how we understand, categorize, and predict complex biological systems. This surge of quantitative data creates an opportunity to apply, develop, and evaluate mathematical models of biological systems and explore novel methods of analysis. Simultaneously, thanks to increased computational power, mathematicians, engineers and physical scientists have developed sophisticated models of biological systems at different scales. Novel modeling schemes can offer deeper understanding of principles in biology, but there is still a disconnect between modeling and experimental biology that limits our ability to fully realize the integration of mathematical modeling and biology. In this work, we explore the urgent need to expand the use of existing mathematical models across biological scales, develop models that are robust to biological heterogeneity, harness feedback loops within the iterative modeling process, and nurture a cultural shift towards interdisciplinary and cross-field interactions. Better integration of biological experimentation and robust mathematical modeling will transform our ability to understand and predict complex biological systems. 

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3. Cross-validation for training and testing co-occurrence network inference algorithms

   https://doi.org/10.1186/s12859-025-06083-7  

   Agyapong, Daniel; Propster, Jeffrey Ryan; Marks, Jane; Hocking, Toby Dylan (December 2025, BMC Bioinformatics)

   Abstract <bold>Background</bold>Microorganisms are found in almost every environment, including soil, water, air and inside other organisms, such as animals and plants. While some microorganisms cause diseases, most of them help in biological processes such as decomposition, fermentation and nutrient cycling. Much research has been conducted on the study of microbial communities in various environments and how their interactions and relationships can provide insight into various diseases. Co-occurrence network inference algorithms help us understand the complex associations of micro-organisms, especially bacteria. Existing network inference algorithms employ techniques such as correlation, regularized linear regression, and conditional dependence, which have different hyper-parameters that determine the sparsity of the network. These complex microbial communities form intricate ecological networks that are fundamental to ecosystem functioning and host health. Understanding these networks is crucial for developing targeted interventions in both environmental and clinical settings. The emergence of high-throughput sequencing technologies has generated unprecedented amounts of microbiome data, necessitating robust computational methods for network inference and validation. <bold>Results</bold>Previous methods for evaluating the quality of the inferred network include using external data, and network consistency across sub-samples, both of which have several drawbacks that limit their applicability in real microbiome composition data sets. We propose a novel cross-validation method to evaluate co-occurrence network inference algorithms, and new methods for applying existing algorithms to predict on test data. Our method demonstrates superior performance in handling compositional data and addressing the challenges of high dimensionality and sparsity inherent in real microbiome datasets. The proposed framework also provides robust estimates of network stability. <bold>Conclusions</bold>Our empirical study shows that the proposed cross-validation method is useful for hyper-parameter selection (training) and comparing the quality of inferred networks between different algorithms (testing). This advancement represents a significant step forward in microbiome network analysis, providing researchers with a reliable tool for understanding complex microbial interactions. The method’s applicability extends beyond microbiome studies to other fields where network inference from high-dimensional compositional data is crucial, such as gene regulatory networks and ecological food webs. Our framework establishes a new standard for validation in network inference, potentially accelerating discoveries in microbial ecology and human health. 

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4. (Vision Paper) A Vision for Spatio-Causal Situation Awareness, Forecasting, and Planning

   https://doi.org/10.1145/3672556  

   Azad, Fahim Tasneema; Candan, K Selçuk; Kapkiç, Ahmet; Li, Mao-Lin; Liu, Huan; Mandal, Pratanu; Sheth, Paras; Arslan, Bilgehan; Chowell-Puente, Gerardo; Sabo, John; et al (June 2024, ACM Transactions on Spatial Algorithms and Systems)

   Successfully tackling many urgent challenges in socio-economically critical domains, such as public health and sustainability, requires a deeper understanding of causal relationships and interactions among a diverse spectrum of spatio-temporally distributed entities. In these applications, the ability to leverage spatio-temporal data to obtain causally based situational awareness and to develop informed forecasts to provide resilience at different scales is critical. While the promise of a causally grounded approach to these challenges is apparent, the core data technologies needed to achieve these are in the early stages and lack a framework to help realize their potential. In this article, we argue that there is an urgent need for a novel paradigm of spatio-causal research built on computational advances in spatio-temporal data and model integration, causal learning and discovery, large scale data- and model-driven simulations, emulations, and forecasting, as well as spatio-temporal data-driven and model-centric operational recommendations, and effective causally driven visualization and explanation. We thus provide a vision, and a road map, for spatio-causal situation awareness, forecasting, and planning. 

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5. Unraveling complex causal processes that affect sustainability requires more integration between empirical and modeling approaches

   https://doi.org/10.1073/pnas.2215676120  

   Schlüter, Maja; Brelsford, Christa; Ferraro, Paul J.; Orach, Kirill; Qiu, Minghao; Smith, Martin D. (October 2023, Proceedings of the National Academy of Sciences)

   Scientists seek to understand the causal processes that generate sustainability problems and determine effective solutions. Yet, causal inquiry in nature–society systems is hampered by conceptual and methodological challenges that arise from nature–society interdependencies and the complex dynamics they create. Here, we demonstrate how sustainability scientists can address these challenges and make more robust causal claims through better integration between empirical analyses and process- or agent-based modeling. To illustrate how these different epistemological traditions can be integrated, we present four studies of air pollution regulation, natural resource management, and the spread of COVID-19. The studies show how integration can improve empirical estimates of causal effects, inform future research designs and data collection, enhance understanding of the complex dynamics that underlie observed temporal patterns, and elucidate causal mechanisms and the contexts in which they operate. These advances in causal understanding can help sustainability scientists develop better theories of phenomena where social and ecological processes are dynamically intertwined and prior causal knowledge and data are limited. The improved causal understanding also enhances governance by helping scientists and practitioners choose among potential interventions, decide when and how the timing of an intervention matters, and anticipate unexpected outcomes. Methodological integration, however, requires skills and efforts of all involved to learn how members of the respective other tradition think and analyze nature–society systems. 

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