arXiv preprints from January 1, 2026 through September 19, 2026 — 23:05:07 EST
Linking individual-level processes, such as survival and reproduction, to ecosystem dynamics is challenging due to interactions among populations and species. These interactions depend on organism traits, such as age, body size, and mass, and are influenced by fluctuations in population structure. Integral projection models (IPMs)...
Successful discovery, integration and reuse of data relies on the availability of rich, well-structured and machine-readable metadata to describe every aspect of the data, from sample sources to collection processes to experimental protocols. The use of standardised terminologies to express concepts in a harmonised fashion lies at the...
Biased migration up chemical gradients and proliferation are fundamental drivers of collective invasion in several biological processes ranging from embryonic morphogenesis to cancer. Nonetheless, our understanding of how their interplay yields distinct invasion patterns remains incomplete. In this work, we propose a multiscale...
Sparse autoencoders (SAEs), and other interpretability methods could turn AI models in Biology and other fields into engines of scientific discovery by explaining the superhuman capabilities of those models. However, a latent is only useful if we know three things: whether it is coherent, whether it can be described, and whether that...
The evolutionary fate of proteins is driven by both folding stability and biological function, dual constraints that often conflict, creating frustration and imposing functional costs beyond stability. These costs can be captured by a "dark energy": the difference between the evolutionary energy of protein sequences and their physical...
Recent research grounded in experiments has connected neural ring models of vision to how animals navigate a complex landscape of attractive targets. In this paper we investigate the mathematical and biological implications of a three-stage model where animals pre-process visual stimuli to identify a discrete set of targets, process...
Ancient DNA and new inference methods have transformed the study of human origins, but consensus has not followed. Evidence increasingly indicates that hominin populations were pervasively structured and admixed, so complexity rather than simplicity is the appropriate prior. Here I highlight two blind spots that impede resolving that...
Motivation: Accurate prediction of mutation-induced protein--protein binding free-energy changes is important for antibody affinity maturation, yet scarce labels and complex interface geometry limit generalization. Heterogeneous predictors may process three-dimensional complexes without preserving the cross-chain signals most relevant...
Large-scale, standardized datasets have driven many advances in AI-based scientific modeling, from protein structure prediction to natural language processing. Infectious disease epidemiology is increasingly adopting AI methods for forecasting, surveillance, and outbreak analytics, but the time-series data available to train them...
Ordinary differential equations are commonly used throughout the sciences to build mechanistic models of time-dependent processes. Often, such models are Markov models describing the time-evolution of different interconnected "states". When these models have no "sources" or "sinks", they naturally conserve the total population of the...
Parcellations distributed in Connectivity Informatics Technology Initiative (CIFTI) format cannot be used directly in many analysis programs that require volume input. Existing conversion options may leave voxels in cortical gray matter unlabeled or assign labels outside gray matter, depending on the mapping parameters. We present...
Reproducible biomarkers that monitor motor and cognitive dysfunction in amyotrophic lateral sclerosis (ALS) are needed. Previous work reported reduced beta-band event-related desynchronization (ERD) and attenuated post-movement event-related synchronization (ERS) in frontal and parietal channels during the sustained attention to...
Objective: Choosing between noninvasive respiratory support (NIRS) and invasive mechanical ventilation (IMV) for patients with acute respiratory failure is a complex, time-sensitive decision with heterogeneous treatment effects across patient subgroups. Although clinical trials and guidelines provide population-level guidance, it...
Protein language models organize sequence and structure at scale, but a global representation of how proteins respond to mutation remains lacking. We present RegimeFormer, a large protein perturbation model coupled to RegimeAtlas, constructed by harmonizing and indexing 202,556,313 non-redundant protein sequences across the tree of...
Spreading processes on networks often interact with other dynamics on the same nodes. Neurodegenerative disease provides one example: pathological proteins spread through anatomical connections, while neuronal activity influences and is altered by their spread, forming a spreading-activity feedback loop. However, models coupling...
Protein language models (pLMs) encode information about protein sequences which enable downstream tasks such as structure prediction, but their internal representations are not well understood. Sparse autoencoders (SAEs) provide a promising tool to disentangle latent pLM representations into interpretable features, but existing...
With activity against multidrug-resistant pathogens and mechanisms distinct from conventional antibiotics, antimicrobial peptides (AMPs) offer a promising approach to combating antibiotic-resistant infections. However, their potency varies substantially across pathogen species, making accurate prediction of the minimum inhibitory...
Dementia comprises biologically heterogeneous disorders, yet current risk assessment provides limited insight into how subtype-specific risk emerges and diverges before clinical diagnosis. We developed NetMoint, a multimodal framework integrating partially observed plasma proteomic, structural magnetic resonance imaging and cerebral...
In the Derrida--Higgs model of sympatric speciation, a sexually reproducing population with finite binary genomes can mate only when the genetic overlap between two individuals exceeds a threshold $q_{\min}$. Depending on the genome length $L$, the population either remains genetically connected or fragments into reproductively...
The coordinated movement of animal groups is one of the most widespread social behaviors, which are generally attributed to high-order cognitive processing in the brain. Yet, collective coordination can seemingly emerge from rapid, local interactions between individuals, suggesting the existence of decentralized mechanisms of online...
Communication requires a shared code, and any change to it must be coordinated between senders and receivers to avoid a breakdown of communication. The honeybee waggle dance illustrates this problem: species with horizontal combs point directly at a food source, while species with vertical combs cannot point directly and instead...
Continuous-time Markov chains (CTMCs) provide the backbone for modeling discrete stochastic dynamics across applied, physical, and biological sciences. Their integration with modern gradient-based machine learning, however, is limited by the hard categorical event selection intrinsic to Gillespie-type simulation algorithms. We exploit...
Phylogenetic trees are used in evolutionary biology to represent the evolutionary history of a collection of taxa. As we have incomplete information about any evolutionary history, recovering trees from partial information is a focus of phylogenetic combinatorics. However, in some cases the available data does not describe a single...
We describe a systematic approach for spawning and aggregating multi-class cryo-EM reconstruction jobs. This approach formalizes standard ad hoc strategies of iterative classification and filtering typically used by practitioners to sort impure, heterogeneous samples. To our knowledge, this is the first method that can successfully...
RNA inverse folding asks for an RNA sequence whose prescribed secondary structure is the unique maximum-base-pair compatible fold. In the four-letter Watson-Crick model (A-U and C-G pairs only, no pseudoknots, and zero minimum base-pair span), Hales et al. introduced a separated-coloring certificate and an even-odd device, while Boury...