Prokaryotic viruses, which infect bacteria and archaea, are key players in microbial communities. Predicting the hosts of prokaryotic viruses helps decipher the dynamic relationship between microbes. Experimental methods for host prediction cannot keep pace with the fast accumulation of sequenced phages. Thus, there is a need for computational host prediction. Despite some promising results, computational host prediction remains a challenge because of the limited known interactions and the sheer amount of sequenced phages by high-throughput sequencing technologies. The state-of-the-art methods can only achieve 43\% accuracy at the species level. In this work, we formulate host prediction as link prediction in a knowledge graph that integrates multiple protein and DNA-based sequence features. Our implementation named CHERRY can be applied to predict hosts for newly discovered viruses and to identify viruses infecting targeted bacteria. We demonstrated the utility of CHERRY for both applications and compared its performance with 11 popular host prediction methods. To our best knowledge, CHERRY has the highest accuracy in identifying virus-prokaryote interactions. It outperforms all the existing methods at the species level with an accuracy increase of 37\%. In addition, CHERRY's performance on short contigs is more stable than other tools.

A new Bayesian modelling framework is introduced for piece-wise homogeneous variable-memory Markov chains, along with a collection of effective algorithmic tools for change-point detection and segmentation of discrete time series. Building on the recently introduced Bayesian Context Trees (BCT) framework, the distributions of different segments in a discrete time series are described as variable-memory Markov chains. Inference for the presence and location of change-points is then performed via Markov chain Monte Carlo sampling. The key observation that facilitates effective sampling is that, using one of the BCT algorithms, the prior predictive likelihood of the data can be computed exactly, integrating out all the models and parameters in each segment. This makes it possible to sample directly from the posterior distribution of the number and location of the change-points, leading to accurate estimates and providing a natural quantitative measure of uncertainty in the results. Estimates of the actual model in each segment can also be obtained, at essentially no additional computational cost. Results on both simulated and real-world data indicate that the proposed methodology performs better than or as well as state-of-the-art techniques.

Applied category theory has recently developed libraries for computing with morphisms in interesting categories, while machine learning has developed ways of learning programs in interesting languages. Taking the analogy between categories and languages seriously, this paper defines a probabilistic generative model of morphisms in free monoidal categories over domain-specific generating objects and morphisms. The paper shows how acyclic directed wiring diagrams can model specifications for morphisms, which the model can use to generate morphisms. Amortized variational inference in the generative model then enables learning of parameters (by maximum likelihood) and inference of latent variables (by Bayesian inversion). A concrete experiment shows that the free category prior achieves competitive reconstruction performance on the Omniglot dataset.

This paper studies the cooperative learning of two generative flow models, in which the two models are iteratively updated based on the jointly synthesized examples. The first flow model is a normalizing flow that transforms an initial simple density into a target density by applying a sequence of invertible transformations. The second flow model is a Langevin flow that runs finite steps of gradient-based MCMC toward an energy-based model. We start from proposing a generative framework that trains an energy-based model with a normalizing flow as an amortized sampler to initialize the MCMC chains of the energy-based model. In each learning iteration, we generate synthesized examples by using a normalizing flow initialization followed by a short-run Langevin flow revision toward the current energy-based model. Then we treat the synthesized examples as fair samples from the energy-based model and update the model parameters with the maximum likelihood learning gradient, while the normalizing flow directly learns from the synthesized examples by maximizing the tractable likelihood. Under the short-run non-mixing MCMC scenario, the estimation of the energy-based model is shown to follow the perturbation of maximum likelihood, and the short-run Langevin flow and the normalizing flow form a two-flow generator that we call CoopFlow. We provide an understating of the CoopFlow algorithm by information geometry and show that it is a valid generator as it converges to a moment matching estimator. We demonstrate that the trained CoopFlow is capable of synthesizing realistic images, reconstructing images, and interpolating between images. Normalizing flows (Dinh et al., 2015; 2017; Kingma & Dhariwal, 2018) are a family of generative models that construct a complex distribution by transforming a simple probability density, such as Gaussian distribution, through a sequence of invertible and differentiable mappings. Due to the tractability of the exact log-likelihood and the efficiency of the inference and synthesis, normalizing flows have gained popularity in density estimation (Kingma & Dhariwal, 2018; Ho et al., 2019; Yang et al., 2019; Prenger et al., 2019; Kumar et al., 2020) and variational inference (Rezende & Mohamed, 2015; Kingma et al., 2016).

Observational studies are regarded as economic alternatives to randomized trials, often used in their stead to investigate and determine treatment efficacy. Due to lack of sample size, observational studies commonly combine data from multiple sources or different sites/centers. Despite the benefits of an increased sample size, a naïve combination of multicenter data may result in incongruities stemming from center-specific protocols for generating cohorts or reactions towards treatments distinct to a given center, among other things. These issues arise in a variety of other contexts, including capturing a treatment effect related to an individual's unique biological characteristics. Existing methods for estimating heterogeneous treatment effects have not adequately addressed the multicenter context, but rather treat it simply as a means to obtain sufficient sample size. Additionally, previous approaches to estimating treatment effects do not straightforwardly generalize to the multicenter design, especially when required to provide treatment insights for patients from a new, unobserved center. To address these shortcomings, we propose Multiple Domain Causal Networks (MDCN), an approach that simultaneously strengthens the information sharing between similar centers while addressing the selection bias in treatment assignment through learning of a new feature embedding. In empirical evaluations, MDCN is consistently more accurate when estimating the heterogeneous treatment effect in new centers compared to benchmarks that adjust solely based on treatment imbalance or general center differences. Finally, we justify our approach by providing theoretical analyses that demonstrate that MDCN improves on the generalization bound of the new, unobserved target center.

Due to the latest advances in technology, telescopes with significant sky coverage will produce millions of astronomical alerts per night that must be classified both rapidly and automatically. Currently, classification consists of supervised machine learning algorithms whose performance is limited by the number of existing annotations of astronomical objects and their highly imbalanced class distributions. In this work, we propose a data augmentation methodology based on Generative Adversarial Networks (GANs) to generate a variety of synthetic light curves from variable stars. Our novel contributions, consisting of a resampling technique and an evaluation metric, can assess the quality of generative models in unbalanced datasets and identify GAN-overfitting cases that the Fr\'echet Inception Distance does not reveal. We applied our proposed model to two datasets taken from the Catalina and Zwicky Transient Facility surveys. The classification accuracy of variable stars is improved significantly when training with synthetic data and testing with real data with respect to the case of using only real data.

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For years, tech companies have relied on something called the Fitzpatrick scale to classify skin tones for their computer vision algorithms. Originally designed for dermatologists in the 1970s, the system comprises only six skin tones, a possible contributor to AI's well-documented failures in identifying people of color. Now Google is beginning to incorporate a 10-skin tone standard across its products, called the Monk Skin Tone (MST) scale, from Google Search Images to Google Photos and beyond. The development has the potential to reduce bias in data sets used to train AI in everything from health care to content moderation. Google first signaled plans to go beyond the Fitzpatrick scale last year; internally, the project dates back to a summer 2020 effort to make AI "work better for people of color," according to a Twitter thread from Xango Eyeé, a responsible AI product manager at the company.

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Counterfactual explanations (CFEs) highlight what changes to a model's input would have changed its prediction in a particular way. CFEs have gained considerable traction as a psychologically grounded solution for explainable artificial intelligence (XAI). Recent innovations introduce the notion of computational plausibility for automatically generated CFEs, enhancing their robustness by exclusively creating plausible explanations. However, practical benefits of such a constraint on user experience and behavior is yet unclear. In this study, we evaluate objective and subjective usability of computationally plausible CFEs in an iterative learning design targeting novice users. We rely on a novel, game-like experimental design, revolving around an abstract scenario. Our results show that novice users actually benefit less from receiving computationally plausible rather than closest CFEs that produce minimal changes leading to the desired outcome. Responses in a post-game survey reveal no differences in terms of subjective user experience between both groups. Following the view of psychological plausibility as comparative similarity, this may be explained by the fact that users in the closest condition experience their CFEs as more psychologically plausible than the computationally plausible counterpart. In sum, our work highlights a little-considered divergence of definitions of computational plausibility and psychological plausibility, critically confirming the need to incorporate human behavior, preferences and mental models already at the design stages of XAI approaches. In the interest of reproducible research, all source code, acquired user data, and evaluation scripts of the current study are available: https://github.com/ukuhl/PlausibleAlienZoo