Unifying (Machine) Vision via Counterfactual World Modeling

Leading approaches in machine vision employ different architectures for different tasks, trained on costly task-specific labeled datasets. This complexity has held back progress in areas, such as robotics, where robust task-general perception remains a bottleneck. In contrast, "foundation models" of natural language have shown how large pre-trained neural networks can provide zero-shot solutions to a broad spectrum of apparently distinct tasks. Here we introduce Counterfactual World Modeling (CWM), a framework for constructing a visual foundation model: a unified, unsupervised network that can be prompted to perform a wide variety of visual computations. CWM has two key components, which resolve the core issues that have hindered application of the foundation model concept to vision. The first is structured masking, a generalization of masked prediction methods that encourages a prediction model to capture the low-dimensional structure in visual data. The model thereby factors the key physical components of a scene and exposes an interface to them via small sets of visual tokens. This in turn enables CWM's second main idea -- counterfactual prompting -- the observation that many apparently distinct visual representations can be computed, in a zero-shot manner, by comparing the prediction model's output on real inputs versus slightly modified ("counterfactual") inputs. We show that CWM generates high-quality readouts on real-world images and videos for a diversity of tasks, including estimation of keypoints, optical flow, occlusions, object segments, and relative depth. Taken together, our results show that CWM is a promising path to unifying the manifold strands of machine vision in a conceptually simple foundation

Generic flow profiles induced by a beating cilium

We describe a multipole expansion for the low Reynolds number fluid flows generated by a localized source embedded in a plane with a no-slip boundary condition. It contains 3 independent terms that fall quadratically with the distance and 6 terms that fall with the third power. Within this framework we discuss the flows induced by a beating cilium described in different ways: a small particle circling on an elliptical trajectory, a thin rod and a general ciliary beating pattern. We identify the flow modes present based on the symmetry properties of the ciliary beat.Comment: 12 pages, 6 figures, to appear in EPJ

Single-cell analysis of CD4+ T-cell differentiation reveals three major cell states and progressive acceleration of proliferation

Background: Differentiation of lymphocytes is frequently accompanied by cell cycle changes, interplay that is of central importance for immunity but is still incompletely understood. Here, we interrogate and quantitatively model how proliferation is linked to differentiation in CD4+ T cells. Results: We perform ex vivo single-cell RNA-sequencing of CD4+ T cells during a mouse model of infection that elicits a type 2 immune response and infer that the differentiated, cytokine-producing cells cycle faster than early activated precursor cells. To dissect this phenomenon quantitatively, we determine expression profiles across consecutive generations of differentiated and undifferentiated cells during Th2 polarization in vitro. We predict three discrete cell states, which we verify by single-cell quantitative PCR. Based on these three states, we extract rates of death, division and differentiation with a branching state Markov model to describe the cell population dynamics. From this multi-scale modelling, we infer a significant acceleration in proliferation from the intermediate activated cell state to the mature cytokine-secreting effector state. We confirm this acceleration both by live imaging of single Th2 cells and in an ex vivo Th1 malaria model by single-cell RNA-sequencing. Conclusion: The link between cytokine secretion and proliferation rate holds both in Th1 and Th2 cells in vivo and in vitro, indicating that this is likely a general phenomenon in adaptive immunity

Reduced Transmissibility of East African Indian Strains of Mycobacterium tuberculosis

BACKGROUND: Mycobacterium tuberculosis (MTB) has been classified into 4 main lineages. Some reports have associated certain lineages with particular clinical phenotypes, but there is still insufficient information regarding the clinical and epidemiologic implications of MTB lineage variation. METHODS: Using large sequence polymorphisms we classified MTB isolates from a population-based study in Montreal, Canada into the 4 major lineages, and identified the associated clinical and epidemiologic features. In addition, IS6110-RFLP and spoligotyping were used as indicators of recent TB transmission. The study population was divided into a derivation cohort, diagnosed between 2001 and 2007, and a separate validation cohort, diagnosed between 1996 and 2000. RESULTS: In the derivation cohort, when compared to the other MTB lineages, the East African-Indian (EAI) lineage was associated with lower rates of TB transmission, as measured by: positive TST among close contacts of pulmonary TB cases (adjusted odds ratio 0.6: [95% confidence interval 0.4-0.9]), and clustered TB cases (0.3: [<0.001-0.6]). Severe forms of TB were also less likely among the EAI group (0.4: [<0.001-0.8]). There were no significant differences when comparing patients with the other MTB lineages. In the validation cohort, the EAI lineage was associated with lower rates of positive TST among contacts (0.5: [0.3-0.9]) and a trend towards less clustered TB cases (0.5: [0.1-1.8]) when compared to the other lineages. Disease severity among the different groups was not significantly different in the validation cohort. CONCLUSIONS: We conclude that in Montreal, EAI strains were associated with reduced transmission compared to other MTB lineages

Introduction to "Working Across Species"

Comparison between different animal species is omnipresent in the history of science and medicine but rarely subject to focussed historical analysis. The articles in the ‘‘Working Across Species’’ topical collection address this deficit by looking directly at the practical and epistemic work of cross-species comparison. Drawn from papers presented at a Wellcome-Trust-funded workshop in 2016, these papers investigate various ways that comparison has been made persuasive and successful, in multiple locations, by diverse disciplines, over the course of two centuries. They explore the many different animal features that have been considered to be (or else made) comparable, and the ways that animals have shaped science and medicine through the use of comparison. Authors demonstrate that comparison between species often transcended the range of practices typically employed with experimental animal models, where standardised practises and apparatus were applied to standardised bodies to produce generalizable, objective data; instead, comparison across species has often engaged diverse groups of nonstandard species, made use of subjective inferences about phenomena that cannot be directly observed, and inspired analogies that linked physiological and behavioural characteristics with the apparent affective state of non-human animals. Moreover, such comparative practices have also provided unusually fruitful opportunities for collaborative connections between different research traditions and disciplines

Origin of Polar Order in Dense Suspensions of Phototactic Micro-Swimmers

A main question for the study of collective motion in living organisms is the origin of orientational polar order, i.e., how organisms align and what are the benefits of such collective behaviour. In the case of micro-organisms swimming at a low Reynolds number, steric repulsion and long-range hydrodynamic interactions are not sufficient to explain a homogeneous polar order state in which the direction of motion is aligned. An external symmetry-breaking guiding field such as a mechanism of taxis appears necessary to understand this phonemonon. We have investigated the onset of polar order in the velocity field induced by phototaxis in a suspension of a motile micro-organism, the algae Chlamydomonas reinhardtii, for density values above the limit provided by the hydrodynamic approximation of a force dipole model. We show that polar order originates from a combination of both the external guiding field intensity and the population density. In particular, we show evidence for a linear dependence of a phototactic guiding field on cell density to determine the polar order for dense suspensions and demonstrate the existence of a density threshold for the origin of polar order. This threshold represents the density value below which cells undergoing phototaxis are not able to maintain a homogeneous polar order state and marks the transition to ordered collective motion. Such a transition is driven by a noise dominated phototactic reorientation where the noise is modelled as a normal distribution with a variance that is inversely proportional to the guiding field strength. Finally, we discuss the role of density in dense suspensions of phototactic micro-swimmers

Phase Synchronization of fluid-fluid interfaces as hydrodynamically coupled oscillators

Hydrodynamic interactions play a role in synchronized motions of coupled oscillators in fluids, and understanding the mechanism will facilitate development of applications in fluid mechanics. For example, synchronization phenomenon in two-phase flow will benefit the design of future microfluidic devices, allowing spatiotemporal control of microdroplet generation without additional integration of control elements. In this work, utilizing a characteristic oscillation of adjacent interfaces between two immiscible fluids in a microfluidic platform, we discover that the system can act as a coupled oscillator, notably showing spontaneous in-phase synchronization of droplet breakup. With this observation of in-phase synchronization, the coupled droplet generator exhibits a complete set of modes of coupled oscillators, including out-of-phase synchronization and nonsynchronous modes. We present a theoretical model to elucidate how a negative feedback mechanism, tied to the distance between the interfaces, induces the in-phase synchronization. We also identify the criterion for the transition from in-phase to out-of-phase oscillations

Efficiency of regional agriculture state support

The study analyzed data on state support for agricultural production in the Samara region. The regional level is the main source of budgetary funding for the agro-industrial complex. The Samara region is a pilot region in the research field into the results impact effectiveness of support measures on the agricultural organizations activities. The study purpose is to substantiate the need to improve state support in agriculture in the Samara region. It is necessary to solve the following tasks: to analyze the experience of state regulation in the Samara region agro-industrial complex; to classify the existing directions of state support for agriculture; to substantiate the need to correct the existing approach when improving state support for agricultural production. As a result of the consistent policy implementation in the field of agro-industrial complex supporting, agricultural production in the Samara region was able to become quite effective. The twofold excess of taxes in 2019 over the amount of support indicates that agricultural producers were able to switch to expanded reproduction using their resources. If the current situation persists in the long term, then the state role will be reduced to stimulating extremely promising directions for the region's agro-industrial complex development. © Published under licence by IOP Publishing Ltd