bioRxiv Science⌕ Search

Biology subjects

Zhang, L.-Q.

Publications and source records attributed to Zhang, L.-Q..

10 recordsLinked to original sources

Inductive bias anchors a scaling law for biological learning

The speed of animal learning varies substantially across individuals and task domains, and does not always track intuitive notions of task complexity. A nominally simple binary decision task can take thousands of rewards to reach proficiency, whereas seemingly complex naturalistic tasks can be learned within dozens. A long-standing explanation is that learning speed reflects the alignment between an animal's inductive biases and the task at hand. However, without a precise notion of alignment, it is difficult to translate this idea into quantitative predictions. Here, modeling an animal as a Bayesian learner that improves through iterative reward feedback, we use statistical learning theory to derive a scaling law for biological learning. The law makes two predictions. First, inductive bias multiplicatively sets the speed of learning through a single quantity, the effective complexity. This quantity measures how well the task aligns with the animal's prior, and corresponds to the number of bits required to represent the task solution under that prior. We demonstrate this multiplicative scaling in a human motor learning dataset, where behavioral measurements before learning can precisely predict subsequent learning speed. Second, task performance improves as a power law in experience. We validate this power law in a large-scale mouse learning dataset and show that a two-parameter rescaling collapses individual learning curves onto a universal function predicted by the theory. These results suggest that behavioral measurements before learning can be used to predict task-dependent learning speeds, and they explain why learning speed reflects alignment with prior knowledge rather than nominal task complexity.

animal behavior and cognition↗

Mus musculus mice self-organize existing behaviors into structured bouts as they become expert hunters.

In the wild, a mouse must flexibly perform multiple computations at once, rapidly navigating, sampling its environment, forming and using memories, and balancing internal needs. Capturing the self-paced, low-repetition, complex nature of decision making in the wild while preserving the experimental control needed to interpret its process remains a challenge. Here we show that lab mice, without food restriction, learn to forage for hidden resources cued by ambiguous sounds in a dynamic environment by spatiotemporally reorganizing their existing behavioral repertoire. Using a novel closed-loop assay, we required mice to sit still to receive informative but hard-to-localize sound cues emanating from one correct location they must find, out of 157 possible locations in a large arena. With experience, mice become efficient hunters. Efficient hunting cannot be explained by an increase in a particular behavioral module, but instead, mice reorganize existing behaviors into clustered bouts of high-quality sampling and site-checking. Looking forward, this work establishes an approach for studying the neural, molecular, and evolutionary basis of naturalistic decision-making in mice.

animal behavior and cognition↗

Transformation-tolerant object recognition in tree shrews despite lacking a fovea

Object recognition depends on the ability to extract stable representations across changes in how they are viewed, yet it remains unclear how this capacity depends on visual acuity and cortical hierarchy. We combined behavioral testing and computational modeling to determine whether tree shrews, close relatives of primates with lower spatial acuity, can perform transformation-tolerant object recognition. Front-end modeling incorporating species-specific optics and photoreceptor sampling showed that, when scaled for acuity, tree shrew retinal filtering preserves the similarity structure of natural image categories relevant for object recognition. Behaviorally, tree shrews reliably discriminated complex objects across variations in position, scale, and viewpoint, including when embedded within natural scenes, and generalized to novel exemplars. Their recognition behavior was best explained by visual features emphasizing differences in global shape and size between objects and by representations from intermediate and deep layers of hierarchical neural network models. These results demonstrate that visual processing supporting object-level generalization can arise within visual systems lacking high-acuity front-end optics and establish the tree shrew as a key model for understanding the computational and evolutionary origins of high-level vision.

animal behavior and cognition↗

Efflux Pump Activation Confers Mupirocin Resistance and Enhances Rhizosphere Fitness in Pseudomonas

Mupirocin (Mup) is a polyketide antibiotic for clinical MRSA treatment and agricultural biocontrol, acting by binding to IleRS to inhibit protein synthesis. Here, we demonstrate that Pseudomonas viciae 11K1 acquires resistance to mupirocin not through canonical mutations in ileS, the gene encoding the drug target, but via single nucleotide polymorphisms (SNPs) of EmhR, a transcriptional repressor. These SNPs attenuate EmhRs DNA-binding ability, resulting in derepression of the resistance-nodulation-division (RND) efflux pump EmhABC. This leads to a 7-fold (to 800 g/mL) increase in the mupirocin minimum inhibitory concentration (MIC), and confers cross-resistance to multiple other antibiotics. Critically, 11K1 strains harboring EmhR mutations exhibit enhanced competitive fitness in colonizing wheat rhizospheres against the mupirocin-producing Pseudomonas bijieensis 2P24. The conservation of this regulatory mechanism in Pseudomonas aeruginosa, mediated by the EmhR ortholog NalD, underscores its broader biological significance. Our findings establish a direct link between efflux pump regulation and ecological adaptation, highlighting a key mechanism contributing to environmental antimicrobial resistance with important implications for the clinical and agricultural use of mupirocin. IMPORTANCEMupirocin and its producing Pseudomonas strains are widely used in both clinical and agricultural contexts, making mupirocin resistance a significant concern for public health and food security. While canonical mupirocin resistance is primarily attributed to mutations in ileS, the gene encoding the drug target isoleucyl-tRNA synthetase (IleRS), our study identifies a novel resistance mechanism in Pseudomonas viciae strain 11K1 mediated by SNPs in the transcriptional repressor EmhR. These SNPs derepress the RND efflux system EmhABC, and reduce intracellular mupirocin levels. This mechanism not only enhances tolerance to mupirocin but also confers cross-resistance to multiple antimicrobial agents, raising the risk of multidrug-resistant strain spread. EmhR-mutant 11K1 strains exhibit enhanced rhizosphere competitiveness in the presence of mupirocin-producing Pseudomonas bijieensis strain 2P24, indicating an ecological fitness advantage that could promote resistant population expansion in agriculture environments. The same regulatory pathway is conserved in human pathogen Pseudomonas aeruginosa PAO1 via the functional ortholog NalD, suggesting that this mechanism may be widespread in Pseudomonas. These findings fill a critical gap in understanding non-target-based mupirocin resistance, clarify the ecological drivers of antimicrobial resistance (AMR), and offer practical insight for improving mupirocin application to limit the emergence and spread of resistant pathogens.

microbiology↗

The tilt illusion arises from an efficient reallocation of neural coding resources at the contextual boundary

The tilt illusion -- a bias in the perceived orientation of a center stimulus induced by an oriented surround -- illustrates how context shapes visual perception. While the tilt illusion has been the subject of quantitative study for over 85 years, we still lack a comprehensive account of the phenomenon that connects its neural and behavioral characteristics. Here, we demonstrate that the tilt illusion originates from a dynamic change in neural coding precision induced by the surround context. We simultaneously obtained psychophysical and fMRI responses from human subjects while they viewed gratings in the absence and presence of an oriented surround, and extracted sensory encoding precision from their behavioral and neural data. Both measures show that in the absence of a surround, encoding reflects the natural scene statistics of orientation. However, in the presence of an oriented surround, encoding precision is significantly increased for stimuli similar to the surround orientation. This local change in encoding is sufficient to accurately predict the behavioral characteristics of the tilt illusion using a Bayesian observer model. The effect of surround modulation increases along the ventral stream, and is localized to the portion of the visual cortex with receptive fields at the center-surround boundary. The pattern of change in coding accuracy reflects the surround-conditioned orientation statistics in natural scenes, but cannot be explained by local stimulus configuration. Our results suggest that the tilt illusion naturally emerges from a dynamic coding strategy that efficiently reallocates neural coding resources based on the current stimulus context.

neuroscience↗

Telomere-to-telomere sheep genome assembly reveals new variants associated with wool fineness trait

Ongoing efforts to improve sheep reference genome assemblies still leave many gaps and incomplete regions, resulting in a few common failures and errors in sheep genomic studies. Here, we report a complete, gap-free telomere-to-telomere (T2T) genome of a ram (T2T-sheep1.0) with a size of 2.85 Gb, including all autosomes and chromosomes X and Y. It adds 220.05 Mb of previously unresolved regions (PURs) and 754 new genes to the most updated reference assembly, ARS-UI_Ramb_v3.0, and contains four types of repeat units (SatI, SatII, SatIII, and CenY) in the centromeric regions. T2T-sheep1.0 exhibits a base accuracy of >99.999%, corrects several structural errors in previous reference assemblies, and improves structural variant (SV) detection in repetitive sequences. We identified 192,265 SVs, including 16,885 new SVs in the PURs, from the PacBio long-read sequences of 18 global representative sheep. With the whole-genome short-read sequences of 810 wild and domestic sheep representing 158 global populations and seven wild species, the use of T2T-sheep1.0 as the reference genome has improved population genetic analysis based on [~]133.31 million SNPs and 1,265,266 SVs, including 2,664,979 novel SNPs and 196,471 novel SVs. T2T-sheep1.0 improves selective tests by detecting several novel genes and variants, including those associated with domestication (e.g., ABCC4) and selection for the wool fineness trait (e.g., FOXQ1) in tandemly duplicated regions.

genomics↗

Efficient neural codes naturally emerge through gradient descent learning

Animal sensory systems are more sensitive to common features in the environment than uncommon features. For example, small deviations from the more frequently encountered horizontal orientations can be more easily detected than small deviations from the less frequent diagonal ones. Here we find that artificial neural networks trained to recognize objects also have patterns of sensitivity that match the statistics of features in images. To interpret these findings, we show mathematically that learning with gradient descent in deep neural networks preferentially creates representations that are more sensitive to common features, a hallmark of efficient coding. This result suggests that efficient coding naturally emerges from gradient-like learning on natural stimuli.

neuroscience↗

Prior expectations in visual speed perception predict encoding characteristics of neurons in area MT

Bayesian inference provides an elegant theoretical framework for understanding the characteristic biases and discrimination thresholds in visual speed perception. However, the framework is difficult to validate due to its flexibility and the fact that suitable constraints on the structure of the sensory uncertainty have been missing. Here, we demonstrate that a Bayesian observer model constrained by efficient coding not only well explains human visual speed perception but also provides an accurate quantitative account of the tuning characteristics of neurons known for rep-resenting visual speed. Specifically, we found that the population coding accuracy for visual speed in area MT ("neural prior") is precisely predicted by the power-law, slow-speed prior extracted from fitting the Bayesian model to psychophysical data ("behavioral prior") to the point that the two priors are indistinguishable in a cross-validation model comparison. Our results demonstrate a quantitative validation of the Bayesian observer model constrained by efficient coding at both the behavioral and neural levels. Significance StatementStatistical regularities of the environment play an important role in shaping both neural representations and perceptual behavior. Most previous works addressed these two aspects independently. Here we present a quantitative validation of a theoretical framework that makes joint predictions for neural coding and behavior, based on the assumption that neural representations of sensory information are efficient but also optimally used in generating a percept. Specifically, we demonstrate that the neural tuning characteristics for visual speed in brain area MT are precisely predicted by the statistical prior expectations extracted from psychophysical data. As such, our results provide a normative link between perceptual behavior and the neural representation of sensory information in the brain.

neuroscience↗

An Image Reconstruction Framework for Characterizing Early Vision

We developed an image-computable observer model of the initial visual encoding that operates on natural image input, based on the framework of Bayesian image reconstruction from the excitations of the retinal cone mosaic. Our model extends previous work on ideal observer analysis and evaluation of performance beyond psychophysical discrimination, takes into account the statistical regularities of the visual environment, and provides a unifying framework for answering a wide range of questions regarding the visual front end. Using the error in the reconstructions as a metric, we analyzed variations of the number of different photoreceptor types on human retina as an optimal design problem. In addition, the reconstructions allow both visualization and quantification of information loss due to physiological optics and cone mosaic sampling, and how these vary with eccentricity. Furthermore, in simulations of color deficiencies and interferometric experiments, we found that the reconstructed images provide a reasonable proxy for modeling subjects percepts. Lastly, we used the reconstruction-based observer for the analysis of psychophysical threshold, and found notable interactions between spatial frequency and chromatic direction in the resulting spatial contrast sensitivity function. Our method is widely applicable to experiments and applications in which the initial visual encoding plays an important role.

neuroscience↗

Aberrant Sensory Encoding in Patients with Autism

Perceptual anomalies in patients with Autism Spectrum Disorder (ASD) have been attributed to irregularities in the Bayesian interpretation (i.e., decoding) of sensory information. Here we show that how sensory information is encoded and adapts to changing stimulus statistics also characteristically differs between healthy and ASD groups. In a visual estimation task, we extracted the accuracy of sensory encoding directly from psychophysical data, bypassing the decoding stage by using information theoretic measures. Initially, sensory representations in both groups reflected the statistics of visual orientations in natural scenes, but encoding capacity was overall lower in the ASD group. Exposure to an artificial statistical distribution of visual orientations altered the sensory representations of the control group toward the novel experimental statistics, while also increasing their total encoding resources. Neither total encoding resources nor their allocation changed significantly in the ASD group. Most interestingly, across both groups the adaptive re-allocation of encoding resources was correlated with subjects initial encoding capacity. These findings suggest that neural encoding resources are limited in ASD, and this limitation may explain their reduced perceptual flexibility.

neuroscience↗