Rxivist logo

Rxivist.org combines preprints from bioRxiv and medRxiv with data from Twitter to help you find the papers being discussed in your field.
Currently indexing 128,741 papers from 551,614 authors.

Most downloaded biology preprints, all time

Results 1 through 20 out of 1718

in category animal behavior and cognition


1: A tutorial on Gaussian process regression: Modelling, exploring, and exploiting functions

Eric Schulz, Maarten Speekenbrink et al.

32,180 downloads (posted 19 Dec 2016)

This tutorial introduces the reader to Gaussian process regression as an expressive tool to model, actively explore and exploit unknown functions. Gaussian process regression is a powerful, non-parametric Bayesian approach towards regression problems that can be utilized in exploration and exploitation scenarios. This tutorial aims to provide an accessible introduction to these techniques. We will introduce Gaussian processes which generate distributions over functions used for Bayesian non-parametric regression, and demonstrate their use in applications and didactic examples including simple regression problems, a demonstration of kernel-encoded prior assumptions and compositions, a pure exploration scenario within an optimal design framework, and a bandit-like exploration-exploitation scenario where the goal is to recommend movies. Beyond that, we describe a situation modelling risk-averse exploration in which an additional constraint (not to sample below a certain threshold) needs to be accounted for. Lastly, we summarize recent psychological experiments utilizing Gaussian processes. Software and literature pointers are also provided.


2: Detection dogs as a help in the detection of COVID-19: Can the dog alert on COVID-19 positive persons by sniffing axillary sweat samples? Proof-of-concept study

Dominique Grandjean, Riad Sarkis et al.

17,629 downloads (posted 05 Jun 2020)

The aim of this study is to evaluate if the sweat produced by COVID-19 persons (SARS-CoV-2 PCR positive) has a different odour for trained detection dogs than the sweat produced by non COVID-19 persons. The study was conducted on 3 sites, following the same protocol procedures, and involved a total of 18 dogs. A total of 198 armpits sweat samples were obtained from different hospitals. For each involved dog, the acquisition of the specific odour of COVID-19 sweat samples required from one to four hours, with an amount o...


3: Highly Heritable and Functionally Relevant Breed Differences in Dog Behavior

Evan L MacLeant, Noah Snyder-Mackler et al.

10,547 downloads (posted 01 Jan 2019)

Variation across dog breeds presents a unique opportunity for investigating the evolution and biological basis of complex behavioral traits. We integrated behavioral data from more than 17,000 dogs from 101 breeds with breed-averaged genotypic data (N = 5,697 dogs) from over 100,000 loci in the dog genome. Across 14 traits, we found that breed differences in behavior are highly heritable, and that clustering of breeds based on behavior accurately recapitulates genetic relationships. We identify 131 single nucleotide pol...


4: Fast animal pose estimation using deep neural networks

Talmo Periera, D. E. Aldarondo et al.

8,463 downloads (posted 25 May 2018)

Recent work quantifying postural dynamics has attempted to define the repertoire of behaviors performed by an animal. However, a major drawback to these techniques has been their reliance on dimensionality reduction of images which destroys information about which parts of the body are used in each behavior. To address this issue, we introduce a deep learning-based method for pose estimation, LEAP (LEAP Estimates Animal Pose). LEAP automatically predicts the positions of animal body parts using a deep convolutional neur...


5: Live Mouse Tracker: real-time behavioral analysis of groups of mice

Fabrice de Chaumont, Elodie Ey et al.

6,950 downloads (posted 14 Jun 2018)

Preclinical studies of psychiatric disorders require the use of animal models to investigate the impact of environmental factors or genetic mutations on complex traits such as decision-making and social interactions. Here, we present a real-time method for behavior analysis of mice housed in groups that couples computer vision, machine learning and Triggered-RFID identification to track and monitor animals over several days in enriched environments. The system extracts a thorough list of individual and collective behavi...


6: The Eighty Five Percent Rule for Optimal Learning

Robert C. Wilson, Amitai Shenhav et al.

6,827 downloads (posted 27 Jan 2018)

Researchers and educators have long wrestled with the question of how best to teach their clients be they human, animal or machine. Here we focus on the role of a single variable, the difficulty of training, and examine its effect on the rate of learning. In many situations we find that there is a sweet spot in which training is neither too easy nor too hard, and where learning progresses most quickly. We derive conditions for this sweet spot for a broad class of learning algorithms in the context of binary classificati...


7: Robust manipulation of the behavior of Drosophila melanogaster by a fungal pathogen in the laboratory

Carolyn N. Elya, Tin Ching Lok et al.

6,548 downloads (posted 10 Dec 2017)

Many microbes induce striking behavioral changes in their animal hosts, but how they achieve this is poorly understood, especially at the molecular level. Mechanistic understanding has been largely constrained by the lack of a model system with advanced tools for molecular manipulation. We recently discovered a strain of the behavior-manipulating fungal pathogen Entomophthora muscae infecting wild Drosophila, and established methods to infect D. melanogaster in the lab. Lab-infected flies manifest the moribund behaviors...


8: Does training method matter?: Evidence for the negative impact of aversive-based methods on companion dog welfare

Ana Catarina Vieira de Castro, Danielle Fuchs et al.

5,753 downloads (posted 29 Oct 2019)

There is a growing number of dogs kept as companion animals, and the methods by which they are trained range broadly from those using mostly positive punishment and negative reinforcement (aversive-based methods) to those using primarily positive reinforcement (reward-based methods). Although the use of aversive-based methods has been strongly criticized for negatively affecting dog welfare, these claims do not find support in solid scientific evidence. Previous research on the subject lacks companion dog-focused resear...


9: Habits without Values

Kevin J. Miller, Amitai Shenhav et al.

5,384 downloads (posted 03 Aug 2016)

Habits form a crucial component of behavior. In recent years, key computational models have conceptualized habits as arising from model-free reinforcement learning (RL) mechanisms, which typically select between available actions based on the future value expected to result from each. Traditionally, however, habits have been understood as behaviors that can be triggered directly by a stimulus, without requiring the animal to evaluate expected outcomes. Here, we develop a computational model instantiating this traditiona...


10: Cleaner wrasse pass the mark test. What are the implications for consciousness and self-awareness testing in animals?

Masanori Kohda, Safiye Celik et al.

5,295 downloads (posted 21 Aug 2018)

The ability to perceive and recognise a reflected mirror image as self (mirror self-recognition, MSR) is considered a hallmark of cognition across species. Although MSR has been reported in mammals and birds, it is not known to occur in any other major taxon. A factor potentially limiting the ability to test for MSR is that the established assay for MSR, the mark test, shows an interpretation bias towards animals with the dexterity (or limbs) required to touch a mark. Here, we show that the cleaner wrasse fish, Labroide...


11: On the inference speed and video-compression robustness of DeepLabCut

Alexander Mathis, Richard Warren

5,243 downloads (posted 30 Oct 2018)

Pose estimation is crucial for many applications in neuroscience, biomechanics, genetics and beyond. We recently presented a highly efficient method for markerless pose estimation based on transfer learning with deep neural networks called DeepLabCut. Current experiments produce vast amounts of video data, which pose challenges for both storage and analysis. Here we improve the inference speed of DeepLabCut by up to tenfold and benchmark these updates on various CPUs and GPUs. In particular, depending on the frame size,...


12: Big Behavioral Data: Psychology, Ethology and the Foundations of Neuroscience

Alex Gomez-Marin, Joseph J. Paton et al.

4,593 downloads (posted 02 Jul 2014)

Behavior is a unifying organismal process where genes, neural function, anatomy and environment converge and interrelate. Here we review the current state and discuss the future impact of accelerating advances in technology for behavioral studies, focusing on rodents as an exemplar. We frame our perspective in three dimensions: degree of experimental constraint, dimensionality of data, and level of description. We argue that "big behavioral data" presents challenges proportionate to its promise and describe how these ch...


13: No compelling evidence that preferences for facial masculinity track changes in women's hormonal status

Benedict C Jones, Amanda C Hahn et al.

4,443 downloads (posted 11 May 2017)

Although widely cited as strong evidence that sexual selection has shaped human facial attractiveness judgments, evidence that preferences for masculine characteristics in men's faces are related to women's hormonal status is equivocal and controversial. Consequently, we conducted the largest ever longitudinal study of the hormonal correlates of women's preferences for facial masculinity (N=584). Analyses showed no compelling evidence that preferences for facial masculinity were related to changes in women's salivary st...


14: DeepPoseKit, a software toolkit for fast and robust animal pose estimation using deep learning

Jacob M. Graving, Daniel Chae et al.

4,187 downloads (posted 26 Apr 2019)

Quantitative behavioral measurements are important for answering questions across scientific disciplines—from neuroscience to ecology. State-of-the-art deep-learning methods offer major advances in data quality and detail by allowing researchers to automatically estimate locations of an animal’s body parts directly from images or videos. However, currently-available animal pose estimation methods have limitations in speed and robustness. Here we introduce a new easy-to-use software toolkit, DeepPoseKit , that addresses ...


15: Is it impossible to acquire absolute pitch in adulthood?

Yetta Kwailing Wong, Kelvin F. H. Lui et al.

4,035 downloads (posted 03 Jul 2018)

Absolute pitch (AP) refers to the rare ability to name the pitch of a tone without external reference. It is widely believed that acquiring AP in adulthood is impossible, since AP is only for the selected few with rare genetic makeup and early musical training. In three experiments, we trained adults to name pitches for 12 to 40 hours. Within the training period, 14% of the participants were able to name twelve pitches at 90% accuracy or above, a performance level comparable with typical AP possessors. At the group leve...


16: Awake Canine fMRI Predicts Dogs' Preference for Praise Versus Food

Peter F. Cook, Ashley Prichard et al.

3,847 downloads (posted 07 Jul 2016)

Dogs are hypersocial with humans, and their integration into human social ecology makes dogs a unique model for studying cross-species social bonding. However, the proximal neural mechanisms driving dog-human social interaction are unknown. We used fMRI in 15 awake dogs to probe the neural basis for their preferences for social interaction and food reward. In a first experiment, we used the ventral caudate as a measure of intrinsic reward value and compared activation to conditioned stimuli that predicted food, praise, ...


17: Latent space visualization, characterization, and generation of diverse vocal communication signals

Tim Sainburg, Marvin Thielk et al.

3,611 downloads (posted 11 Dec 2019)

Animals produce vocalizations that range in complexity from a single repeated call to hundreds of unique vocal elements patterned in sequences unfolding over hours. Characterizing complex vocalizations can require considerable effort and a deep intuition about each species’ vocal behavior. Even with a great deal of experience, human characterizations of animal communication can be affected by human perceptual biases. We present here a set of computational methods that center around projecting animal vocalizations into l...


18: Ethology as a physical science

Andre E. X. Brown, Benjamin L de Bivort

3,478 downloads (posted 17 Nov 2017)

Behaviour is the ultimate output of an animal's nervous system and choosing the right action at the right time can be critical for survival. The study of the organisation of behaviour in its natural context, ethology, has historically been a primarily qualitative science. A quantitative theory of behaviour would advance research in neuroscience as well as ecology and evolution. However, animal posture typically has many degrees of freedom and behavioural dynamics vary on timescales ranging from milliseconds to years, pr...


19: A theory of learning to infer

Ishita Dasgupta, Eric Schulz et al.

3,447 downloads (posted 20 May 2019)

Bayesian theories of cognition assume that people can integrate probabilities rationally. However, several empirical findings contradict this proposition: human probabilistic inferences are prone to systematic deviations from optimality. Puzzlingly, these deviations sometimes go in opposite directions. Whereas some studies suggest that people under-react to prior probabilities ( base rate neglect ), other studies find that people under-react to the likelihood of the data ( conservatism ). We argue that these deviations ...


20: Positive Sexual Imprinting For Human Eye Color

Lisa M DeBruine, Benedict C Jones et al.

3,336 downloads (posted 08 May 2017)

Human romantic partners tend to have similar physical traits, but the mechanisms causing this homogamy are controversial. One potential explanation is direct matching to own characteristics. Alternatively, studies showing similarity between parent and partner support positive sexual imprinting, where individuals are more likely to choose mates with the physical characteristics of their other-sex parent. This interpretation has been strongly criticized because the same pattern could also be caused by sex-linked heritable...