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2606.11510 2026-06-11 q-bio.QM q-bio.PE stat.ML 新提交

Continuous biome representations from Earth observation embeddings

从地球观测嵌入中提取连续生物群落表示

Maxwell B. Joseph, Flávia De Souza Mendes, Dieu My T. Nguyen, Camile Sothe, Christopher B. Anderson (Planet Labs PBC)

AI总结 针对离散生物群落图压缩生态连续性的问题,提出从卫星图像嵌入中学习连续概率表示,在巴西6个生物群落和4672种植物数据上验证,优于离散标签预测物种分布。

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8 pages, 4 figures
AI中文摘要

生物群落随空间连续变化,但生物群落图通过分类边界压缩了这种变化,特别是在生态过渡带,过渡群落具有独特的生态特征。地球观测基础模型通过密集嵌入编码光谱、空间和时间信息,能否将离散的生物群落图转换为更好地捕捉生态变化的连续表示?本文在Clay v1.5卫星图像嵌入上拟合线性分类器,从分类图中预测生物群落标签。softmax输出产生一个连续概率向量,其维度对应命名的生物群落类别。我们使用巴西六个生物群落、130万个嵌入和10015个保留的森林清查样地(涵盖4672种植物)评估该方法。连续生物群落表示在预测物种出现方面优于离散生物群落标签(10次空间交叉验证中平均每物种AUC 0.618 vs. 0.570)。分解这一增益表明,改进来自分级概率输出的连续性,而非标签重新分配;该模式在距生物群落边界的所有距离上均成立。原始1024维嵌入仍然是我们测试的最强预测因子(平均AUC 0.646 vs. 0.618),但连续表示恢复了嵌入相对于离散标签的大部分增益。这种简单方法为分类地图标签提供了概率替代方案,保留了其含义,同时编码了离散地图抑制的分级变化。

英文摘要

Biotic communities vary continuously across space, yet biome maps impose categorical boundaries that compress this variation, particularly at ecotones where transitional communities are ecologically distinct. Could Earth observation (EO) foundation models, which encode spectral, spatial, and temporal information with dense embeddings, convert discrete biome maps into continuous representations that better capture ecological variation? Here, we fit a linear classifier on Clay v1.5 satellite image embeddings to predict biome labels from a categorical map. The softmax output yields a continuous probability vector whose dimensions correspond to named biome classes. We evaluate this approach using six Brazilian biomes, 1.3 million embeddings, and 10,015 withheld forest inventory plots spanning 4,672 plant species. The continuous biome representation outperforms discrete biome labels for predicting species occurrence (mean per-species AUC 0.618 vs. 0.570 across 10 spatial cross-validation folds). Decomposing this gain shows that continuity in the graded probability output, rather than label reassignment, accounts for the improvement; the pattern holds across all distances from biome boundaries. The raw 1024-dimensional embedding remains the strongest predictor we tested (mean AUC 0.646 vs. 0.618), but the continuous representation recovers most of the embedding's gain over discrete labels. This simple approach provides a probabilistic replacement for categorical map labels, preserving their meaning while encoding graded variation that discrete maps suppress.

2606.11259 2026-06-11 nlin.AO cond-mat.stat-mech cs.SI math.DS q-bio.PE 新提交

Stabilizing Role of Uninformed Participants in Collective Decision Making

无信息参与者在集体决策中的稳定作用

Leonardo Colombo, Marıa Emma Eyrea Irazu, Laura P. Schaposnik, James Unwin

AI总结 通过耗散哈密顿量建模,发现无信息参与者通过方向无关的耗散延迟极化转变,稳定集体决策。

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23 pages, 6 images
AI中文摘要

对于没有严格等级制度的群体,集体决策通常通过妥协产生。我们使用耗散哈密顿量公式开发了一个集体决策的二阶网络模型,其中知情代理引入偏好方向,而无信息参与者仅贡献方向无关的耗散。我们表明,在低冲突下,该模型允许一个局部唯一、指数稳定的妥协状态。使用结构化模块网络,我们进一步表明,随着冲突增加,局部妥协分支通过鞍节点折叠终止,而不是通过平滑的平均场对称破缺转变。模块化极化状态在局部与妥协分支分离的分支上持续存在。方向无关的耗散不会改变静态结构阈值,但会延迟从鞍节点幽灵的逃逸,并将极化的可观察起始点推向更大的冲突。我们的工作确定了一种耗散介导的机制,与基于连通性的解释互补,通过该机制,无信息参与者稳定了生物和工程群体中的集体行为。

英文摘要

For groups without strict hierarchy, collective decisions often emerge through compromise. We develop a second-order network model of collective decision-making using a dissipative Hamiltonian formulation, in which informed agents introduce preferred directions while uninformed participants contribute only direction-free dissipation. We show that under low conflict, the model admits a locally unique, exponentially stable compromise state. Using a structured modular network we further show that as conflict increases the local compromise branch terminates through a saddle-node fold rather than through a smooth mean-field symmetry-breaking transition. Modular polarized states persist on branches that are locally separated from the compromise branch. Direction-free dissipation does not shift the static structural threshold, but it delays escape from the saddle-node ghost and pushes the observable onset of polarization to larger conflicts. Our work identifies a dissipation-mediated mechanism, complementary to connectivity-based accounts, through which uninformed participants stabilize collective behavior in biological and engineered swarms.

2511.04327 2026-06-11 q-bio.PE nlin.AO physics.bio-ph

Feasibility and Single Parameter Scaling of Extinctions in Large Ecological Communities

大规模生态群落中灭绝可行性的单参数标度

Philippe Jacquod

AI总结 研究通过随机矩阵理论分析了大规模生态群落中物种共存的可行性及灭绝触发机制,推导出灭绝概率的解析表达式并提出单参数标度律。

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Journal ref
Phys. Rev. E 113, L62202 (2026)
Comments
Final version; to appear in Phys. Rev. E Letters
AI中文摘要

由广义利克特-沃尔特方程建模的多物种生态系统表现出稳定的种群丰度,其中大量物种往往共存。理解这种共存在何种条件下可行以及触发物种灭绝的因素是理论生态学中的关键问题。通过标准的随机矩阵理论方法,我证明在弱相互作用范围内,物种丰度分布在平衡时呈高斯分布。一个结果是,对于足够多的物种,可行性通常在稳定性之前被破坏。我进一步推导了n=0,1,2,...个物种灭绝的概率解析表达式,并推测物种灭绝遵循单参数标度律。这些结果通过在广泛系统参数范围内的数值模拟得到验证。

英文摘要

Multispecies ecosystems modelled by generalized Lotka-Volterra equations exhibit stationary population abundances, where large number of species often coexist. Understanding the precise conditions under which this is at all feasible and what triggers species extinctions is a key, outstanding problem in theoretical ecology. Using standard methods of random matrix theory, I show that distributions of species abundances are Gaussian at equilibrium, in the weakly interacting regime. One consequence is that feasibility is generically broken before stability, for large enough number of species. I further derive an analytical expression for the probability that $n=0,1,2,...$ species go extinct and conjecture that a single-parameter scaling law governs species extinctions. These results are corroborated by numerical simulations in a wide range of system parameters.

2604.25701 2026-06-11 physics.bio-ph physics.data-an q-bio.BM q-bio.MN q-bio.PE 版本更新

Bayesian Rate Inference for Sequence Motif Dynamics in Systems of Reactive Nucleic Acids

反应性核酸系统中序列基序动力学的贝叶斯速率推断

Johannes Harth-Kitzerow, Ulrich Gerland, Torsten A. Enßlin

AI总结 提出贝叶斯推断框架,从链反应器模拟的连接计数数据中推断基序速率方程参数,为匹配简化模型与复杂模拟提供方法,并迈向从实验数据直接推断反应速率常数。

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18 pages, 8 figures, pre-submission
AI中文摘要

RNA世界假说提出了生命在早期地球上出现的一条途径。它假设生命始于基于RNA的系统,能够存储、传递和复制信息,设想单体和短RNA寡聚体相互作用形成更长的链,最终成为具有催化活性的核酶。RNA池中的关键反应是杂交、去杂交、模板化连接和切割。这些反应依赖于许多环境参数以及相互作用链之间广泛可能的构型。为了扫描如此高维的参数空间,需要高效的描述。基序速率方程将复杂的链反应器动力学投影到序列基序空间。这里我们提出了一个贝叶斯推断框架,从链反应器模拟产生的连接计数数据中推断其参数。这提供了一个将更简单的基序速率方程与更复杂的模拟相匹配的框架。此外,这是朝着直接从实验数据推断反应速率常数(包括严格的 uncertainty 估计)迈出的一步。这可能是连接理论与实验、加深我们对生命出现所必需的基本特征理解的关键步骤。

英文摘要

The RNA world hypothesis suggests a pathway of how life emerged on early earth. It assumes that life started with RNA based systems, capable of storing, transmitting and replicating information, envisioning that monomers and short RNA oligomers interact to form longer strands, eventually becoming catalytically active ribozymes. Key reactions in RNA pools are hybridization, dehybridization, templated ligation, and cleavage. Those reactions depend on many environmental parameters and the wide range of possible configurations among interacting strands. In order to scan such high dimensional parameter spaces, efficient descriptions are needed. Motif rate equations project complex strand reactor dynamics onto sequence motif space. Here we present a Bayesian inference framework to infer their parameters from ligation count data produced by strand reactor simulations. This provides a framework to match the simpler motif rate equations to more complex simulations. Additionally, it is a step towards inferring reaction rate constants directly from experimental data, including rigorous uncertainty estimation. This could be an essential procedure to connect theory and experiment, and deepen our understanding of the essential features necessary for life to emerge.

2602.20266 2026-06-11 math.PR math.ST q-bio.PE 版本更新

Multiple Poisson-Dirichlet diffusions on generalized Kingman simplices

广义Kingman单纯形上的多重Poisson-Dirichlet扩散

Cristina Costantini, Matteo Ruggiero

AI总结 构造了有限标记广义Kingman单纯形上的无穷维扩散过程,通过分块斜积分解和极限过程,得到了多重Poisson-Dirichlet平稳分布。

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Comments
Revised version; dedicated to the memory of T.G. Kurtz
AI中文摘要

我们在带有有限个标记的广义Kingman单纯形上构造了一类新的无穷维扩散过程。该模型描述了由有限个$H$标记标记的无穷多种类型的相对频率的时间演化,但在每个标记内类型是无标记的。我们首先建立了有限类型Wright-Fisher扩散的分块斜积表示,扩展了Dirichlet律的聚合-重归一化自相似性质。该分解将控制演化中的随机标记质量的$H$维Wright-Fisher扩散与$H$个Wright-Fisher扩散(每个在其自己的随机时钟上运行)分开,后者描述了每个标记内相对频率的演化。在对标记内频率进行降序排序后,我们确定了当每个标记的类型数趋于无穷大时的分布极限,并在适当定义域上推导出其无穷小生成元的显式形式。极限扩散以多重Poisson-Dirichlet分布作为平稳分布;当所有类型共享相同标记时,它恢复为无穷多中性等位基因扩散,而当有两个标记时,它产生Thoma单纯形上的扩散。

英文摘要

We construct a new class of infinite-dimensional diffusions with values in a generalized Kingman simplex with finitely many marks. The model describes the temporal evolution of the relative frequencies of infinitely many types that are labeled by a finite number $H$ of marks, but unlabeled within each mark. We first establish a blockwise skew-product representation for a finite-type Wright-Fisher diffusion, extending the aggregation-renormalization self-similarity property of Dirichlet laws. The decomposition separates an $H$-dimensional Wright-Fisher diffusion governing the evolving random mark masses, from $H$ Wright-Fisher diffusions, each run on its own random clock, which describe the evolution of the relative frequencies within each mark. After ranking the within-mark frequencies in decreasing order, we identify the distributional limit as the number of types per mark tends to infinity and we derive an explicit form of its infinitesimal generator on a suitable domain. The limiting diffusion admits the multiple Poisson-Dirichlet distribution as a stationary distribution; it recovers the infinitely-many-neutral-alleles diffusion when all types share the same mark and yields a diffusion on the Thoma simplex when there are two marks.

2501.09172 2026-06-11 q-bio.PE 版本更新

Towards a less spherical cow: Species differences dilute the stabilizing effect of higher-order interactions

走向更少球形的牛:物种差异稀释了高阶相互作用的稳定效应

Marc Duran-Sala, Sandro Meloni, Violeta Calleja-Solanas

AI总结 通过分析包含成对和高阶相互作用的竞争群落模型,发现高阶相互作用单独不能保证共存,其稳定效应在物种差异存在时减弱,挑战了高阶相互作用作为通用稳定机制的观点。

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AI中文摘要

生态模型传统上通过物种间的成对相互作用来解释稳定性和共存。然而,相互作用也可能涉及三个或更多物种的群体,即高阶相互作用,最近的理论表明这可以稳定群落。然而,在成对和高阶相互作用同时发生的群落中,高阶相互作用足以稳定共存的条件仍然未知。本研究通过分析包含一定比例成对和高阶相互作用的竞争群落模型来填补这一空白。利用经验数据、数值模拟和解析方法,我们表明高阶相互作用单独不能保证共存。我们发现,虽然一小部分高阶相互作用可以稳定相同物种群落的动态,但在更现实的条件下,如出生率和死亡率的变化或明确的相互作用结构,这种效应会减弱。我们的结果挑战了高阶相互作用作为通用稳定机制的普遍观点,提供了定量证据,表明成对和高阶相互作用以及网络结构和物种参数对于理解生态稳定性共同重要。

英文摘要

Ecological models traditionally explain stability and coexistence through pairwise interactions among species. However, interactions can also involve groups of three or more species, higher-order interactions, which recent theory suggests can stabilize communities. Yet, the conditions under which higher-order interactions are sufficient to stabilize coexistence in communities where pairwise and higher-order interactions occur simultaneously remain unknown. This work addresses this gap by analyzing a model of competitive communities that incorporates a proportion of pairwise and higher-order interactions. Using empirical data, numerical simulations, and analytical methods, we show that higher-order interactions alone cannot guarantee coexistence. We find that, while a small fraction of higher-order interactions can stabilize dynamics in communities of identical species, this effect weakens under more realistic conditions, such as variability in birth and mortality rates or explicit interaction structures. Our results challenge the prevailing view of higher-order interactions as a universal stabilizing mechanism, providing quantitative evidence of the joint importance of both pairwise and higher-order interactions, together with network structure and species parameters, for understanding ecological stability.