Quantitative Biology
Genomic foundation models such as Evo 2 learn rich sequence representations, but their value for biosecurity screening is largely unexplored. We ask how much biosecurity-relevant signal is linearly accessible in these representations by…
Transient synaptic memory has emerged as a potential mechanism for maintaining short-term information even in the absence of persistent neuronal activity. However, it remains unclear whether the hidden synaptic state alone contains…
Recent advances in generative and embodied AI have been driven by large-scale predictive learning over multimodal data. However, the resulting systems remain largely based on passive training regimes where linguistic regularities create the…
Humans recognize movements effortlessly, even from noisy and complex visual input. But what information in the stimulus allows humans to rapidly classify movements? No framework has systematically compared different strategies of movement…
All-optical two-photon holographic optogenetics enables causal circuit mapping by stimulating defined neurons or ensembles while imaging population activity. Yet exhaustive connectivity mapping remains experimentally prohibitive because of…
Phylogenetic networks generalize phylogenetic trees to evolutionary histories that include reticulate events such as recombination, horizontal gene transfer, and hybridization. Under a Markov model of nucleotide substitution, a phylogenetic…
Falling detection is vital for elderly care and intelligent surveillance; however, prevailing vision-based approaches predominantly frame it as static pose classification or discrete temporal pattern matching, fundamentally overlooking the…
Evolved sequences can be used to infer the rules of evolution. Orally transmitted folk melodies are evolved sequences whose similarity to protein sequences (one-dimensional, drawn from a limited alphabet) invites application of…
The fundamental relationship among protein sequence, structure, function, and physicochemical properties is a central principle in biology. While in principle protein function and properties should be able to be derived directly from…
Cancer progression is driven by the ability of cells with identical driver mutations to adopt biologically distinct adaptive phenotypes. Yet the population dynamics implied by intratumour phenotypic heterogeneity is poorly understood.…
DNA methylation can function as a toxic alkylation reaction exploited by chemotherapeutic agents to induce cancer cell death. However, finely tuned DNA methylation plays a fundamental role in cellular physiology, particularly in the…
Accurate diagnostic classification and disease-severity prediction for Alzheimer's disease are hampered by the incompleteness and heterogeneity of real-world clinical data. Left unaddressed, these barriers prevent reliable disease modelling…
Depth of anesthesia is a complex but important vital state to analyze during a surgery or other procedure. One parameter to estimate this state is the bispectral index (BIS), a value ranging from 0 to 100 with a target of 40 to 60 for a…
These are lecture notes for an advanced topics course in the master's programme at Bonn University. It aims to give a concise review of some of the work that has been done around the topic of adaptive dynamics from a rigorous stochastic…
Tumor evolution is shaped by cell division, cell death, competition, and constraints imposed by the local microenvironment. Because these dynamics are usually not observed directly, phylogenetic trees inferred from somatic variation in…
Decoding brain activity is useful for characterizing brain processes and understanding the functional architecture underlying cognition. However, the inter-individual variability in brain response patterns limits the development of decoders…
Energy landscapes provide a common framework for describing learning, embryonic development, and collective dynamics. Although such landscapes may evolve over time, their dynamics are typically prescribed externally rather than generated by…
We model human motor cortex during a wrist-extension BCI task as a port-Hamiltonian system (pHS): a conservative interconnection (gyroscopic coupling between neural phasors) plus a dissipative port (power-law energy decay driven by a GNN…
Dimensionality reduction has proven powerful for identifying neural manifolds, which are low-dimensional structures underlying high-dimensional neural activity. These low-dimensional representations have improved the interpretability of…
Background: Dynamic programming in biological sequence analysis computes probabilities or partition functions by summing over exponentially many latent paths, alignments, derivation trees, or RNA secondary structures. Their backward and…