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Publication Open Access High-throughput automated phenotyping of two genetic mouse models of huntington's disease(Public Library of Science, 2013) Oakeshott, Stephen; Shamy, Jul Lea T; El-Khodor, Bassem Fouad; Filippov, Igor V.; Mushlin, Richard A.; Port, Russell G.; Connor, David; Paintdakhi, Ahmad; Menalled, Liliana B.; Ramboz, Sylvie; Howland, David S.; Kwak, Seung; Brunner, Dani; Department of Psychology; Balcı, Fuat; Faculty Member; Department of Psychology; College of Social Sciences and Humanities; 51269Phenotyping with traditional behavioral assays constitutes a major bottleneck in the primary screening, characterization, and validation of genetic mouse modelsof disease, leading to downstream delays in drug discovery efforts. We present a novel and comprehensive one-stop approach to phenotyping, the PhenoCube™. This system simultaneously captures the cognitive performance, motor activity, and circadian patterns of group-housed mice by use of home-cage operant conditioning modules (IntelliCage) and custom-built computer vision software. We evaluated two different mouse models of Huntington's Disease (HD), the R6/2 and the BACHD in the PhenoCube™ system. Our results demonstrated that this system can efficiently capture and track alterations in both cognitive performance and locomotor activity patterns associated with these disease models. This work extends our prior demonstration that PhenoCube™ can characterize circadian dysfunction in BACHD mice and shows that this system, with the experimental protocols used, is a sensitive and efficient tool for a first pass high-throughput screening of mouse disease models in general and mouse models of neurodegeneration in particularPublication Open Access Craft: a benchmark for causal reasoning about forces and in teractions(Association for Computational Linguistics (ACL), 2022) Ateş, Tayfun; Ateşoğlu, M. Şamil; Yiğit, Çağatay; Department of Computer Engineering; Department of Psychology; Erdem, Aykut; Göksun, Tilbe; Yüret, Deniz; Kesen, İlker; Kobaş, Mert; Faculty Member; Faculty Member; Faculty Member; Master Student; Department of Computer Engineering; Department of Psychology; Koç Üniversitesi İş Bankası Yapay Zeka Uygulama ve Araştırma Merkezi (KUIS AI)/ Koç University İş Bank Artificial Intelligence Center (KUIS AI); Graduate School of Sciences and Engineering; College of Engineering; College of Social Sciences and Humanities; 20331; 47278; 179996; N/A; N/A; N/AHumans are able to perceive, understand and reason about causal events. Developing models with similar physical and causal understanding capabilities is a long-standing goal of artificial intelligence. As a step towards this direction, we introduce CRAFT1, a new video question answering dataset that requires causal reasoning about physical forces and object interactions. It contains 58K video and question pairs that are generated from 10K videos from 20 different virtual environments, containing various objects in motion that interact with each other and the scene. Two question categories in CRAFT include previously studied descriptive and counterfactual questions. Additionally, inspired by the Force Dynamics Theory in cognitive linguistics, we introduce a new causal question category that involves understanding the causal interactions between objects through notions like cause, enable, and prevent. Our results show that even though the questions in CRAFT are easy for humans, the tested baseline models, including existing state-of-the-art methods, do not yet deal with the challenges posed in our benchmark.Publication Open Access Virtual dance mirror: a functional approach to avatar representation through movement in immersive VR(Association for Computing Machinery (ACM), 2022) Öztürk, Aslı; Topal, Onur Sümer; Department of Media and Visual Arts; Department of Psychology; N/A; Yantaç, Asım Evren; Eskenazi, Terry; Akbaş, Saliha; Şemsioğlu, Sinem; Kuşçu, Kemal; Faculty Member; Department of Media and Visual Arts; Department of Psychology; College of Social Sciences and Humanities; Graduate School of Social Sciences and Humanities; School of Medicine; 52621; 258780; N/A; N/A; N/AImmersive Virtual Reality (VR) technologies offer new possibilities for studying embodied interaction with different sets of constraints and affordances for action-taking while using one's physical body. In this study, we designed and prototyped a VR dance experience, Virtual Dance Mirror, where a dancer's bodily movements are reflected on a 3D avatar model using a motion-capture suit. We investigated the novel possibilities for avatar design based on the expression of movements available for dancers in VR environment. After a preliminary briefing session, we conducted a user-study with five dancers with semi-structured interviews. Our findings support HCI literature on virtual body design to facilitate collaboration and non-verbal communication between VR users.Publication Open Access Editorial to the special issue on temporal illusions(Brill, 2020) Vatakis, Argiro; Department of Psychology; Balcı, Fuat; Faculty Member; Department of Psychology; College of Social Sciences and Humanities; 51269Publication Open Access On measuring social biases in prompt-based multi-task learning(Association for Computational Linguistics (ACL), 2022) Akyürek; A.F.; Paik, S.; Koçyiğit, M.Y.; Akbıyık, S.; Wijaya, D.; Department of Psychology; Runyun, Şerife Leman; PhD Student; Department of Psychology; Graduate School of Social Sciences and HumanitiesLarge language models trained on a mixture of NLP tasks that are converted into a textto- text format using prompts, can generalize into novel forms of language and handle novel tasks. A large body of work within prompt engineering attempts to understand the effects of input forms and prompts in achieving superior performance. We consider an alternative measure and inquire whether the way in which an input is encoded affects social biases promoted in outputs. In this paper, we study T0, a large-scale multi-task text-to-text language model trained using prompt-based learning. We consider two different forms of semantically equivalent inputs: question-answer format and premise-hypothesis format. We use an existing bias benchmark for the former BBQ (Parrish et al., 2021) and create the first bias benchmark in natural language inference BBNLI with hand-written hypotheses while also converting each benchmark into the other form. The results on two benchmarks suggest that given two different formulations of essentially the same input, T0 conspicuously acts more biased in question answering form, which is seen during training, compared to premisehypothesis form which is unlike its training examples.Publication Open Access The confidence database(Nature Publishing Group (NPG), 2020) Rahnev, Dobromir; Desender, Kobe; Lee, Alan L. F.; Adler, William T.; Aguilar-Lleyda, David; Akdoğan, Başak; Arbuzova, Polina; Atlas, Lauren Y.; Bang, Ji Won; Bègue, Indrit; Birney, Damian P; Brady, Timothy F.; Calder-Travis, Joshua; Chetverikov, Andrey; Clark, Torin K.; Davranche, Karen; Denison, Rachel N.; Dildine, Troy C.; Double, Kit S.; Faivre, Nathan; Fallow, Kaitlyn; Filevich, Elisa; Gajdos, Thibault; Gallagher, Regan M.; de Gardelle, Vincent; Gherman, Sabina; Haddara, Nadia; Hainguerlot, Marine; Hsu, Tzu-Yu; Hu, Xiao; Iturrate, Iñaki; Jaquiery, Matt; Kantner, Justin; Koculak, Marcin; Konishi, Mahiko; Koß, Christina; Kwok, Sze Chai; Lebreton, Maël; Lempert, Karolina M.; Ming Lo, Chien; Luo, Liang; Maniscalco, Brian; Martin, Antonio; Massoni, Sébastien; Matthews, Julian; Mazancieux, Audrey; Merfeld, Daniel M.; O’Hora, Denis; Palser, Eleanor R.; Paulewicz, Borysław; Pereira, Michael; Peters, Caroline; Philiastides, Marios G.; Pfuhl, Gerit; Prieto, Fernanda; Rausch, Manuel; Recht, Samuel, Reyes, Gabriel; Rouault, Marion; Sackur, Jérôme; Sadeghi, Saeedeh; Samaha, Jason; Seow, Tricia X. F.; Shekhar, Medha, Sherman, Maxine T.; Siedlecka, Marta; Skóra, Zuzanna; Song, Chen; Soto, David; Sun, Sai; van Boxtel, Jeroen J. A.; Wang, Shuo; Weidemann, Christoph T.; Weindel, Gabriel; Wierzchoń, Michał; Xu, Xinming; Ye, Qun; Yeon, Jiwon; Zou, Futing; Zylberberg, Ariel; Department of Psychology; Balcı, Fuat; Duyan, Yalçın Akın; Faculty Member; PhD Student; Department of Psychology; College of Social Sciences and Humanities; 51269; N/A; N/AUnderstanding how people rate their confidence is critical for the characterization of a wide range of perceptual, memory, motor and cognitive processes. To enable the continued exploration of these processes, we created a large database of confidence studies spanning a broad set of paradigms, participant populations and fields of study. The data from each study are structured in a common, easy-to-use format that can be easily imported and analysed using multiple software packages. Each dataset is accompanied by an explanation regarding the nature of the collected data. At the time of publication, the Confidence Database (which is available at ) contained 145 datasets with data from more than 8,700 participants and almost 4 million trials. The database will remain open for new submissions indefinitely and is expected to continue to grow. Here we show the usefulness of this large collection of datasets in four different analyses that provide precise estimations of several foundational confidence-related effects.Publication Open Access Effectiveness of Self-Help Plus in preventing mental disorders in refugees and asylum seekers in Western Europe: a multinational randomized controlled trial(Karger Publishers, 2021) Purgato, Marianna; Carswell, Kenneth; Tedeschi, Federico; Anttila, Minna; Au, Teresa; Bajbouj, Malek; Baumgartner, Josef; Biondi, Massimo; Churchill, Rachel; Cuijpers, Pim; Koesters, Markus; Gastaldon, Chiara; Lantta, Tella; Nose, Michela; Ostuzzi, Giovanni; Papola, Davide; Popa, Mariana; Roselli, Valentina; Sijbrandij, Marit; Tarsitani, Lorenzo; Turrini, Giulia; Valimaki, Maritta; Walker, Lauren; Wancata, Johannes; Zanini, Elisa; White, Ross; van Ommeren, Mark; Barbui, Corrado; Department of Psychology; Acartürk, Ceren; İlkkurşun, Zeynep; Faculty Member; Master Student; Department of Psychology; College of Social Sciences and Humanities; Graduate School of Social Sciences and Humanities; 39271; N/AIntroduction: Self-Help Plus (SH+) is a group-based psychological intervention developed by the World Health Organization for managing stress. Objective: to assess the effectiveness of SH+ in preventing mental disorders in refugees and asylum seekers in Western Europe. Methods: we conducted a randomized controlled trial in 5 European countries. Refugees and asylum seekers with psychological distress (General Health Questionnaire score >= 3), but without a Diagnostic and Statistical Manual of Mental Disorders, 5th edition (DSM-5) or ICD/10 diagnosis of mental disorder, as assessed with the Mini International Neuropsychiatric Interview (MINI), were randomized to SH+ or enhanced treatment as usual (ETAU). The primary outcome was the frequency of mental disorders with the MINI at 6 months. Secondary outcomes included the frequency of mental disorders at postintervention, self-identified problems, psychological symptoms, and other outcomes. Results: four hundred fifty-nine individuals were randomly assigned to SH+ or ETAU. For the primary outcome, we found no difference in the frequency of mental disorders at 6 months (Cramer V = 0.007, p = 0.90, RR = 0.96; 95% CI 0.52-1.78), while the difference significantly favored SH+ at after the intervention (secondary outcome, measured within 2 weeks from the last session; Cramer V = 0.13, p = 0.01, RR = 0.50; 95% CI 0.29-0.87). Conclusions: this is the first randomized indicated prevention study with the aim of preventing the onset of mental disorders in asylum seekers and refugees in Western Europe. As a prevention effect of SH+ was not observed at 6 months, but rather after the intervention only, modalities to maintain its beneficial effect in the long term need to be identified.Publication Open Access Optimal time discrimination(Sage, 2015) Department of Psychology; Çoşkun, Filiz; Sayalı, Zeynep Ceyda; Gürbüz, Emine; Balcı, Fuat; Undergraduate Student; Faculty Member; Department of Psychology; College of Social Sciences and Humanities; N/A; N/A; N/A; 51269In the temporal bisection task, participants categorize experienced stimulus durations as short or long based on their similarity to previously acquired reference durations. Reward maximization in this task requires integrating endogenous timing uncertainty as well as exogenous probabilities of the reference durations into temporal judgements. We tested human participants on the temporal bisection task with different short and long reference duration probabilities (exogenous probability) in two separate test sessions. Incorrect categorizations were not penalized in Experiment 1 but were penalized in Experiment 2, leading to different levels of stringency in the reward functions that participants tried to maximize. We evaluated the judgements within the framework of optimality. Our participants adapted their choice behaviour in a nearly optimal fashion and earned nearly the maximum possible expected gain they could attain given their level of endogenous timing uncertainty and exogenous probabilities in both experiments. These results point to the optimality of human temporal risk assessment in the temporal bisection task. The long categorization response times (RTs) were overall faster than short categorization RTs, and short but not long categorization RTs were modulated by reference duration probability manipulations. These observations suggested an asymmetry between short and long categorizations in the temporal bisection task.Publication Open Access Automated, quantitative cognitive/behavioral screening of mice: for genetics, pharmacology, animal cognition and undergraduate instruction(Journal of Visualized Experiments (JoVE), 2014) Gallistel, C. R.; Freestone, David; Kheifets, Aaron; King, Adam; Department of Psychology; Balcı, Fuat; Faculty Member; Department of Psychology; College of Social Sciences and Humanities; 51269We describe a high-throughput, high-volume, fully automated, live-in 24/7 behavioral testing system for assessing the effects of genetic and pharmacological manipulations on basic mechanisms of cognition and learning in mice. A standard polypropylene mouse housing tub is connected through an acrylic tube to a standard commercial mouse test box. The test box has 3 hoppers, 2 of which are connected to pellet feeders. All are internally illuminable with an LED and monitored for head entries by infrared (IR) beams. Mice live in the environment, which eliminates handling during screening. They obtain their food during two or more daily feeding periods by performing in operant (instrumental) and Pavlovian (classical) protocols, for which we have written protocol-control software and quasi-real-time data analysis and graphing software. The data analysis and graphing routines are written in a MATLAB-based language created to simplify greatly the analysis of large time-stamped behavioral and physiological event records and to preserve a full data trail from raw data through all intermediate analyses to the published graphs and statistics within a single data structure. The data-analysis code harvests the data several times a day and subjects it to statistical and graphical analyses, which are automatically stored in the "cloud" and on in-lab computers. Thus, the progress of individual mice is visualized and quantified daily. The data-analysis code talks to the protocol-control code, permitting the automated advance from protocol to protocol of individual subjects. The behavioral protocols implemented are matching, autoshaping, timed hopper-switching, risk assessment in timed hopper-switching, impulsivity measurement, and the circadian anticipation of food availability. Open-source protocol-control and data-analysis code makes the addition of new protocols simple. Eight test environments fit in a 48 in x 24 in x 78 in cabinet; two such cabinets (16 environments) may be controlled by one computer.Publication Open Access Trajectories of psychosocial symptoms and wellbeing in asylum seekers and refugees exposed to traumatic events and resettled in Western Europe, Turkey, and Uganda(Taylor _ Francis, 2022) Purgato, Marianna; Tedeschi, Federico; Turrini, Giulia; Anttila, Minna; Augustinavicious, Jura; Baumgartner, Josef; Bryant, Richard; Churchill, Rachel; Karyotaki, Eirini; Klein, Thomas; Koesters, Markus; Lantta, Tella; Leku, Marx R.; Nose, Michela; Ostuzzi, Giovanni; Popa, Mariana; Prina, Eleonora; Sijbrandij, Marit; Uygun, Ersin; Valimaki, Maritta; Walker, Lauren; Wancata, Johannes; White, Ross G.; Cuijpers, Pim; Tol, Wietse; Barbui, Corrado; Department of Psychology; Acartürk, Ceren; İlkkurşun, Zeynep; Faculty Member; Master Student; Department of Psychology; College of Social Sciences and Humanities; Graduate School of Social Sciences and Humanities; 39271; N/ABackground: longitudinal studies examining mental health trajectories in refugees and asylum seekers are scarce. Objectives: to investigate trajectories of psychological symptoms and wellbeing in refugees and asylum seekers, and identify factors associated with these trajectories. Method: 912 asylum seekers and refugees from the control arm of three trials in Europe (n = 229), Turkey (n = 320), and Uganda (n = 363) were included. We described trajectories of psychological symptoms and wellbeing, and used trauma exposure, age, marital status, education, and individual trial as predictors. Then, we assessed the bidirectional interactions between wellbeing and psychological symptoms, and the effect of each predictor on each outcome controlling for baseline values. Results: symptom improvement was identified in all trials, and for wellbeing in 64.7% of participants in Europe and Turkey, versus 31.5% in Uganda. In Europe and Turkey domestic violence predicted increased symptoms at post-intervention (ss = 1.36, 95% CI 0.17-2.56), whilst murder of family members at 6-month follow-up (ss = 1.23, 95% CI 0.27-2.19). Lower wellbeing was predicted by murder of family member (ss = -1.69, 95% CI -3.06 to -0.32), having been kidnapped (ss = -1.67, 95% CI -3.19 to -0.15), close to death (ss = -1.38, 95% CI -2.70 to -0.06), and being in the host country >= 2 years (ss = -1.60, 95% CI -3.05 to -0.14). In Uganda at post-intervention, having been kidnapped predicted increased symptoms (ss = 2.11, 95% CI 0.58-3.65), and lack of shelter (ss = -2.51, 95% CI -4.44 to -0.58) and domestic violence predicted lower wellbeing (ss = -1.36, 95% CI -2.67 to -0.05). Conclusion: many participants adapt to adversity, but contextual factors play a critical role in determining mental health trajectories. / Antecedentes: estudios longitudinales que examinan las trayectorias de la salud mental en losrefugiados y solicitantes de asilo son escasos. Objetivos: investigar las trayectorias de los síntomas psicológicos y el bienestar en refugiadosy solicitantes de asilo, e identificar factores asociados a estas trayectorias.Métodos:Se incluyeron 912 solicitantes de asilos y refugiados del brazo control de tresensayos clínicos en Europa (n= 229), Turquía (n= 320) y Uganda (n= 363). Describimos las trayectorias psicológicas de los síntomas y el bienestar, y utilizamos la exposición traumática, laedad, el estado marital, la educación y el juicio individual como predictores. Después,evaluamos las interacciones bidireccionales entre el bienestar y los síntomas psicológicos, yel efecto de cada uno de los predictores en cada resultado controlando por los valores iniciales.Resultados: se identificó una mejoría en los síntomas en todos los ensayos, y del bienestar en el64.7% de los participantes en Europa y Turquía, versus el 31.5% en Uganda. En Europa y en Turquía,la violencia doméstica predijo el incremento de síntomas de después de la intervención (ß= 1.36,95% CI 0.17 a 2.56), mientras que el homicidio de algún miembro familiar a los 6 meses deseguimiento (ß= 1.23, 95% CI 0.27 a 2.19). Un menor bienestar fue predicho por el homicidio dealgún miembro de la familia (ß=?1.69, 95% CI?3.06 a?0.32), haber sido secuestrado (ß=?1.67, 95% CI?3.19 a?0.15), haber estado próximo a la muerte (ß=?1.38, 95% CI?2.70 a?0.06), y estar en el país de acogida?2años(ß=?1.60, 95% CI?3.05 a?0.14). En Uganda,después de la intervención, haber sido secuestrado predijo un aumento de los síntomas(ß=2.11, 95% CI 0.58 a 3.65), y la falta de refugio (ß=?2.51, 95% CI?4.44 a?0.58) y laviolencia doméstica predijo un menor bienestar (ß=?1.36, 95% CI?2.67 a?0.05).Conclusión: muchos participantes se adaptan a la adversidad, pero los factores contextualesjuegan un papel crítico en determinar las trayectorias de la salud mental.