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4. Of Mice and Mates: Automated Classification and Modelling of Mouse Behaviour in Groups using a Single Model across Cages

Author

Camilleri, Michael P. J., Bains, Rasneer S., and Williams, Christopher K. I.

Subjects
Computer Science - Computer Vision and Pattern Recognition, Computer Science - Machine Learning, Statistics - Machine Learning
Abstract

Behavioural experiments often happen in specialised arenas, but this may confound the analysis. To address this issue, we provide tools to study mice in the home-cage environment, equipping biologists with the possibility to capture the temporal aspect of the individual's behaviour and model the interaction and interdependence between cage-mates with minimal human intervention. Our main contribution is the novel Group Behaviour Model (GBM) which summarises the joint behaviour of groups of mice across cages, using a permutation matrix to match the mouse identities in each cage to the model. In support of the above, we also (a) developed the Activity Labelling Module (ALM) to automatically classify mouse behaviour from video, and (b) released two datasets, ABODe for training behaviour classifiers and IMADGE for modelling behaviour., Comment: International Journal of Computer Vision (2024)

Published
2023
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5. Light Curves and Colors of the Ejecta from Dimorphos after the DART Impact

Author

Graykowski, Ariel, Lambert, Ryan A., Marchis, Franck, Cazeneuve, Dorian, Dalba, Paul A., Esposito, Thomas M., Peluso, Daniel O'Conner, Sgro, Lauren A., Blaclard, Guillaume, Borot, Antonin, Malvache, Arnaud, Marfisi, Laurent, Powell, Tyler M., Huet, Patrice, Limagne, Matthieu, Payet, Bruno, Clarke, Colin, Murabana, Susan, Owen, Daniel Chu, Wasilwa, Ronald, Fukui, Keiichi, Goto, Tateki, Guillet, Bruno, Huth, Patrick, Ishiyama, Satoshi, Kukita, Ryuichi, Mitchell, Mike, Primm, Michael, Randolph, Justus, Rivett, Darren A., Ryno, Matthew, Shimizu, Masao, Toullec, Jean-Pierre, Will, Stefan, Yue, Wai-Chun, Camilleri, Michael, Graykowski, Kathy, Janetzke, Ron, Janke, Des, Kardel, Scott, Loose, Margaret, Pickering, John W., Smith, Barton A., and Transom, Ian M.

Subjects
Astrophysics - Earth and Planetary Astrophysics
Abstract

On 26 September 2022 the Double Asteroid Redirection Test (DART) spacecraft impacted Dimorphos, a satellite of the asteroid 65803 Didymos. Because it is a binary system, it is possible to determine how much the orbit of the satellite changed, as part of a test of what is necessary to deflect an asteroid that might threaten Earth with an impact. In nominal cases, pre-impact predictions of the orbital period reduction ranged from ~8.8 - 17.2 minutes. Here we report optical observations of Dimorphos before, during and after the impact, from a network of citizen science telescopes across the world. We find a maximum brightening of 2.29 $\pm$ 0.14 mag upon impact. Didymos fades back to its pre-impact brightness over the course of 23.7 $\pm$ 0.7 days. We estimate lower limits on the mass contained in the ejecta, which was 0.3 - 0.5% Dimorphos' mass depending on the dust size. We also observe a reddening of the ejecta upon impact., Comment: Accepted by Nature

Published
2023
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7. Automated identification and behaviour classification for modelling social dynamics in group-housed mice

Author

Camilleri, Michael, Williams, Christopher, King, Ruth, and Sanguinetti, Guido

Subjects
Automated Identification, Behaviour Classification, Modelling Social Dynamics, Social Dynamics, Group-Housed Mice
Abstract

Mice are often used in biology as exploratory models of human conditions, due to their similar genetics and physiology. Unfortunately, research on behaviour has traditionally been limited to studying individuals in isolated environments and over short periods of time. This can miss critical time-effects, and, since mice are social creatures, bias results. This work addresses this gap in research by developing tools to analyse the individual behaviour of group-housed mice in the home-cage over several days and with minimal disruption. Using data provided by the Mary Lyon Centre at MRC Harwell we designed an end-to-end system that (a) tracks and identifies mice in a cage, (b) infers their behaviour, and subsequently (c) models the group dynamics as functions of individual activities. In support of the above, we also curated and made available a large dataset of mouse localisation and behaviour classifications (IMADGE), as well as two smaller annotated datasets for training/evaluating the identification (TIDe) and behaviour inference (ABODe) systems. This research constitutes the first of its kind in terms of the scale and challenges addressed. The data source (side-view single-channel video with clutter and no identification markers for mice) presents challenging conditions for analysis, but has the potential to give richer information while using industry standard housing. A Tracking and Identification module was developed to automatically detect, track and identify the (visually similar) mice in the cluttered home-cage using only single-channel IR video and coarse position from RFID readings. Existing detectors and trackers were combined with a novel Integer Linear Programming formulation to assign anonymous tracks to mouse identities. This utilised a probabilistic weight model of affinity between detections and RFID pickups. The next task necessitated the implementation of the Activity Labelling module that classifies the behaviour of each mouse, handling occlusion to avoid giving unreliable classifications when the mice cannot be observed. Two key aspects of this were (a) careful feature-selection, and (b) judicious balancing of the errors of the system in line with the repercussions for our setup. Given these sequences of individual behaviours, we analysed the interaction dynamics between mice in the same cage by collapsing the group behaviour into a sequence of interpretable latent regimes using both static and temporal (Markov) models. Using a permutation matrix, we were able to automatically assign mice to roles in the HMM, fit a global model to a group of cages and analyse abnormalities in data from a different demographic.

Published
2023
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13. Persistent Animal Identification Leveraging Non-Visual Markers

Author

Camilleri, Michael P. J., Zhang, Li, Bains, Rasneer S., Zisserman, Andrew, and Williams, Christopher K. I.

Subjects
Computer Science - Computer Vision and Pattern Recognition, Mathematics - Combinatorics
Abstract

Our objective is to locate and provide a unique identifier for each mouse in a cluttered home-cage environment through time, as a precursor to automated behaviour recognition for biological research. This is a very challenging problem due to (i) the lack of distinguishing visual features for each mouse, and (ii) the close confines of the scene with constant occlusion, making standard visual tracking approaches unusable. However, a coarse estimate of each mouse's location is available from a unique RFID implant, so there is the potential to optimally combine information from (weak) tracking with coarse information on identity. To achieve our objective, we make the following key contributions: (a) the formulation of the object identification problem as an assignment problem (solved using Integer Linear Programming), and (b) a novel probabilistic model of the affinity between tracklets and RFID data. The latter is a crucial part of the model, as it provides a principled probabilistic treatment of object detections given coarse localisation. Our approach achieves 77% accuracy on this animal identification problem, and is able to reject spurious detections when the animals are hidden.

Published
2021
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15. ACG Clinical Guideline: Gastroparesis.

Author

Abell, Thomas, Camilleri, Michael, Kuo, Braden, Nguyen, Linda, Vaughn, Vida, Petrey, Jessica, Greer, Katarina, and Yadlapati, Rena

Subjects
Adult, Gastric Emptying, Gastroenterology, Gastroparesis, Humans, Pylorus, Risk Factors
Abstract

Gastroparesis is characterized by symptoms suggesting retention of food in the stomach with objective evidence of delayed gastric emptying in the absence of mechanical obstruction in the gastric outflow. This condition is increasingly encountered in clinical practice. These guidelines summarize perspectives on the risk factors, diagnosis, and management of gastroparesis in adults (including dietary, pharmacological, device, and interventions directed at the pylorus), and they represent the official practice recommendations of the American College of Gastroenterology. The scientific evidence for these guidelines was assessed using the Grading of Recommendations, Assessment, Development, and Evaluation process. When the evidence was not appropriate for Grading of Recommendations, Assessment, Development, and Evaluation, we used expert consensus to develop key concept statements. These guidelines should be considered as preferred but are not the only approaches to these conditions.

Published
2022

18. Clinical and translational research studies in gastrointestinal motility and functional disorders

Author

Camilleri, Michael

Abstract

The body of my work has advanced knowledge and learning in the areas of gastrointestinal, colonic and anorectal physiology, pathophysiology, pharmacology, pharmacogenetics, diagnosis and management of motility and functional gastrointestinal disorders. The work has impacted the diagnosis and management of disorders such as gastroparesis, chronic constipation, irritable bowel syndrome, functional dyspepsia, and carcinoid diarrhea. These publications are selected from around 800 articles published (625 original articles, >175 invited reviews or editorials in journals) over more than 35 years. They have been selected to show the sustained and consistent contribution I have made to the translational and clinical science research in gastroenterology. These original contributions have usually been made jointly with students I have supervised, or fellows and collaborators I have worked with. This work has been published in international journals and has been cited extensively by others. In many instances, this work has achieved a long-term impact and has led to further developments by others and citations over a long time. According to Google Scholar, my published work has been cited over 65372 times, with 22400 in the last 5 years, and my current h-index is 133. In addition to articles pertaining to original research detailed under 9 different categories below, I have selected 20 articles cited >100 times (based on Thomson Web of Science) and these are single author reviews (as in the New England Journal of Medicine), national or international guidelines that have impacted the field significantly, or original research. All the selected papers are in English. As recommended in the instructions, I have identified 20 papers with some of the highest numbers of citations in the literature, and provided the Journal, Title of the article, full list of authors and number of times cited according to the Web of Science database. I have also added my role in the article, and this is verifiable by the name of the corresponding or senior author of each article, or by first authorship. This information appears in the table, and pdfs of the articles are attached in the same order.

Published
2022

26. Genome-wide analysis of 53,400 people with irritable bowel syndrome highlights shared genetic pathways with mood and anxiety disorders

Author

Eijsbouts, Chris, Zheng, Tenghao, Kennedy, Nicholas A, Bonfiglio, Ferdinando, Anderson, Carl A, Moutsianas, Loukas, Holliday, Joanne, Shi, Jingchunzi, Shringarpure, Suyash, Voda, Alexandru-Ioan, Farrugia, Gianrico, Franke, Andre, Hübenthal, Matthias, Abecasis, Gonçalo, Zawistowski, Matthew, Skogholt, Anne Heidi, Ness-Jensen, Eivind, Hveem, Kristian, Esko, Tõnu, Teder-Laving, Maris, Zhernakova, Alexandra, Camilleri, Michael, Boeckxstaens, Guy, Whorwell, Peter J, Spiller, Robin, McVean, Gil, D’Amato, Mauro, Jostins, Luke, and Parkes, Miles

Subjects
Human Genome, Behavioral and Social Science, Mental Health, Neurosciences, Chronic Pain, Genetics, Pain Research, Digestive Diseases, Brain Disorders, 2.1 Biological and endogenous factors, Aetiology, Oral and gastrointestinal, Mental health, Neurological, Aged, Anxiety Disorders, CD56 Antigen, Cell Adhesion Molecules, Cytoskeletal Proteins, Female, Genetic Predisposition to Disease, Genome-Wide Association Study, Guanine Nucleotide Exchange Factors, Homeodomain Proteins, Humans, Irritable Bowel Syndrome, Male, Middle Aged, Molecular Chaperones, Mood Disorders, Polymorphism, Single Nucleotide, United Kingdom, 23andMe Research Team, Bellygenes Initiative, Biological Sciences, Medical and Health Sciences, Developmental Biology
Abstract

Irritable bowel syndrome (IBS) results from disordered brain-gut interactions. Identifying susceptibility genes could highlight the underlying pathophysiological mechanisms. We designed a digestive health questionnaire for UK Biobank and combined identified cases with IBS with independent cohorts. We conducted a genome-wide association study with 53,400 cases and 433,201 controls and replicated significant associations in a 23andMe panel (205,252 cases and 1,384,055 controls). Our study identified and confirmed six genetic susceptibility loci for IBS. Implicated genes included NCAM1, CADM2, PHF2/FAM120A, DOCK9, CKAP2/TPTE2P3 and BAG6. The first four are associated with mood and anxiety disorders, expressed in the nervous system, or both. Mirroring this, we also found strong genome-wide correlation between the risk of IBS and anxiety, neuroticism and depression (rg > 0.5). Additional analyses suggested this arises due to shared pathogenic pathways rather than, for example, anxiety causing abdominal symptoms. Implicated mechanisms require further exploration to help understand the altered brain-gut interactions underlying IBS.

Published
2021

37. VJA\'G\'G -- A Thick-Client Smart-Phone Journey Detection Algorithm

Author

Camilleri, Michael P. J., Muscat, Adrian, Buttigieg, Victor, and Attard, Maria

Subjects
Computer Science - Information Retrieval, Computer Science - Computers and Society
Abstract

In this paper we describe $Vja\dot{g}\dot{g}$, a battery-aware journey detection algorithm that executes on the mobile device. The algorithm can be embedded in the client app of the transport service provider or in a general purpose mobility data collector. The thick client setup allows the customer/participant to select which journeys are transferred to the server, keeping customers in control of their personal data and encouraging user uptake. The algorithm is tested in the field and optimised for both accuracy in registering complete journeys and battery power consumption. Typically the algorithm can run for a full day without the need of recharging and more than 88% of journeys are correctly detected from origin to destination, whilst 12% would be missing part of the journey.

Published
2019

38. The Extended Dawid-Skene Model: Fusing Information from Multiple Data Schemas

Author

Camilleri, Michael P. J. and Williams, Christopher K. I.

Subjects
Statistics - Machine Learning, Computer Science - Human-Computer Interaction, Computer Science - Machine Learning
Abstract

While label fusion from multiple noisy annotations is a well understood concept in data wrangling (tackled for example by the Dawid-Skene (DS) model), we consider the extended problem of carrying out learning when the labels themselves are not consistently annotated with the same schema. We show that even if annotators use disparate, albeit related, label-sets, we can still draw inferences for the underlying full label-set. We propose the Inter-Schema AdapteR (ISAR) to translate the fully-specified label-set to the one used by each annotator, enabling learning under such heterogeneous schemas, without the need to re-annotate the data. We apply our method to a mouse behavioural dataset, achieving significant gains (compared with DS) in out-of-sample log-likelihood (-3.40 to -2.39) and F1-score (0.785 to 0.864)., Comment: Updated with Author-Preprint version following Publication in P. Cellier and K. Driessens (Eds.): ECML PKDD 2019 Workshops, CCIS 1167, pp. 121 - 136, 2020

Published
2019
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41. Phenotype tailored lifestyle intervention on weight loss and cardiometabolic risk factors in adults with obesity: a single-centre, non-randomised, proof-of-concept study

Author

Cifuentes, Lizeth, Ghusn, Wissam, Feris, Fauzi, Campos, Alejandro, Sacoto, Daniel, De la Rosa, Alan, McRae, Alison, Rieck, Thom, Mansfield, Sara, Ewoldt, Jason, Friend, Jamie, Grothe, Karen, Lennon, Ryan J., Hurtado, Maria D., Clark, Matthew M., Camilleri, Michael, Hensrud, Donald D., and Acosta, Andres

Published
2023
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44. Contributors

Author

Accorsi–Mendonça, Daniela, primary, Adams, David J., additional, Allen, Andrew M., additional, Alvarenga, Marlies, additional, Ardell, Jeffrey L., additional, Arnold, Amy C., additional, Ashton, Jesse L., additional, Badrov, Mark B., additional, Ballantyne, Brennan A., additional, Bardsley, Emma N., additional, Barez-Lopez, Soledad, additional, Barman, Susan M., additional, Barrett, Carolyn J., additional, Bauer, Deborah, additional, Bell, Christopher, additional, Ben-Tal, Alona, additional, Benarroch, Eduardo E., additional, Biaggioni, Italo, additional, Brandl, Katharina, additional, Brooks, Virginia L., additional, Brown, Amy E., additional, Browning, Kirsteen N., additional, Bryarly, Meredith, additional, Camargo, Livia L., additional, Camilleri, Michael, additional, Campbell, Preston J., additional, Caron, Marc G., additional, Carter, Jason R., additional, Chapleau, Mark W., additional, Charkoudian, Nisha, additional, Chelimsky, Gisela, additional, Chelimsky, Thomas C., additional, Chompoopong, Pitcha, additional, Claydon, Victoria E., additional, Clément, Gilles, additional, Convertino, Victor A., additional, Coon, Elizabeth A., additional, Cortelli, Pietro, additional, Davis, Stephen N., additional, Diedrich, André, additional, DiPette, Donald J., additional, Diz, Debra I., additional, Drake, Marcus J., additional, Eisenhofer, Graeme, additional, Elefteriou, Florent, additional, Elijovich, Fernando, additional, Elmenhorst, Eva-Maria, additional, English, Brett A., additional, Esler, Murray, additional, Esler, Rosemary, additional, Fadel, Paul J., additional, Fahrenholz, John M., additional, Fanciulli, Alessandra, additional, Fang, John Y., additional, Fealey, Robert D., additional, Ferreira, Nathanne S., additional, Filogonio, Renato, additional, Fink, Gregory D., additional, Fisher, James P., additional, Floras, John S., additional, Fountain, Samuel J., additional, Fu, Qi, additional, Fudim, Marat, additional, Furlan, Raffaello, additional, Gamboa, Alfredo, additional, Garland, Emily M., additional, Gibbons, Christopher H., additional, Giritharan, Andrew, additional, Goldstein, David S., additional, Golombék, Diego A., additional, Gomez-Sanchez, Elise P., additional, Gomez-Sanchez, Celso E., additional, Graham, Robert M., additional, Grassi, Guido, additional, Greenlund, Ian M., additional, Grubb, Blair P., additional, Guekht, Alla, additional, Guild, Sarah-Jane, additional, Guo, Ling, additional, Gurevich, Vsevolod V., additional, Habermann, Ralf, additional, Hadaya, Joseph, additional, Hahn, Maureen K., additional, Hanna, Peter, additional, Henderson, Luke A., additional, Herring, Neil, additional, Hilz, Max J., additional, Hunter, Peter, additional, Hyland, Keith, additional, Hyland, Lauren A., additional, Jackson, Edwin Kerry, additional, Jacob, Giris, additional, Jänig, Wilfrid, additional, Japundžić-Žigon, Nina, additional, Jones, Carrie K., additional, Joos, Karen M., additional, Jordan, Jens, additional, Joyce, William, additional, Kaidonis, Xenia, additional, Kaufmann, Horacio, additional, Kaye, David, additional, Khan Minhas, Abdul Mannan, additional, Kim, Joyce S., additional, Kitta, Takeya, additional, Kline, David D., additional, Konecny, Thomas, additional, Koons, Natalie J., additional, Kumar, Ambrish, additional, Laffer, Cheryl L., additional, Lagrange, Andre H., additional, Laiken, Nora, additional, Lambert, Gavin, additional, Lambert, Elisabeth, additional, Lamotte, Guillaume, additional, Lenders, Jacques W.M., additional, Levine, Benjamin D., additional, Leys, Fabian, additional, Limper, Ulrich, additional, Lin, Mabelle, additional, Listik, Eduardo, additional, Longmuir, Reid, additional, Low, David A., additional, Low, Phillip A., additional, Luther, James M., additional, Macefield, Vaughan G., additional, Machado, Benedito H., additional, Madel, Maria-Bernadette, additional, Martelli, Davide, additional, Mathias, Christopher J., additional, Mauermann, Michelle L., additional, McAllen, Robin M., additional, McBryde, Fiona D., additional, McKeon, Andrew, additional, McKinley, Michael J., additional, Menuet, Clément, additional, Milam, Douglas F., additional, Mohl, Marion C., additional, Montgomery, Johanna M., additional, Moraes, Davi J.A., additional, Morrison, Shaun F., additional, Murphy, David, additional, Nichols, Charles D., additional, Niewiński, Piotr, additional, Norcliffe-Kaufmann, Lucy, additional, Okamoto, Luis E., additional, Osanlouy, Mahyar, additional, Osborn, John W., additional, Oubaid, Viktor, additional, Palma, Jose-Alberto, additional, Pamporaki, Christina, additional, Parsons, Brian A., additional, Paterson, David J., additional, Paton, Julian F.R., additional, Peltier, Amanda C., additional, Pensato, Umberto, additional, Peterson, Sean M., additional, Phibbs, Fenna T., additional, Pierangeli, Giulia, additional, Potts, Jay D., additional, Rabinstein, Alejandro A., additional, Raizada, Mohan K., additional, Raj, Satish R., additional, Rand, Casey M., additional, Reichmann, Heinz, additional, Robertson, Calum, additional, Robertson, Rose Marie, additional, Robinson, Michael B., additional, Ruzieh, Mohammed, additional, Sandroni, Paola, additional, Sato, Takayuki, additional, Schiffrin, Ernesto L., additional, Schlaich, Markus, additional, Schondorf, Ronald, additional, Schultz, Harold D., additional, Scott, Michael M., additional, Seravalle, Gino, additional, Shannon, John R., additional, Sheikh, Abu Baker, additional, Shibao, Cyndya A., additional, Shivkumar, Kalyanam, additional, Shouman, Kamal, additional, Siepmann, Timo, additional, Singer, Wolfgang, additional, Soltani, Elias, additional, Somers, Virend, additional, Sridharan, Aadhavi, additional, Stefanova, Nadia, additional, Stewart, Julian, additional, Stiles, Lauren E., additional, Sunagawa, Kenji, additional, Tank, Jens, additional, Thijs, Roland D., additional, Tomek, Jakub, additional, Touyz, Rhian M., additional, Tracy, Jennifer A., additional, Travagli, R. Alberto, additional, Undem, Bradley J., additional, Urs, Nikhil, additional, Vernino, Steven, additional, Vianna, Lauro C., additional, Vigo, Daniel E., additional, Vizzard, Margaret A., additional, Wahba, Amr, additional, Waheed, Waqar, additional, Wang, Han-Jun, additional, Wang, Tobias, additional, Wang, Qin, additional, Wang, Ruihao, additional, Weese-Mayer, Debra E., additional, Wenning, Gregor K., additional, Wieling, Wouter, additional, Williams, Kevin W., additional, Winzer-Serhan, Ursula H., additional, Wood, Scott, additional, Yap, Kai Lee, additional, Yoshimura, Naoki, additional, Zavalin, Kirill A., additional, Zhuravlev, Dmitry, additional, Zoccal, Daniel B., additional, and Zubcevic, Jasenka, additional

Published
2023
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