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Principles of Gestalt Psychology

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... The development of artificial intelligence now urgently requires computational models for visual perception 1 . The Gestalt theory, formulated by psychologists Wolfgang Köhler, Kurt Koffka, and Max Wertheimer in the early 20th century and has been developed to this day, provides a classic framework for understanding visual perception [2][3][4] . Especially, Gestalt theory demonstrates the extraction of global properties in visual perception through experiments [5][6][7][8][9][10] . ...
... Since visual topology theory utilizes classical algebraic topology to interpret Gestalt theory, and persistent homology makes algebraic topology concepts efficiently computable, persistent homology can be employed to calculate key Gestalt principles, e.g., similarity, proximity, closure, good continuation and pragnanz 3,4,35 . In this paper, we will elaborate on the underlying mechanisms of these principles within the context of persistent homology, and develop the computational model for Gestalt theory. ...
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Widely employed in cognitive psychology, Gestalt theory elucidates basic principles in visual perception, but meanwhile presents significant challenges for computation. The advancement of artificial intelligence requires the emulation of human cognitive behavior, for which Gestalt theory serves as a fundamental framework describing human visual cognitive behavior. In this paper, we utilize persistent homology, a mathematical tool in computational topology, to develop a computational model for Gestalt theory, addressing the challenges of quantification and computation. The Gestalt computational model not only holds promise for applications in artificial intelligence and computer vision, but also opens a new research direction of computational visual perception.
... The Gestalt theorists (Köhler 1929) proposed the concept of isomorphism, suggesting that there is a corresponding neurobiological form and dynamic (embodied) for every experiential form and dynamic. In the Gestalt perspective, perception is not merely the sum of individual sensory elements; it transcends them and is also an immediate and automatic process (Koffka 1935). Interestingly, the idea of perception as related to automatic processes regulated by experiential scripts, as well as the concept of isomorphism, evoke the concept of embodied simulation. ...
... These ingredients emerge from the facts with immediate evidence […]. "Everything says what it is," wrote K. Koffka, "… a fruit says 'eat me'; water says 'drink me'; thunder says 'be afraid of me'; and a woman says 'love me.'" (Koffka 1935). (Bozzi 1998, p. 100). ...
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This paper proposes an integration of embodied and phenomenological perspectives to understand the restorative capacity of natural environments. It emphasizes the role of embodied simulation mechanisms in evoking positive affects and cognitive functioning. Perceptual symbols play a crucial role in generating the restorative potential in environments, highlighting the significance of the encounter between the embodied individual and the environment. This study reviews Stress Reduction Theory (SRT) and Attention Restoration Theory (ART), finding commonalities in perceptual fluency and connectedness to nature. It also explores a potential model based on physiognomic perception, where the environment’s pervasive qualities elicit an affective response. Restorativeness arises from a direct encounter between the environment’s phenomenal structure and the embodied perceptual processes of individuals. Overall, this integrative approach sheds light on the intrinsic affective value of environmental elements and their influence on human well-being.
... General machine learning paradigms can often benefit from key concepts when applied to specific domains. For computer vision and especially for localization-geared tasks like object detection, one of these concepts is 'region': Widely-accepted physiological theories [40] suggest that human perception will group similar elements and parts together to parse complex scenes and objects. This hypothesis is empirically validated by the R-CNN series [29] (note that the 'R' stands for 'region', which can be pre-computed [54] or jointly learned [50]). ...
... One crucial difference between the two is that language consists of semantically meaningful words, while images are raw signals recorded in pixels. Meanwhile, in vision, objects can serve as a natural counterpart to words -they are constantly referred and manipulated as we interact with the visual world [40,66], and they can often be captured by regions [54,2]. By enhancing MAE's region awareness, we hope to uncover novel ways to bridge the gap between the two fields. ...
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Vision-specific concepts such as "region" have played a key role in extending general machine learning frameworks to tasks like object detection. Given the success of region-based detectors for supervised learning and the progress of intra-image methods for contrastive learning, we explore the use of regions for reconstructive pre-training. Starting from Masked Autoencoding (MAE) both as a baseline and an inspiration, we propose a parallel pre-text task tailored to address the one-to-many mapping between images and regions. Since such regions can be generated in an unsupervised way, our approach (R-MAE) inherits the wide applicability from MAE, while being more "region-aware". We conduct thorough analyses during the development of R-MAE, and converge on a variant that is both effective and efficient (1.3% overhead over MAE). Moreover, it shows consistent quantitative improvements when generalized to various pre-training data and downstream detection and segmentation benchmarks. Finally, we provide extensive qualitative visualizations to enhance the understanding of R-MAE's behaviour and potential. Code will be made available at https://github.com/facebookresearch/r-mae.
... Gestalt theory has sought to understand (1) why one perception is subjectively experienced while alternative perceptions are not (e.g., why one sees ten people as "a group" rather than as "ten individuals") and (2) why a perception is stable or not (e.g., why one continues to see "a group" instead of vacillating between seeing "a group" and "individuals") (Koffka 1935;Wagemans, Elder, et al. 2012;Wertheimer 1924). A Gestalt theorist assumes that a visual perception emerges and is sustained owing to the relationships among the elements in a visual display (i.e., principles of visual organization). ...
... Perceptual structure is a hypothesized property of a perception that is based on the Gestalt theory assumption that perceptions can vary in their degree of gestaltet (i.e., structure, design) (Koffka 1935;Wagemans, Feldman, et al. 2012;Wertheimer 1924). The Gestalt and related literatures suggest that structured perceptions have five characteristics: cohesive, homogeneous, predictable, stable, and systematic. ...
Article
Visual marketing communications consist of two components: (1) semantic content (e.g., headings, images, copy) that communicates a brand’s positioning, benefits, and personality and (2) visual design (e.g., font selection, image size, the organization of the content) that encourages inferences about brand claims. We investigate how visual design can be used to encourage inferences that support brand claims and improve brand performance. We find that brands with a utilitarian positioning perform better when the visual design of their marketing communications encourages structured perceptions, whereas brands with a hedonic positioning perform better when the visual design of their marketing communications encourages unstructured perceptions. In both cases, (un)structured perceptions encourage inferences that reinforce brand claims and, consequently, improve brand performance. This research offers actionable insights into how marketing communication specialists can coordinate logo design, product design, package design, visual merchandising, and retail environments to reinforce brand claims.
... Understandably, defining general-purpose metrics for quantifying explanation properties is not trivial [6], as the perceived quality depends on the data itself, on the target user, and the downstream task. Focussing on explanations of video DeepFake classifiers, we discuss a set of desirable human-centric properties [10,38,51] and formulate quantitative metrics for their evaluation. ...
... texture details or high-frequency patterns [26,84]. Instead, we expect models that focus on human-interpretable cues [38] such as small manipulation artefacts, teeth misalignment, non-circular pupils, or irregular skin complexion, to produce smoother, sparser and more localized heatmaps. ...
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The proliferation of DeepFake technology is a rising challenge in today's society, owing to more powerful and accessible generation methods. To counter this, the research community has developed detectors of ever-increasing accuracy. However, the ability to explain the decisions of such models to users is lacking behind and is considered an accessory in large-scale benchmarks, despite being a crucial requirement for the correct deployment of automated tools for content moderation. We attribute the issue to the reliance on qualitative comparisons and the lack of established metrics. We describe a simple set of metrics to evaluate the visual quality and informativeness of explanations of video DeepFake classifiers from a human-centric perspective. With these metrics, we compare common approaches to improve explanation quality and discuss their effect on both classification and explanation performance on the recent DFDC and DFD datasets.
... We would be studying how far it can be transmitted compositionally in syntax starting with the whole, but not holistically. (This sounds like a distant memory in psychology too; see Koffka 1936). ...
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TheBench is a tool to study monadic structures in natural language. It is for writing monadic grammars to explore analyses, compare diverse languages through their categories, and to train models of grammar from form-meaning pairs where syntax is latent variable. Monadic structures are binary combinations of elements that employ semantics of composition only. TheBench is essentially old-school categorial grammar to syntacticize the idea, with the implication that although syntax is autonomous (recall \emph{colorless green ideas sleep furiously}), the treasure is in the baggage it carries at every step, viz. semantics, more narrowly, predicate-argument structures indicating choice of categorial reference and its consequent placeholders for decision in such structures. There is some new thought in old school. Unlike traditional categorial grammars, application is turned into composition in monadic analysis. Moreover, every correspondence requires specifying two command relations, one on syntactic command and the other on semantic command. A monadic grammar of TheBench contains only synthetic elements (called `objects' in category theory of mathematics) that are shaped by this analytic invariant, viz. composition. Both ingredients (command relations) of any analytic step must therefore be functions (`arrows' in category theory). TheBench is one implementation of the idea for iterative development of such functions along with grammar of synthetic elements.
... The neural pleasure associated with this type of successful perception has its parallels in other perceptual engagements, for example in the responses identified a hundred years ago by the Gestalt psychologists, Wertheimer, Koffka, and Köhler. They noticed the way our perception of phenomena is influenced by their display of particular properties, including good 'fig-ure/ground' differentiation, 'similarity', 'symmetry', 'continuity', 'closure' and 'grouping' (Koffka 1935). Such neurally driven preferences for particular Gestalts have been selected for in our genetic make-up because they help us to see, by facilitating the discrimination of objects in our visual environment. ...
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In this chapter, I will make a case that neuroscience can help with the understanding of any art, and that in the context of rock art, with its deep history, it offers particular advantages. Most importantly it can give us new access to the minds of its makers and users, something much needed in the absence of the verbal commentaries associated with most other categories of material. That access, I suggest, can be obtained by using the latest knowledge of the extent to which the formation of the individual brain is affected by the environment to which it is exposed. This knowledge can help not only to reconstruct salient aspects of the neural resources of any individual or group whose material and social environment is sufficiently familiar to us, but also to infer how those resources are likely to have influenced such art-related behaviours as their motor inclinations and visual preferences. When these insights are supported by an understanding of such other newly discovered properties of our brains as its neural plasticity and neural mirroring, we can build up a new understanding of the mental activities behind the similarities and the differences in the way people living at different places and times have marked rock walls. A neural approach also allows us to re-evaluate assumptions about the history of culture that have been taken for granted in the fields of archaeology, anthropology, and art history, such as the pre-eminence of the role of language in the formation of culture and the associated insistence that art is necessarily a symbolic activity. In this way neuroscience can add a new dimension to cultural history.
... Gibson fully acknowledges his indebtedness to the Gestalt concept of "Demand Character", i.e., a characteristic that we perceive that can place demands on us (Koffka, 1935). However, Gibson was skeptical of the strict divide that Gestalt theorists saw between the physical or objective and the phenomenal or subjective. ...
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Psychological and philosophical studies have extended J. J. Gibson’s notion of affordances. Affordances are possibilities for bodily action presented to us by the objects of our perception. Recent work has argued that we should extend the actions afforded by perception to mental action. I argue that we can extend the notion of affordance itself. What I call ‘Introspective Affordances’ are possibilities for mental action presented to us by introspectively accessible states. While there are some prima facie worries concerning the non-perceptual nature of introspection, I will argue that our internal mental lives share enough commonalities with experiences in our environment to warrant this extension. I will demonstrate the value of introspective affordances by showing how they allow us to explain an underexplored aspect of thought insertion.
... So, what happens when auditory information is removed during sport performance? Although Gestalt psychologists have mainly dealt with visual perception (Koffka 1935;Wertheimer 1923), some of them also extended Gestalt principles to multisensory integration (see, for example, Werner 1934). They would probably say that the "whole" experience (i.e., the multisensory integration of information) is somehow disrupted when a piece of information is removed, even if its contribution to the "whole" appears limited. ...
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Starting approximately from the beginning of the new millennium, a series of studies highlighted that auditory information deriving from biological motion can significantly influence the behavioral, cognitive and neurophysiological processes involved in the perception and execution of complex movements. In particular, it was observed that an appropriate use of sounds deriving from one’s own movement promotes improvements in the movement execution itself. Two main approaches can be used, namely the sonification one or the ecological sound one; the former is based on the conversion of physiological and/or physical movement data into sound, while the latter is based on the use of auditory recordings of movement sounds as models. In the present article, some of the main applications of both approaches—especially the latter—to the domains of sport and motor rehabilitation are reviewed, with the aim of addressing two questions: Is it possible to consider rhythm as a Gestalt of human movement? If so, is it possible to build up cognitive strategies to improve/standardize movement performance from this Gestalt? As with most topics in science, a definitive answer is not possible, yet the evidence leads us to lean toward a positive answer to both questions.
... After outlining the results, we will discuss what they mean for our research questions, their interpretive limits, and what our findings prompt for future study. (Koffka 1935) into cognitive linguistics first by Fillmore (1968) and later by Talmy (2000Talmy ( [1975). For the purposes of this paper, a Figure can be understood as an object or point that is "moving or conceptually movable" while a Ground functions as a reference point that situates that Figure (419). ...
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This paper is a systematic investigation of motion expressions in programmatic music description. To address issues with defining the Source MOTION and the Target MUSIC, we utilize Gestalt models (Figure-Ground and Source-Path-Goal) while also critically examining the ontological complexity of the Target MUSIC. We also investigate music motion descriptions considering the role of the describer’s perspective and communicative goals. As previous research has demonstrated, an attentional Goal-bias is common in physical motion description, yet this has been found also to lessen due to audience accommodation effects. We investigate whether this also occurs in music description. Using cognitive linguistic frameworks, we conducted an analysis of 21 English speakers’ written descriptions of dynamic orchestral excerpts. All participants gave a description of one excerpt reporting their own personal experiences and the other excerpt reporting the events of the excerpt for a fictional future participant. We find that addressee accommodation shapes the choice of the ontological types of Figures used from being more subjective and creative in describing music for oneself versus being more objective in describing music for others. However, our investigation does not find sufficient evidence for a Goal-bias in music like there is in physical motion event descriptions.
... The Gestalt school noted the proclivity for humans to perceive complex sensory information in the simplest, most meaningful, and most complete way. In simple terms, the law of Prägnanz is a case of cognitive parsimony: a principle asserting that our cognitive systems prefer economical and elegant representations of reality (Koffka 1935;Wertheimer 1923). Sudden insights exemplify this principle, as they succinctly encapsulate the most pertinent and likely solution. ...
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The Gestalt psychologists’ theory of insight problem-solving was based on a direct parallelism between perceptual experience and higher-order forms of cognition (e.g., problem-solving). Similarly, albeit not exclusively, to the sudden recognition of bistable figures, these psychologists contended that problem-solving involves a restructuring of one’s initial representation of the problem’s elements, leading to a sudden leap of understanding phenomenologically indexed by the “Aha!” feeling. Over the last century, different scholars have discussed the validity of the Gestalt psychologists’ perspective, foremost using the behavioral measures available at the time. However, in the last two decades, scientists have gained a deeper understanding of insight problem-solving due to the advancements in cognitive neuroscience. This review aims to provide a retrospective reading of Gestalt theory based on the knowledge accrued by adopting novel paradigms of research and investigating their neurophysiological correlates. Among several key points that the Gestalt psychologists underscored, we focus specifically on the role of the visual system in marking a discrete switch of knowledge into awareness, as well as the perceptual experience and holistic standpoints. While the main goal of this paper is to read the previous theory in light of new evidence, we also hope to initiate an academic discussion and encourage further research about the points we raise.
... Profiling, as proposed by Rubin (1921), derives from gestalt perception principles (Koffka 1935;Wertheimer 1938); it is a very general feature of cognition (Langacker 2008, 58) and concerns the distinction between a figure and its background. Gestalt perception, in its turn, represents holistic object processing and it draws on innate visual processing mechanisms (see, e.g., Dalrymple et al., 2013). ...
Article
The paper seeks to provide a cognitive-linguistic re-interpretation of the centuries-old notion of whole-text structure . The investigation presented here draws on 317 data sources selected through a scoping literature review. The paper demonstrates how text structure, narrative structure, rhetorical structure , etc. all represent metonymically one and the same multi-faceted underlying concept. That concept is argued to result from the amalgamated operation of conceptual metaphor and conceptual metonymy combined with the simultaneous and dynamic operation of (what are known in gestalt psychology as) profiling shifts. The paper further demonstrates how such shifts in profiling operate on text-worlds and discourse-worlds to bring about perceptions of a text’s ‘progression’ and of whole-text structure .
... Notes 1 See Freud's (1940) Outline of Psycho-Analysis first published as Abriss der Psychoanalyse; (Koffka 1935); (Schrödinger 1935); and C. S. Lewis's (1941) excursion into the demonic that first appeared in serial form with "The Screwtape Letters" in The Guardian (2 May 1941-28 November 1941). ...
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Charles Scott Sherrington (1857–1952) is widely acclaimed as the most important neurophysiologist in history. He became a legend in his own time, coined the term “synapse”, and in 1932 received the Nobel Prize in medicine for his discoveries on the function of neurons. By the time he presented the Gifford Lectures 1937–38, he represented the best that science had to offer on behalf of the relationship of the mind to the natural world. The lectures, including one never publicly presented, were published as Man on His Nature (1941). Here neurology meets theology at the busy and often treacherous intersection of science and religion. Examining Sherrington’s views in some detail, the standard rendering of Sherrington as a theist cannot be sustained by their contents; he ends up as at least a humanist and perhaps an atheist. Views by neurologists and philosophers of mind some seventy to eighty years later are compared and contrasted with Sherrington’s. Although expectations of a materialist/reductionist answer to the mind/body problem have not been realized, neuroscientist Raymond Tallis appears as a parallel figure to Sherrington: both are clearly naturalistic humanists. A theistic response is presented addressing the mind/body problem from a hylomorphic process theology perspective, along with some comments regarding natural theology in general. In the end, this essay has two complementary aims: (1) to relocate Sherrington’s neurotheology—if it can be called that—in a more appropriate historiographical category; and (2) to offer a viable answer to the mind/body problem.
... Hurley 2001). One instance of such a holistic program is gestalt psychology (Koffka 1935;Wertheimer 1938;Köhler 1959). Roughly, the gestalt approach to human perception and understanding viewed these as processes in which the whole configurations (Gestalten in German) are perceived and understood as opposed to the component parts of the whole. ...
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Basal cognition investigates cognition working upwards from non-neuronal organisms. Since it is committed to empirically testable hypotheses, a methodological challenge arises: how can experiments avoid using zoo-centric assumptions that ignore the ecological contexts that might elicit cognitively driven behaviour in non-neuronal organisms? To meet this challenge, I articulate the Principle of Dynamic Holism (PDH), a methodological principle for guiding research on non-neuronal cognition. PDH’s relation to holistic research programmes in human-focused cognitive science and psychology is described and then an argument from analogy based on holistic developmental biology is presented. Lastly, two experiments exemplifying the need for PDH are examined.
... Cette forme, d'autre part, résiste aux perturbations si elle parvient à s'imposer avec force à la perception de l'observateur. Dans ce contexte, la perception n'est pas comprise comme une somme de diverses expériences sensorielles, mais comme la totalité de l'expérience immédiate prise en soi (KOFKA, 1975). ...
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The article presents an experience of analysis of the activities of the garbage collection worker in a city, based on the device of the Photo Workshop and having as a theoretical reference the Clinic of the Activity. The focus of the study is on the analysis of the activity of workers who work as garbage collectors in a city in the state of Rio de Janeiro. The Photo Workshop was chosen as a research and intervention device in order to use the images as triggers for the co-analysis of the work, giving rise to a collective reality, present in all work activities. The purpose of this device is to trigger, from the production of images, questions and reflections about the work activity. In this sense, through the results collected from this research and intervention, it became evident that the Photo Workshop can be a possible device in the development of the workers’ power to act, thus enabling collective exchanges, with the professional genre being a decisive instrument of the workers’ power to act. involved.
... According to the Gestalt psychologist Kurt Koffka, simple combinations do not represent the totality of things, but rather the combined whole, with its connectedness, is the perfectly unified structure [9] .Here, the village of Zhang Guying has unique genetic qualities and abundant cultural resources that have created a hereditary spatial order and cultural identity.In terms of the identification of genetic elements, by subdividing and extracting the genetic traits of traditional villages, two major genetic bodies were obtained and core elements were extracted , Table 2.Its gene subjects can be divided into Characteristic and Introverted genes. Architectural layout of the hierarchical order, courtyard relationship, which reflects the order of respect, filial respect for ancestors and other rituals. ...
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This study analyzes the spatial genes of traditional villages by taking Zhang Guying village in northern Hunan Province as an example.Starting from the theory of heterogeneous isomorphism, we discover the methods and paths of identifying, presenting and translating the spatial genes of traditional villages in Hunan region.Through the gene identification extraction method, it analyzes the spatial and cultural genes of Zhang Guying village and obtains the genetic elements and composition of the traditional villages.Based on the design model of gene translation, the “Duanwu family” is systematically analyzed, and it can build a traditional village regeneration and development system.In view of this, his research relies on the application of “heterogeneous isomorphism” theory, which can be obtained from the gene translation method, isomorphic design model.It can promote the regenerative continuation of traditional villages and low-carbon ecological development.
... In a sense, our perception of the world is defined by what kinds of interactions we can perform. Related ideas of functional visual understanding (what actions does a given scene afford an agent?) were discussed in the 1930s by the Gestalt psychologists [35] and later described by J.J. Gibson [21] as affordances. Although this direction inspired many efforts in vision and psychology research, a comprehensive computational model of affordance perception remains elusive. ...
Preprint
We study the problem of inferring scene affordances by presenting a method for realistically inserting people into scenes. Given a scene image with a marked region and an image of a person, we insert the person into the scene while respecting the scene affordances. Our model can infer the set of realistic poses given the scene context, re-pose the reference person, and harmonize the composition. We set up the task in a self-supervised fashion by learning to re-pose humans in video clips. We train a large-scale diffusion model on a dataset of 2.4M video clips that produces diverse plausible poses while respecting the scene context. Given the learned human-scene composition, our model can also hallucinate realistic people and scenes when prompted without conditioning and also enables interactive editing. A quantitative evaluation shows that our method synthesizes more realistic human appearance and more natural human-scene interactions than prior work.
... Next, how should we incorporate them into the 3D space? The Gestalt principle is a fundamental theory in cognitive psychology that points out that a visual image is first recognized as a global entity and then understood as content specific to the local [36]. It coincides with the diagnosis process by pathologists, and two subprinciples within it can support the fusion process in the model. ...
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Artificial intelligence-enabled histopathological data analysis has become a valuable assistant to the pathologist. However, existing models lack representation and inference abilities compared with those of pathologists, especially in cancer subtype diagnosis, which is unconvincing in clinical practice. For instance, pathologists typically observe the lesions of a slide from global to local, and then can give a diagnosis based on their knowledge and experience. In this paper, we propose a Data and Knowledge Co-driving (D&K) model to replicate the process of cancer subtype classification on a histopathological slide like a pathologist. Specifically, in the data-driven module, the bagging mechanism in ensemble learning is leveraged to integrate the histological features from various bags extracted by the embedding representation unit. Furthermore, a knowledge-driven module is established based on the Gestalt principle in psychology to build the three-dimensional (3D) expert knowledge space and map histological features into this space for metric. Then, the diagnosis can be made according to the Euclidean distance between them. Extensive experimental results on both public and in-house datasets demonstrate that the D&K model has a high performance and credible results compared with the state-of-the-art methods for diagnosing histopathological subtypes. Code: https://github.com/Dennis-YB/Data-and-Knowledge-Co-driving-for-Cancer-Subtypes-Classification
... In this work, we follow an object-centric approach inspired by the Gestalt school of perception that captures an object as a whole shape [32,47] invariant to its pose and scale [31]. A holistic approach builds up a prior for each object category, that then enables object recognition in different complex scenes with varying configurations. ...
Preprint
We introduce Equivariant Neural Field Expectation Maximization (EFEM), a simple, effective, and robust geometric algorithm that can segment objects in 3D scenes without annotations or training on scenes. We achieve such unsupervised segmentation by exploiting single object shape priors. We make two novel steps in that direction. First, we introduce equivariant shape representations to this problem to eliminate the complexity induced by the variation in object configuration. Second, we propose a novel EM algorithm that can iteratively refine segmentation masks using the equivariant shape prior. We collect a novel real dataset Chairs and Mugs that contains various object configurations and novel scenes in order to verify the effectiveness and robustness of our method. Experimental results demonstrate that our method achieves consistent and robust performance across different scenes where the (weakly) supervised methods may fail. Code and data available at https://www.cis.upenn.edu/~leijh/projects/efem
... 34 Wearenotusedtosuchawayofwritinganymore or different. Since it was first explored by Wertheimer and Köhler in the 1920s 35 , an extensive amount of literature has studied how shape recognition works and what its main drivers are [240][241][242]. The 'Gestalt principles' (or sometimes 'Gestalt Laws') are nowadays common concepts when working on visual representations. ...
Thesis
The popularization of sequencing technologies in the past twenty years led to a high increase of the number of sequenced genomes. The diversity of the newly sequenced reference genomes highlighted the biases of using a single reference, which is not enough to access all the diversity within a species. There are many examples of intraspecific variations within plants, including presence / absence and copy number variations. These variations can have a strong effect on plant phenotypes, as exemplified by the African rice in which the presence of the gene Sub1A is linked to drought tolerance. The concept of pangenome appeared to better integrate these variations within genomics approaches. A pangenome can be built from genes only or from any genomic fragments found within a group, and is useful to compare their distributions between multiple individuals. Depending on the presence rate, many categories of elements can be defined; the main ones are the elements present in all the individuals (part of the ‘core’ genome) and these absent in at least one of them (part of the ‘variable’ genome). Pangenomics still lacks tools, especially for visualization. This is particularly true for eukaryotes (including plants) which have larger and more complex genomes than bacteria. Pangenomes were first built for bacteria, but their related tools cannot properly work on bigger genomes. My PhD investigated the creation of novel visual representations and tools for the visualization of plant pangenomes (and eukaryotes in general).Within this dissertation, I introduce the state of the art of pangenome visualization: I distinguish pan-gene from pangenomes, the latter often being represented by pangenome graphs where each sequence is a node and each observed sequence succession forms an edge; I also identify unspecific, qualifying, positioned, structural and composite visualization tools. The first chapter introduce ten principles for creating a genomic visualization tool, for future biology or bioinformatics scientists interested in datavisualization. The second chapter describes my first pangenome visualization, published in the journal Bioinformatics under the name ‘Panache: a Web Browser-Based Viewer for Linearized Pangenomes’. I detail the visual representation used within Panache and the creation of the resulting web application built in JavaScript, enabling the dynamic exploration of pangenomic data. The third and final chapter details the design of a composite visualization tools for pangenomes, called SaVanache, and enabling the navigation between four view scales. There are four of them: one for global diversity, one for structural variations, one for the presence / absence variations, and one for nucleotide variations. I propose a new approach for the annotation and visual representation of structural variations within a pangenome graph, based on a pivot path within the graph used as a reference coordinate system.
... We did not choose these alternatives in order to satisfy DG5 (configure DataPilot to support one, none, or both of quality and usage information); the bi-colored glyphs were more aesthetic as they retained a consistent circular shape while using different colors to describe different dimensions across configurations. Next, we picked a discrete three-class (high, medium, low) scale over a continuous scale to help users perceptually distinguish between (and form groups of) attributes by color hue instead of the less effective saturation [67]. For the five-class rating scales in the Attribute Details View, we considered a progress bar-like continuous widget that encodes the size (length), but eventually chose discrete icon arrays as they are easy to read [41]. ...
Preprint
Selecting relevant data subsets from large, unfamiliar datasets can be difficult. We address this challenge by modeling and visualizing two kinds of auxiliary information: (1) quality - the validity and appropriateness of data required to perform certain analytical tasks; and (2) usage - the historical utilization characteristics of data across multiple users. Through a design study with 14 data workers, we integrate this information into a visual data preparation and analysis tool, DataPilot. DataPilot presents visual cues about "the good, the bad, and the ugly" aspects of data and provides graphical user interface controls as interaction affordances, guiding users to perform subset selection. Through a study with 36 participants, we investigate how DataPilot helps users navigate a large, unfamiliar tabular dataset, prepare a relevant subset, and build a visualization dashboard. We find that users selected smaller, effective subsets with higher quality and usage, and with greater success and confidence.
... Rather, questions arise as to how we experience spaces, how we manage to experience them and how we deal with them" (translation MT). 7 Von Ehrenfels 1890; Kanizsa 1976;Köhler 1920Köhler , 1929Koffka 1935;Pinna 2011;Rubin 1921;Wertheimer 1923Wertheimer , 1925 elementary school. In other words, to perceive a polygon with three edges as a triangle is not a universal principle independent of cultural heritage and subjective encoding preferences. ...
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The term common sense is often misunderstood as intuitive, but it is implicit. Implicit refers back to cognitive psychology research arguing in favor of procedural, that is, highly automatized knowledge of mental computation processes. The hypothesis is that common sense geography processes-ancient and current-are based on procedural knowledge of cognitive computation. This computation is in constant interaction with the environment. Le terme bon sens est souvent mal compris comme intuitif, mais il est implicite. Implicite renvoie à la recherche en psychologie cognitive qui plaide en faveur de la procédure, c'est-à-dire une connaissance hautement automatisée des processus de calcul mental. L'hypothèse est que les processus de géographie de bon sens-anciens et actuels-sont basés sur la connaissance procédurale du calcul cognitif. Ce calcul est en interaction constante avec l'environnement.
... Hareketin bu algısal önceliği, görsel iletişimde en dikkat çeken unsur olmasını ve hareketli bir anlatımın, hareketsiz bir anlatıma göre çok daha etkili olmasını sağlamıştır. Algısal önceliğe bağlı olarak, izleyicilerin hareket sayesinde daha az sıkıldığı, başka yöne bakamadığı ve zamanın daha hızlı geçtiği hissine kapıldıkları da görülmüştür (Koffka 1935;Hass vd. 2008). ...
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