Biology subjects

Spicer, R.

Publications and source records attributed to Spicer, R..

3 recordsLinked to original sources

bioRxiv2025

Evaluating the Significance of Embedding-Based Protein Sequence Alignment with Clustering and Double Dynamic Programming for Remote Homology

Accurate detection of protein sequence homology is essential for understanding evolutionary relationships and predicting protein functions, particularly for detecting remote homology in the "twilight zone" (20-35% sequence similarity), where traditional sequence alignment methods often fail. Recent studies show that embeddings from protein language models (pLM) can improve remote homology detection over traditional methods. Alignment-based approaches, such as those combining pLMs with dynamic programming alignment, further improve performance but often suffer from noise in the resulting similarity matrices. To address this, we evaluate a newly developed embedding-based sequence alignment approach that refines residue-level embedding similarity using K-means clustering and double dynamic programming (DDP). We show that the incorporation of clustering and DDP contributes substantially to the improved performance in detecting remote homology. Experimental results demonstrate that our approach outperforms both traditional and state-of-the-art approaches based on pLMs on several benchmarks. Our study illustrates embedding-based alignment refined with clustering and DDP offers a powerful approach for identifying remote homology, with potential to evolve further as pLMs continue to advance.

bioinformatics↗

bioRxiv2020

Cultural Evolution of Genetic Heritability

Behavioral genetics and cultural evolution have both revolutionized our understanding of human behavior, but largely independently of each other. Here we reconcile these two fields using a dual inheritance approach, which offers a more nuanced understanding of the interaction between genes and culture, and a resolution to several long-standing puzzles. For example, by neglecting how human environments are extensively shaped by cultural dynamics, behavioral genetic approaches systematically inflate heritability estimates and thereby overestimate the genetic basis of human behavior. A WEIRD (Western, educated, industrialized, rich, democratic) gene problem obscures this inflation. Considering both genetic and cultural evolutionary forces, heritability scores become less a property of a trait and more a moving target that responds to cultural and social changes. Ignoring cultural evolutionary forces leads to an over-simplified model of gene-to-phenotype causality. When cumulative culture functionally overlaps with genes, genetic effects become masked, or even reversed, and the causal effect of an identified gene is confounded with features of the cultural environment, specific to a particular society at a particular time. This framework helps explain why it is easier to discover genes for deficiencies than genes for abilities. With this framework, we predict the ways in which heritability should differ between societies, between socioeconomic levels within some societies but not others, and over the life course. An integrated cultural evolutionary behavioral genetics cuts through the nature-nurture debate and elucidates controversial topics such as general intelligence.

genetics↗

bioRxiv2019

Embodiment improves performance on an immersive brain computer interface in head-mounted virtual reality

Brain computer interfaces (BCI) can be used to provide individuals with neurofeedback of their own brain activity and train them to learn how to control their brain activity. Neurofeedback-based BCIs used for motor rehabilitation aim to close the loop between attempted motor commands and sensory feedback by providing supplemental sensory information when individuals successfully establish specific brain patterns. Existing neurofeedback-based BCIs have used a variety of displays to provide feedback, ranging from devices that provide a more immersive and compelling experience (e.g., head-mounted virtual reality (HMD-VR) or CAVE systems) to devices that are considered less immersive (e.g., computer screens). However, it is not clear whether more immersive systems (i.e., HMD-VR) improve neurofeedback performance compared to computer screens, and whether there are individual performance differences in HMD-VR versus screen-based neurofeedback. In this pilot experiment, we compared neurofeedback performance in HMD-VR versus on a computer screen in twelve healthy individuals. We also examined whether individual differences in presence or embodiment correlated with neurofeedback performance in either environment. Participants were asked to control a virtual right arm by imagining right hand movements. Real-time brain activity indicating motor imagery, which was measured via electroencephalography (EEG) as desynchronized sensorimotor rhythms (SMR; 8-24 Hz) in the left motor cortex, drove the movement of the virtual arm towards (increased SMR desynchronization) or away from (decreased SMR desynchronization) targets. Participants performed two blocks of 30 trials, one for each condition (Screen, HMD-VR), with the order of conditions counterbalanced across participants. After completing each block, participants were asked questions relating to their sense of presence and embodiment in each environment. We found that, while participants performance on the neurofeedback-based BCI task was similar between conditions, the participants reported levels of embodiment was significantly different between conditions. Specifically, participants experienced higher levels of embodiment in HMD-VR compared to the computer screen. We further found that reported levels of embodiment positively correlated with neurofeedback performance only in the HMD-VR condition. Overall, these preliminary results suggest that embodiment may improve performance on a neurofeedback-based BCI and that HMD-VR may increase embodiment during a neurofeedback-based BCI task compared to a standard computer screen.

neuroscience↗