Daily Papers

The coronavirus disease (COVID-19) has resulted in a pandemic crippling the a breadth of services critical to daily life. Segmentation of lung infections in computerized tomography (CT) slices could be be used to improve diagnosis and understanding of COVID-19 in patients. Deep learning systems lack interpretability because of their black box nature. Inspired by human communication of complex ideas through language, we propose a symbolic framework based on emergent languages for the segmentation of COVID-19 infections in CT scans of lungs. We model the cooperation between two artificial agents - a Sender and a Receiver. These agents synergistically cooperate using emergent symbolic language to solve the task of semantic segmentation. Our game theoretic approach is to model the cooperation between agents unlike Generative Adversarial Networks (GANs). The Sender retrieves information from one of the higher layers of the deep network and generates a symbolic sentence sampled from a categorical distribution of vocabularies. The Receiver ingests the stream of symbols and cogenerates the segmentation mask. A private emergent language is developed that forms the communication channel used to describe the task of segmentation of COVID infections. We augment existing state of the art semantic segmentation architectures with our symbolic generator to form symbolic segmentation models. Our symbolic segmentation framework achieves state of the art performance for segmentation of lung infections caused by COVID-19. Our results show direct interpretation of symbolic sentences to discriminate between normal and infected regions, infection morphology and image characteristics. We show state of the art results for segmentation of COVID-19 lung infections in CT.

The Universal Morphology (UniMorph) project is a collaborative effort providing broad-coverage instantiated normalized morphological inflection tables for hundreds of diverse world languages. The project comprises two major thrusts: a language-independent feature schema for rich morphological annotation and a type-level resource of annotated data in diverse languages realizing that schema. This paper presents the expansions and improvements made on several fronts over the last couple of years (since McCarthy et al. (2020)). Collaborative efforts by numerous linguists have added 67 new languages, including 30 endangered languages. We have implemented several improvements to the extraction pipeline to tackle some issues, e.g. missing gender and macron information. We have also amended the schema to use a hierarchical structure that is needed for morphological phenomena like multiple-argument agreement and case stacking, while adding some missing morphological features to make the schema more inclusive. In light of the last UniMorph release, we also augmented the database with morpheme segmentation for 16 languages. Lastly, this new release makes a push towards inclusion of derivational morphology in UniMorph by enriching the data and annotation schema with instances representing derivational processes from MorphyNet.

Measuring the morphological parameters of galaxies is a key requirement for studying their formation and evolution. Surveys such as the Sloan Digital Sky Survey (SDSS) have resulted in the availability of very large collections of images, which have permitted population-wide analyses of galaxy morphology. Morphological analysis has traditionally been carried out mostly via visual inspection by trained experts, which is time-consuming and does not scale to large (gtrsim10^4) numbers of images. Although attempts have been made to build automated classification systems, these have not been able to achieve the desired level of accuracy. The Galaxy Zoo project successfully applied a crowdsourcing strategy, inviting online users to classify images by answering a series of questions. Unfortunately, even this approach does not scale well enough to keep up with the increasing availability of galaxy images. We present a deep neural network model for galaxy morphology classification which exploits translational and rotational symmetry. It was developed in the context of the Galaxy Challenge, an international competition to build the best model for morphology classification based on annotated images from the Galaxy Zoo project. For images with high agreement among the Galaxy Zoo participants, our model is able to reproduce their consensus with near-perfect accuracy (> 99%) for most questions. Confident model predictions are highly accurate, which makes the model suitable for filtering large collections of images and forwarding challenging images to experts for manual annotation. This approach greatly reduces the experts' workload without affecting accuracy. The application of these algorithms to larger sets of training data will be critical for analysing results from future surveys such as the LSST.

A compartmental deterministic model that allows (1) immunity from two stages of infection and carriage, and (2) disease induced death, is used in studying the dynamics of meningitis epidemic process in a closed population. It allows for difference in the transmission rate of infection to a susceptible by a carrier and an infective. It is generalized to allow a proportion ({\phi}) of those susceptibles infected to progress directly to infectives in stage I. Both models are used in this study. The threshold conditions for the spread of carrier and infectives in stage I are derived for the two models. Sensitivity analysis is performed on the reproductive number derived from the next generation matrix. The case-carrier ratio profile for various parameters and threshold values are shown. So also are the graphs of the total number ever infected as influenced by {\epsilon} and {\phi}. The infection transmission rate (eta), the odds in favor of a carrier, over an infective, in transmitting an infection to a susceptible ({\epsilon}) and the carrier conversion rate ({\phi}) to an infective in stage I, are identified as key parameters that should be subject of attention for any control intervention strategy. The case-carrier ratio profiles provide evidence of a critical case-carrier ratio attained before the number of reported cases grows to an epidemic level. They also provide visual evidence of epidemiological context, in this case, epidemic incidence (in later part of dry season) and endemic incidence (during rainy season). Results from total proportion ever infected suggest that the model, in which {\phi}=0 obtained, can adequately represent, in essence, the generalized model for this study.

We present Galaxy Zoo DECaLS: detailed visual morphological classifications for Dark Energy Camera Legacy Survey images of galaxies within the SDSS DR8 footprint. Deeper DECaLS images (r=23.6 vs. r=22.2 from SDSS) reveal spiral arms, weak bars, and tidal features not previously visible in SDSS imaging. To best exploit the greater depth of DECaLS images, volunteers select from a new set of answers designed to improve our sensitivity to mergers and bars. Galaxy Zoo volunteers provide 7.5 million individual classifications over 314,000 galaxies. 140,000 galaxies receive at least 30 classifications, sufficient to accurately measure detailed morphology like bars, and the remainder receive approximately 5. All classifications are used to train an ensemble of Bayesian convolutional neural networks (a state-of-the-art deep learning method) to predict posteriors for the detailed morphology of all 314,000 galaxies. When measured against confident volunteer classifications, the networks are approximately 99% accurate on every question. Morphology is a fundamental feature of every galaxy; our human and machine classifications are an accurate and detailed resource for understanding how galaxies evolve.

Image-based or morphological profiling is a rapidly expanding field wherein cells are "profiled" by extracting hundreds to thousands of unbiased, quantitative features from images of cells that have been perturbed by genetic or chemical perturbations. The Cell Painting assay is the most popular imaged-based profiling assay wherein six small-molecule dyes label eight cellular compartments and thousands of measurements are made, describing quantitative traits such as size, shape, intensity, and texture within the nucleus, cytoplasm, and whole cell (Cimini et al., 2023). We have created the Cell Painting Gallery, a publicly available collection of Cell Painting datasets, with granular dataset descriptions and access instructions. It is hosted by AWS on the Registry of Open Data (RODA). As of January 2024, the Cell Painting Gallery holds 656 terabytes (TB) of image and associated numerical data. It includes the largest publicly available Cell Painting dataset, in terms of perturbations tested (Joint Undertaking for Morphological Profiling or JUMP (Chandrasekaran et al., 2023)), along with many other canonical datasets using Cell Painting, close derivatives of Cell Painting (such as LipocyteProfiler (Laber et al., 2023) and Pooled Cell Painting (Ramezani et al., 2023)).

The galaxy population is strongly bimodal in both colour and morphology, and the two measures correlate strongly, with most blue galaxies being late-types (spirals) and most early-types, typically ellipticals, being red. This observation has led to the use of colour as a convenient selection criteria to make samples which are then labelled by morphology. Such use of colour as a proxy for morphology results in necessarily impure and incomplete samples. In this paper, we make use of the morphological labels produced by Galaxy Zoo to measure how incomplete and impure such samples are, considering optical (ugriz), NUV and NIR (JHK) bands. The best single colour optical selection is found using a threshold of g-r = 0.742, but this still results in a sample where only 56% of red galaxies are smooth and 56% of smooth galaxies are red. Use of the NUV gives some improvement over purely optical bands, particularly for late-types, but still results in low purity/completeness for early-types. No significant improvement is found by adding NIR bands. With any two bands, including NUV, a sample of early-types with greater than two-thirds purity cannot be constructed. Advances in quantitative galaxy morphologies have made colour-morphology proxy selections largely unnecessary going forward; where such assumptions are still required, we recommend studies carefully consider the implications of sample incompleteness/impurity.

Pathogen identification is pivotal in diagnosing, treating, and preventing diseases, crucial for controlling infections and safeguarding public health. Traditional alignment-based methods, though widely used, are computationally intense and reliant on extensive reference databases, often failing to detect novel pathogens due to their low sensitivity and specificity. Similarly, conventional machine learning techniques, while promising, require large annotated datasets and extensive feature engineering and are prone to overfitting. Addressing these challenges, we introduce PathoLM, a cutting-edge pathogen language model optimized for the identification of pathogenicity in bacterial and viral sequences. Leveraging the strengths of pre-trained DNA models such as the Nucleotide Transformer, PathoLM requires minimal data for fine-tuning, thereby enhancing pathogen detection capabilities. It effectively captures a broader genomic context, significantly improving the identification of novel and divergent pathogens. We developed a comprehensive data set comprising approximately 30 species of viruses and bacteria, including ESKAPEE pathogens, seven notably virulent bacterial strains resistant to antibiotics. Additionally, we curated a species classification dataset centered specifically on the ESKAPEE group. In comparative assessments, PathoLM dramatically outperforms existing models like DciPatho, demonstrating robust zero-shot and few-shot capabilities. Furthermore, we expanded PathoLM-Sp for ESKAPEE species classification, where it showed superior performance compared to other advanced deep learning methods, despite the complexities of the task.