Haplotype phasing, the process of resolving parental allele inheritance patterns in diploid genomes, is critical for precision medicine and population genetics, yet the underlying optimization is NP-hard, posing a scalability challenge. To address this, we introduce QHap, a haplotype phasing tool that leverages quantum-inspired optimization. By reformulating haplotype phasing as a Max-Cut problem and deploying a GPU-accelerated ballistic simulated bifurcation solver, QHap accelerates phasing while maintaining accuracy comparable to established phasing tools. On the highly polymorphic human major histocompatibility complex region, QHap demonstrates 4- to 20-fold acceleration with zero switch error across multiple long read sequencing platforms. The framework implements two strategies: a read-based method for regional phasing, and a single nucleotide polymorphism-based method that, through quality-weighted probabilistic edge construction, efficiently scales to chromosome-scale tasks. Integration of chromatin conformation capture data extends phase block contiguity by up to 15-fold, enabling near-chromosome-spanning haplotype reconstruction. QHap demonstrates that quantum-inspired algorithms operating on classical hardware offer a promising approach to addressing the growing computational demands of sequencing data, establishing a new paradigm for applying physics-inspired optimization to fundamental challenges in computational genomics.

Protein structural ensembles from NMR spectroscopy capture biologically important conformational heterogeneity, but it remains difficult to determine whether observed variation reflects coordinated motion or noise-like artifacts. We evaluate the Spectral Coherence Index (SCI), a model-free, rotation-invariant summary derived from the participation-ratio effective rank of the inter-model pairwise distance-variance matrix. Under grouped primary analysis of a Main110 cohort of 110 NMR ensembles (30--403 residues; 10--30 models per entry), SCI separated experimental ensembles from matched synthetic incoherent controls with AUC-ROC $= 0.973$ and Cliff's $\delta = -0.945$. Relative to an internal 27-protein pilot, discrimination softened modestly, showing that pilot-era thresholds do not transfer perfectly to a larger, more heterogeneous cohort: the primary operating point $\tau = 0.811$ yielded 95.5\% sensitivity and 89.1\% specificity. PDB-level sensitivity remained nearly unchanged (AUC $= 0.972$), and an independent 11-protein holdout reached AUC $= 0.983$. Across 5-fold grouped stratified cross-validation and leave-one-function-class-out testing, SCI remained strong (AUC $= 0.968$ and $0.971$), although $\sigma_{R_g}$ was the stronger single-feature discriminator and a QC-augmented multifeature model generalized best (AUC $= 0.989$ and $0.990$). Residue-level validation linked SCI-derived contributions to experimental RMSF across 110 proteins and showed broad concordance with GNM-based flexibility patterns. Rescue analyses showed that Main110 softening arose mainly from size and ensemble normalization rather than from loss of spectral signal. Together, these results establish SCI as an interpretable, bounded coherence summary that is most useful when embedded in a multimetric QC workflow for heterogeneous protein ensembles.

Phylogenetic comparative methods (PCMs) are widely used to study trait evolution. However, many evolutionary histories involve reticulate evolutionary scenarios, such as hybridization, that violate core assumptions of these methods. In this study, we evaluate how such violations affect the performance of PCMs. In particular, we focus on the ancestral character estimation, evolutionary rate estimation, and model selection. We simulate continuous trait evolution on various phylogenetic network topologies and assess the performance of PCMs that assume a bifurcating tree (i.e., major tree of the network) as the underlying model of evolution. We found that the performance of the tested PCMs was suboptimal. Using random forest, generalized linear models, and model-based clustering, we identified key factors contributing to these inaccuracies. Our results show that frequent and/or recent hybridization accompanied by one ore more transgressive events and rapidly evolving traits (i.e., high evolutionary rate) lead to significant estimation error, especially with respect to rate estimation and model choice. These factors substantially shift trait values away from tree-based model expectations, leading to overall increased error in parameter estimates. Our study demonstrates cases in which PCMs that rely on trees are likely to misinterpret biological histories and offers recommendations for researchers studying systems with complex evolutionary histories.

Predicting whether someone with mild cognitive impairment (MCI) will progress to Alzheimer's disease (AD) is crucial in the early stages of neurodegeneration. This uncertainty limits enrollment in clinical trials and delays urgent treatment. The Boundary Sharpness Coefficient (BSC) measures how well-defined the gray-white matter boundary looks on structural MRI. This study measures how BSC changes over time, namely, how fast the boundary degrades each year works much better than looking at a single baseline scan for predicting MCI-to-AD conversion. This study analyzed 1,824 T1-weighted MRI scans from 450 ADNI subjects (95 converters, 355 stable; mean follow-up: 4.84 years). BSC voxel-wise maps were computed using tissue segmentation at the gray-white matter cortical ribbon. Previous studies have used CNN and RNN models that reached 96.0% accuracy for AD classification and 84.2% for MCI conversion, but those approaches disregard specific regions within the brain. This study focused specifically on the gray-white matter interface. The approach uses temporal slope features capturing boundary degradation rates, feeding them into Random Survival Forest, a non-parametric ensemble method for right-censored survival data. The Random Survival Forest trained on BSC slopes achieved a test C-index of 0.63, a 163% improvement over baseline parametric models (test C-index: 0.24). Structural MRI costs a fraction of PET imaging ($800--$1,500 vs. $5,000--$7,000) and does not require CSF collection. These temporal biomarkers could help with patient-centered safety screening as well as risk assessment.

The rapid scaling of Protein Language Models (PLMs) has unlocked unprecedented accuracy in protein structure prediction and design, but the quadratic memory growth of the Key-Value (KV) cache during inference remains a prohibitive barrier for single-GPU deployment and high-throughput generation. While 8-bit quantization is now standard, 3-bit quantization remains elusive due to severe numerical outliers in activations. This paper presents TurboESM, an adaptation of Google's TurboQuant to the PLM domain. We solve the fundamental incompatibility between Rotary Position Embeddings (RoPE) and orthogonal transformations by deriving a RoPE-first rotation pipeline. We introduce a head-wise SVD calibration method tailored to the amino acid activation manifold, a dual look-up table (LUT) strategy for asymmetric K/V distributions, and a 1-bit Quantized Johnson-Lindenstrauss (QJL) residual correction. All experiments are conducted on ESM-2 650M, where our implementation achieves a 7.1x memory reduction (330 MB to 47 MB) while maintaining cosine similarity > 0.96 in autoregressive decoding across diverse protein families, including short peptides, transmembrane helices, enzyme active site fragments, and intrinsically disordered regions. We further implement a Triton-based fused decode attention kernel that eliminates intermediate dequantization memory allocations, achieving a 1.96x speedup over the PyTorch two-step path for the KV fetch operation alone; however, TurboESM incurs a prefill overhead of 21-27 ms relative to the original model due to KV quantization and packing, making it most suitable for memory-bound scenarios rather than latency-critical short-sequence workloads. Analysis reveals that PLMs exhibit sharper outlier profiles than large language models (LLMs) due to amino acid vocabulary sparsity, and our method effectively addresses these distributions.

This work analyzes the RAID dataset to evaluate human responses to affine image distortions, including rotation, translation, scaling, and Gaussian noise. Using Mean Squared Error (MSE), the study establishes human detection thresholds for these distortions, enabling comparison across types. Statistical analysis with ANOVA and Tukey Kramer tests reveals that observers are significantly more sensitive to Gaussian noise, which consistently produced the lowest detection thresholds. Fourier analysis further shows that high-frequency components act as a visual mask for Gaussian noise, demonstrating a strong correlation between high frequency energy and detection thresholds. Additionally, spectral orientation influences the perception of rotation. Finally, the study employs the PixelCNN model to show that image probability significantly correlates with detection thresholds for most distortions, suggesting that statistical likelihood affects human visual tolerance.

Biological systems are governed by coupled interactions between intracellular metabolism and bioreactor operation that span multiple time scales. Constraint-based metabolic models are widely used to describe intracellular metabolism, but repeatedly solving the optimization problem at each time step in dynamic models introduces numerical challenges related to infeasibility and computational efficiency. This work presents a multi-scale modeling framework that integrates genome-scale, constraint-based metabolic models with dynamic bioreactor simulations. Intracellular metabolism is described using positive flux variables in a parsimonious flux balance analysis, and the resulting embedded optimization problem is replaced by a neural network surrogate. The surrogate provides a smooth approximation of the embedded optimization mapping and eliminates repeated linear program solves during simulation. The approach is demonstrated for fed-batch fermentation of Escherichia coli, in which the surrogate model yields intracellular fluxes under substrate-limited conditions, whereas the underlying linear program would otherwise be infeasible. The framework provides a continuous representation of intracellular metabolism suitable for dynamic simulation of genome-scale models in bioreactor configurations.

Connectivity structure shapes neural computation, but inferring this structure from population recordings is degenerate: multiple connectivity structures can generate identical dynamics. Recent work uses low-rank recurrent neural networks (lrRNNs) to infer low-dimensional latent dynamics and connectivity structure from observed activity, enabling a mechanistic interpretation of the dynamics. However, standard approaches for training lrRNNs can recover spurious structures irrelevant to the underlying dynamics. We first characterize the identifiability of connectivity structures in lrRNNs and determine conditions under which a unique solution exists. Then, to find such solutions, we develop an inference framework based on maximum entropy and continuous normalizing flows (CNFs), trained via flow matching. Instead of estimating a single connectivity matrix, our method learns the maximally unbiased distribution over connection weights consistent with observed dynamics. This approach captures complex yet necessary distributions such as heavy-tailed connectivity found in empirical data. We validate our method on synthetic datasets with connectivity structures that generate multistable attractors, limit cycles, and ring attractors, and demonstrate its applicability in recordings from rat frontal cortex during decision-making. Our framework shifts circuit inference from recovering connectivity to identifying which connectivity structures are computationally required, and which are artifacts of underconstrained inference.

Multicellular self-organization drives development in biological organisms, yet a comprehensive theory is lacking as basic properties of cells can complicate common approaches. Framing such properties by dynamic graphs led to new theoretical propositions for multicellular self-organization in Escherichia coli. Here, corresponding ideas are developed from biologically-general first principles. The resulting perspective could aid both experimental and computational approaches to multicellular biology as well as efforts to control and engineer it.

Machine learning models of chemical bioactivity are increasingly used for prioritizing a small number of compounds in virtual screening libraries for experimental follow-up. In these applications, assessing model accuracy by early hit enrichment such as Positive Predicted Value (PPV) calculated for top N hits (PPV@N) is more appropriate and actionable than traditional global metrics such as AUC. We present KANEL, an ensemble workflow that combines interpretable Kolmogorov-Arnold Networks (KANs) with XGBoost, random forest, and multilayer perceptron models trained on complementary molecular representations (LillyMol descriptors, RDKit-derived descriptors, and Morgan fingerprints).

Recent advances in neurotechnologies and decades of scientific and clinical research have made closed-loop electrical neuromodulation one of the most promising avenues for the treatment of drug-resistant epilepsy (DRE), a condition that affects over 15 million individuals globally. Yet, with the existing clinical state of the art, only 18% of patients with DRE who undergo closed-loop neuromodulation become seizure-free. In a recent study, we demonstrated that a simple proportional feedback policy based on the framework of passivity-based control (PBC) can significantly outperform the clinical state of the art. However, this study was purely numerical and lacked rigorous mathematical analysis. The present study addresses this gap and provides the first rigorous analysis of PBC for the closed-loop control of epileptic seizures. Using the celebrated Epileptor neural mass model of epilepsy, we analytically demonstrate that (i) seizure dynamics are, in their standard form, neither passive nor passivatable, (ii) epileptic dynamics, despite their lack of passivity, can be stabilized by sufficiently strong passive feedback, and (iii) seizure dynamics can be passivated via proper output redesign. To our knowledge, our results provide the first rigorous passivity-based analysis of epileptic seizure dynamics, as well as a theoretically-grounded framework for sensor placement and feedback design for a new form of closed-loop neuromodulation with the potential to transform seizure management in DRE.

Braess's paradox -- where adding network capacity increases travel time -- is typically attributed to selfish agents. Although eusocial colonies maximize collective fitness, we find experimentally that \emph{Diacamma indicum} ants exhibit this paradox: Leaders favour the shortest path even when it slows the colony. We present a quantitative model of the exploration-exploitation trade-off, demonstrating that evolutionary forces selecting for shortest-path identification can force suboptimal global states. This proves the paradox can emerge in highly cooperative systems without individual selfishness.

Background: The identification of optimal signal detection methods is hindered by the lack of reliable reference datasets. Existing datasets do not capture when adverse events (AEs) are officially recognized by regulatory authorities, preventing restriction of analyses to pre-confirmation periods and limiting evaluation of early detection performance. This study addresses this gap by developing a time-indexed reference dataset for the European Union (EU), incorporating the timing of AE inclusion in product labels along with regulatory metadata. Methods: Current and historical Summaries of Product Characteristics (SmPCs) for all centrally authorized products (n=1,513) were retrieved from the EU Union Register of Medicinal Products (data lock: 15 December 2025). Section 4.8 was extracted and processed using DeepSeek V3 to identify AEs. Regulatory metadata, including labelling changes, were programmatically extracted. Time indexing was based on the date of AE inclusion in the SmPC. Results: The database includes 17,763 SmPC versions spanning 1995-2025, comprising 125,026 drug-AE associations. The time-indexed reference dataset, restricted to active products, included 1,479 medicinal products and 110,823 drug-AE associations. Most AEs were identified pre-marketing (74.5%) versus post-marketing (25.5%). Safety updates peaked around 2012. Gastrointestinal, skin, and nervous system disorders were the most represented System Organ Classes. Drugs had a median of 48 AEs across 14 SOCs. Conclusions: The proposed dataset addresses a critical gap in pharmacovigilance by incorporating temporal information on AE recognition for the EU, supporting more accurate assessment of signal detection performance and facilitating methodological comparisons across analytical approaches.

Ultraweak photon emission is the spontaneous emission of extremely low levels of light from a broad range of biological systems. Recent studies have reported that UPE measured extracranially can serve as a potential non-invasive biomarker of brain activity. Here, we show that this interpretation suffers from serious problems. First, when observed under properly dark conditions, the UPE from the head is much weaker than what is reported in certain papers on 'brain UPE' from human heads. Signals detected in these studies are overwhelmingly dominated by background light. Second, photons at wavelengths < 600 nm are strongly attenuated by scalp and skull tissues, and longer wavelengths fall largely outside the effective spectral sensitivity of the photomultiplier tubes (PMTs) used. As a consequence, even if UPE from the head is detected under properly background-free conditions, it is likely to be dominated by emission from the scalp rather than from the brain, certainly as long as PMTs are used. Our results emphasize the importance of careful experimental design to make genuine progress on this important question.

Real world spatio-temporal datasets, and phenomena related to them, are often challenging to visualise or gain a general overview of. In order to summarise information encompassed in such data, we combine two well known statistical modelling methods. To account for the spatial dimension, we use the intrinsic modification of the conditional autoregression, and incorporate it with the hidden Markov model, allowing the spatial patterns to vary over time. We apply our method to parish register data considering deaths caused by measles in Finland in 1750-1850, and gain novel insight of previously undiscovered infection dynamics. Five distinctive, reoccurring states, describing spatially and temporally differing infection burden and potential routes of spread, are identified. We also find that there is a change in the occurrences of the most typical spatial patterns circa 1812, possibly due to changes in communication networks after major administrative transformations in Finland.

A key step in mechanistic modelling of dynamical systems is to conduct a structural identifiability analysis. This entails deducing which parameter combinations can be estimated from a given set of observed outputs. The standard differential algebra approach answers this question by re-writing the model as a higher-order system of ordinary differential equations that depends solely on the observed outputs. Over the last decades, alternative approaches for analysing structural identifiability based on Lie symmetries acting on independent and dependent variables as well as parameters, have been proposed. However, the link between the standard differential algebra approach and that using full symmetries remains elusive. In this work, we establish this link by introducing the notion of parameter symmetries, which are a special type of full symmetry that alter parameters while preserving the observed outputs. Our main result states that a parameter combination is locally structurally identifiable if and only if it is a differential invariant of all parameter symmetries of a given model. We show that the standard differential algebra approach is consistent with the concept of structural identifiability in terms of parameter symmetries. We present an alternative symmetry-based approach for analysing structural identifiability using parameter symmetries. Lastly, we demonstrate our approach on two well-known models in mathematical biology.

Computational phylogenetics has become an established tool in historical linguistics, with many language families now analyzed using likelihood-based inference. However, standard approaches rely on expert-annotated cognate sets, which are sparse, labor-intensive to produce, and limited to individual language families. This paper explores alternatives by comparing the established method to two fully automated methods that extract phylogenetic signal directly from lexical data. One uses automatic cognate clustering with unigram/concept features; the other applies multiple sequence alignment (MSA) derived from a pair-hidden Markov model. Both are evaluated against expert classifications from Glottolog and typological data from Grambank. Also, the intrinsic strengths of the phylogenetic signal in the characters are compared. Results show that MSA-based inference yields trees more consistent with linguistic classifications, better predicts typological variation, and provides a clearer phylogenetic signal, suggesting it as a promising, scalable alternative to traditional cognate-based methods. This opens new avenues for global-scale language phylogenies beyond expert annotation bottlenecks.

A rapidly alternating red and black display known as Ganzflicker induces visual hallucinations that reflect the generative capacity of the visual system. Individuals vary in their degree of visual imagery, ranging from absent to vivid imagery. Recent proposals suggest that differences in the visual system along this imagery spectrum should also influence the complexity of other internally generated visual experiences. Here, we used tools from natural language processing to analyze free-text descriptions of hallucinations from over 4,000 participants, asking whether people with different imagery phenotypes see different things in their mind's eye during Ganzflicker-induced hallucinations. Topic modeling of descriptions revealed that strong imagers described complex, naturalistic content, while weak imagers reported simple geometric patterns. Using crowd-sourced sensorimotor norms, we also found that participants with stronger imagery used language with richer perceptual associations. These findings may reflect individual variation in coordination between early visual areas and higher-order regions relevant for the imagery spectrum.