Latent Transformer Models for out-of-distribution detection

Any clinically-deployed image-processing pipeline must be robust to the full range of inputs it may be presented with. One popular approach to this challenge is to develop predictive models that can provide a measure of their uncertainty. Another approach is to use generative modelling to quantify the likelihood of inputs. Inputs with a low enough likelihood are deemed to be out-of-distribution and are not presented to the downstream predictive model. In this work, we evaluate several approaches to segmentation with uncertainty for the task of segmenting bleeds in 3D CT of the head. We show that these models can fail catastrophically when operating in the far out-of-distribution domain, often providing predictions that are both highly confident and wrong. We propose to instead perform out-of-distribution detection using the Latent Transformer Model: a VQ-GAN is used to provide a highly compressed latent representation of the input volume, and a transformer is then used to estimate the likelihood of this compressed representation of the input. We demonstrate this approach can identify images that are both far- and near- out-of-distribution, as well as provide spatial maps that highlight the regions considered to be out-of-distribution. Furthermore, we find a strong relationship between an image's likelihood and the quality of a model's segmentation on it, demonstrating that this approach is viable for filtering out unsuitable images

Valon biologiset vaikutukset

Uuden valoherkän aistinsolun ("luontaisesti valoherkkä verkkokalvon gangliosolu" tai "melanopsiinia sisältävä verkkokalvon gangliosolu") löytö silmässä, aiemmin tunnettujen tappi- ja sauvasolujen lisäksi, vuonna 2002 on syventänyt kronobiologian ja valaistustekniikan tietämystä. Uuden aistinsolun on havaittu vastaavan ihmisen ja muiden nisäkkäiden sisäisen kellon tahdistamisesta ulkoiseen valo/pimeä-rytmiin sekä muista tässä työssä käsiteltävistä biologista vaikutuksista. Työssä tutkittiin uuden aistinsolun (fotoreseptorin) mahdollisia vaikutuksia valaistustekniikkaan. Aistinsoluun liittyvä biologinen tausta on käyty läpi vain perusteiden tasolla työn keskittyessä lähinnä uuteen aistinsoluun liittyvien valovaikutusten tutkimiseen. Uuden aistinsolun analyysi on tehty kirjallisuuskatsauksena käyttäen olemassa olevia julkaisuja. Käytännön sovellukset kuten vuorotyö, jet lag ja kaamosmasennus ovat käyty läpi vain perusteiden osalta. Kirjallisuuskatsauksen tuloksena paljastui monta mahdollista sovellusta valaistustekniikassa uudelle aistinsolulle. Kuitenkin on huomattavaa, että vaikka kehitys kronobiologisten vasteiden tuntemuksessa viimeisen viiden vuoden aikana on ollut nopeaa liittyen uuteen aistinsoluun, on paljon uuden aistinsolun ominaisuuksista vielä selvittämättä. Ennen kuin fotooppiselle näkemiselle (päivänäkeminen) vastaavia suosituksia uudelle aistinsolulle voidaan tehdä, lisätutkimusta tarvitaan selvittämään eri aivorakenteiden ja perinteisten fotoreseptorien (sauva- ja tappisolut) osuus kronobiologisessa säätelyssä

Modulation spectrale des réponses mélanopsine : rôle de la bistabilité de la mélanopsine dans le réflexe photomoteur

In addition to the canonical photoreceptors, rods and cones, a novelmelanopsin-expressing retinal ganglion cell (mRGC) was recently discovered.The novel photopigment melanopsin in the human retinahas been shown to express invertebrate-like bistable properties bothin vitro and in vivo. In bistable photopigment systems, light elicitsphotosensory responses and drives photoregeneration of the chromophoreto restore photic responsiveness. These studies have shownthat prior light exposure can modulate the amplitude of subsequentphotic responses of melanopsin.In this thesis, the putative bistability of melanopin in humans isexamined. The bistability was studied using 1) pupillary light reflex(PLR) as a tool, 2) developing a method for quantifying the effectsof lens density for melanopsin-mediated photoreception, and 3) providinga quantitative mathematical framework for modeling bistablepigment systems and non-image forming (NIF) visual system.Exploiting the bistable properties of melanopsin could allow foroptimization of spectral light distribution in experimental, industrial,domestic and clinical phototherapy applications by appropriate useof the photoregenerative effects of long wavelength light.Perinteisten fotoreseptorien, sauvasolujen ja tappisolujen, lisäksi verkkokalvoltaon löydetty melanopsiinia sisältäviä gangliosoluja. Fotopigmenttimelanopsiinin on huomattu käyttäytyvän ihmisen verkkokalvollaselkärangattomien eläimien bistabiilin näköjärjestelmän tavoinsekä in vivo- ja in vitro- olosuhteissa. Bistabiileissa fotopigmenttijärjestelmissävalo aiheuttaa sensoristen vasteiden lisäksi kromoforin fogeneraationvastevalmiisen tilaan. Nämä aiemmat tutki-mukset ovatosoittaneet, että aiempi valoaltistus voi moduloida siitä seuraaviamelanopsiinivasteita.Tässä väitöskirjassa melanopsiinin oletettua bistabiiliutta tutkittiinkäyttäen 1) Pupillireaktiota työkaluna, 2) kehittämällä kvantitaviinenmenetelmä mykiöntiheyden vaikutuksiin melanopsiini-fotoreseptiossa,ja 3) kehittäen kvantitatiivisen matemaattisen kehyksen bistabiilien pigmenttijärjestelmien ja ei-visuaalisen näköjärjestelmän mallintamiseen.Melanopsiinin bistabiileita ominaisuuksia on mahdollista optimoidavalon spektrikoostumusta niin tieteellisissä, teollisissa, kotitalouksellisissaja kliinisissä valoterapia sovelluksissa hyväksikäyttämälläpunaisen aallonpituusalueen fotoregeneroivia vaikutuksia.En plus des photorécepteurs canoniques traditionnels (bâtonnets etcônes), des cellules ganglionnaires contenant le photopigment mélanopsineont récemment été découverts. Une étude récente de notrelaboratoire a suggéré que, dans la rétine humaine, ce nouveau photopigmentexprime des propriétés bistables similaires à celles notéeschez les invertébrés tant in vitro qu’in vivo. Dans les systèmes dephotopigments bistables, la lumière déclenche une réponse photosensoriellemais permet aussi la régénération du chromophore pourrétablir la réactivité lumineuse du photopigment. Cette dernière étudea montré qu’une exposition lumineuse antérieure peut moduler l’amplitudedes réponses lumineuses de la mélanopsine.L’objectif de ma thèse est d’étudier (1) la bistabilité présumée de lamélanopsine chez l’Homme en utilisant comme outil le réflexe photomoteurpupillaire. Ma thèse comporte aussi 2) le développementd’une technique d’évaluation quantitative des effets du brunissementdu cristallin oculaire sur la photoréception impliquant la mélanopsine;3) le développement d’un modèle mathématique portant sur lefonctionnement des photopigments bistables et du système photiquenon visuel.L’exploitation des propriétés bistables de la mélanopsine et l’utilisationappropriée des effets photorégénérateurs des longueurs d’ondeslumineuses longues pourraient servir dans l’optimisation de la compositionspectrale des applications photothérapeutiques (expérimentales,industrielles, domestiques et cliniques)

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Embedded deep learning in ophthalmology: making ophthalmic imaging smarter.

10.1177/2515841419827172Ther Adv Ophthalmol112515841419827172

Embedded deep learning in ophthalmology: making ophthalmic imaging smarter

Deep learning has recently gained high interest in ophthalmology due to its ability to detect clinically significant features for diagnosis and prognosis. Despite these significant advances, little is known about the ability of various deep learning systems to be embedded within ophthalmic imaging devices, allowing automated image acquisition. In this work, we will review the existing and future directions for ‘active acquisition’–embedded deep learning, leading to as high-quality images with little intervention by the human operator. In clinical practice, the improved image quality should translate into more robust deep learning–based clinical diagnostics. Embedded deep learning will be enabled by the constantly improving hardware performance with low cost. We will briefly review possible computation methods in larger clinical systems. Briefly, they can be included in a three-layer framework composed of edge, fog, and cloud layers, the former being performed at a device level. Improved egde-layer performance via ‘active acquisition’ serves as an automatic data curation operator translating to better quality data in electronic health records, as well as on the cloud layer, for improved deep learning–based clinical data mining

A Purkinje image-based system for an assessment of the density and transmittance spectra of the human crystalline lens in vivo

10.1038/s41598-020-73541-yScientific Reports10

Does pupil constriction under blue and green monochromatic light exposure change with age?

Many non-visual functions are regulated by light through a photoreceptive system involving melanopsin-expressing retinal ganglion cells that are maximally sensitive to blue light. Several studies have suggested that the ability of light to modulate circadian entrainment and to induce acute effects on melatonin secretion, subjective alertness and gene expression, decreases during aging, particularly for blue light. This could contribute to the documented changes in sleep and circadian regulatory processes with aging. However, age-related modification in the impact of light on steady-state pupil constriction, which regulates the amount of light reaching the retina, is not demonstrated. We measured pupil size in 16 young (22.8±4y) and 14 older (61±4.4y) healthy subjects during 45s exposures to blue (480nm) and green (550nm) monochromatic lights at low (7×10(12) photons/cm(2)/s), medium (3×10(13) photons/cm(2)/s), and high (10(14) photons/cm(2)/s) irradiance levels. Results showed that young subjects had consistently larger pupils than older subjects, for dark adaptation and during all light exposures. Steady-state pupil constriction was greater under blue than green light exposure in both age groups and increased with increasing irradiance. Surprisingly, when expressed in relation to baseline pupil size, no significant age-related differences were observed in pupil constriction. The observed reduction in pupil size in older individuals, both in darkness and during light exposure, may reduce retinal illumination and consequently affect non-visual responses to light. The absence of a significant difference between age groups for relative steady-state pupil constriction suggests that other factors such as tonic, sympathetic control of pupil dilation, rather than light sensitivity per se, account for the observed age difference in pupil size regulation. Compared to other nonvisual functions, the light sensitivity of steady-state pupil constriction appears to remain relatively intact and is not profoundly altered by age

Aging of Non-Visual Spectral Sensitivity to Light in Humans: Compensatory Mechanisms?

<div><p>The deterioration of sleep in the older population is a prevalent feature that contributes to a decrease in quality of life. Inappropriate entrainment of the circadian clock by light is considered to contribute to the alteration of sleep structure and circadian rhythms in the elderly. The present study investigates the effects of aging on non-visual spectral sensitivity to light and tests the hypothesis that circadian disturbances are related to a decreased light transmittance. In a within-subject design, eight aged and five young subjects were exposed at night to 60 minute monochromatic light stimulations at 9 different wavelengths (420–620 nm). Individual sensitivity spectra were derived from measures of melatonin suppression. Lens density was assessed using a validated psychophysical technique. Although lens transmittance was decreased for short wavelength light in the older participants, melatonin suppression was not reduced. Peak of non-visual sensitivity was, however, shifted to longer wavelengths in the aged participants (494 nm) compared to young (484 nm). Our results indicate that increased lens filtering does not necessarily lead to a decreased non-visual sensitivity to light. The lack of age-related decrease in non-visual sensitivity to light may involve as yet undefined adaptive mechanisms.</p></div