RNAs play crucial and versatile roles in biological processes. Computational prediction approaches can help to understand RNA structures and their stabilizing factors, thus providing information on their functions, and facilitating the design of new RNAs. Machine learning (ML) techniques have made tremendous progress in many fields in the past few years. Although their usage in protein-related fields has a long history, the use of ML methods in predicting RNA tertiary structures is new and rare. Here, we review the recent advances of using ML methods on RNA structure predictions and discuss the advantages and limitation, the difficulties and potentials of these approaches when applied in the field. Introduction RNAs are macromolecules of crucial and versatile biological functions. To fully understand their functions, knowledge of the three-dimensional (3D) structures is essential. Since experimental approaches to determinate RNA 3D structures are difficult and expensive, many computational approaches have been developed to this purpose. To date, although template-based and homology-modeling methods could achieve high accuracies, de novo predictions still depends on the size and complexity of the RNA, and further improvement in predicting non-canonical interactions are required, according to the recent RNA-Puzzles round III. For a comprehensive study of the recent work, we refer readers to the relevant literature.

We introduce a unified objective for action and perception of intelligent agents. Extending representation learning and control, we minimize the joint divergence between the world and a target distribution. Intuitively, such agents use perception to align their beliefs with the world, and use actions to align the world with their beliefs. Minimizing the joint divergence to an expressive target maximizes the mutual information between the agent's representations and inputs, thus inferring representations that are informative of past inputs and exploring future inputs that are informative of the representations. This lets us derive intrinsic objectives, such as representation learning, information gain, empowerment, and skill discovery from minimal assumptions. Moreover, interpreting the target distribution as a latent variable model suggests expressive world models as a path toward highly adaptive agents that seek large niches in their environments, while rendering task rewards optional. The presented framework provides a common language for comparing a wide range of objectives, facilitates understanding of latent variables for decision making, and offers a recipe for designing novel objectives. We recommend deriving future agent objectives from the joint divergence to facilitate comparison, to point out the agent's target distribution, and to identify the intrinsic objective terms needed to reach that distribution.

We consider the problem of fitting variational posterior approximations using stochastic optimization methods. The performance of these approximations depends on (1) how well the variational family matches the true posterior distribution, (2) the choice of divergence, and (3) the optimization of the variational objective. We show that even in the best-case scenario when the exact posterior belongs to the assumed variational family, common stochastic optimization methods lead to poor variational approximations if the problem dimension is moderately large. We also demonstrate that these methods are not robust across diverse model types. Motivated by these findings, we develop a more robust and accurate stochastic optimization framework by viewing the underlying optimization algorithm as producing a Markov chain. Our approach is theoretically motivated and includes a diagnostic for convergence and a novel stopping rule, both of which are robust to noisy evaluations of the objective function. We show empirically that the proposed framework works well on a diverse set of models: it can automatically detect stochastic optimization failure or inaccurate variational approximation.

Along with the analysis of time-to-event data, it is common to assume that only partial information is given at hand. In the presence of right-censored data with covariates, the conditional Kaplan-Meier estimator (also referred as the Beran estimator) is known to propose a consistent estimate for the lifetimes conditional survival function. However, a necessary condition is the clear knowledge of whether each individual is censored or not, although, this information might be incomplete or even totally absent in practice. We thus propose a study on the Beran estimator when the censoring indicator is not clearly specified. From this, we provide a new estimator for the conditional survival function and establish its asymptotic normality under mild conditions. We further study the supervised learning problem where the conditional survival function is to be predicted with no censorship indicators. To this aim, we investigate various approaches estimating the conditional expectation for the censoring indicator. Along with the theoretical results, we illustrate how the estimators work for small samples by means of a simulation study and show their practical applicability with the analysis of synthetic data and the study of real data for the prognosis of monoclonal gammopathy.

Learning classifier systems (LCSs) are population-based predictive systems that were originally envisioned as agents to act in reinforcement learning (RL) environments. These systems can suffer from population bloat and so are amenable to compaction techniques that try to strike a balance between population size and performance. A well-studied LCS architecture is XCSF, which in the RL setting acts as a Q-function approximator. We apply XCSF to a deterministic and stochastic variant of the FrozenLake8x8 environment from OpenAI Gym, with its performance compared in terms of function approximation error and policy accuracy to the optimal Q-functions and policies produced by solving the environments via dynamic programming. We then introduce a novel compaction algorithm (Greedy Niche Mass Compaction - GNMC) and study its operation on XCSF's trained populations. Results show that given a suitable parametrisation, GNMC preserves or even slightly improves function approximation error while yielding a significant reduction in population size. Reasonable preservation of policy accuracy also occurs, and we link this metric to the commonly used steps-to-goal metric in maze-like environments, illustrating how the metrics are complementary rather than competitive.

Probabilistic circuits (PCs) represent a probability distribution as a computational graph. Enforcing structural properties on these graphs guarantees that several inference scenarios become tractable. Among these properties, structured decomposability is a particularly appealing one: it enables the efficient and exact computations of the probability of complex logical formulas, and can be used to reason about the expected output of certain predictive models under missing data. This paper proposes Strudel, a simple, fast and accurate learning algorithm for structured-decomposable PCs. Compared to prior work for learning structured-decomposable PCs, Strudel delivers more accurate single PC models in fewer iterations, and dramatically scales learning when building ensembles of PCs. It achieves this scalability by exploiting another structural property of PCs, called determinism, and by sharing the same computational graph across mixture components. We show these advantages on standard density estimation benchmarks and challenging inference scenarios. Keywords: Probabilistic circuits; structure learning; structured decomposability.

Clustering techniques have been proved highly suc-cessful for Takagi-Sugeno (T-S) fuzzy model identification. Inparticular, fuzzyc-regression clustering based on type-2 fuzzyset has been shown the remarkable results on non-sparse databut their performance degraded on sparse data. In this paper, aninnovative architecture for fuzzyc-regression model is presentedand a novel student-tdistribution based membership functionis designed for sparse data modelling. To avoid the overfitting,we have adopted a Bayesian approach for incorporating aGaussian prior on the regression coefficients. Additional noveltyof our approach lies in type-reduction where the final output iscomputed using Karnik Mendel algorithm and the consequentparameters of the model are optimized using Stochastic GradientDescent method. As detailed experimentation, the result showsthat proposed approach outperforms on standard datasets incomparison of various state-of-the-art methods.

In this work we take a Category Theoretic perspective on the relationship between probabilistic modeling and function approximation. We begin by defining two extensions of function composition to stochastic process subordination: one based on the co-Kleisli category under the comonad (Omega x -) and one based on the parameterization of a category with a Lawvere theory. We show how these extensions relate to the category Stoch and other Markov Categories. Next, we apply the Para construction to extend stochastic processes to parameterized statistical models and we define a way to compose the likelihood functions of these models. We conclude with a demonstration of how the Maximum Likelihood Estimation procedure defines an identity-on-objects functor from the category of statistical models to the category of Learners. Code to accompany this paper can be found at https://github.com/dshieble/Categorical_Stochastic_Processes_and_Likelihood

We introduce a non-parametric hierarchical Bayesian approach for open-ended 3D object categorization, named the Local Hierarchical Dirichlet Process (Local-HDP). This method allows an agent to learn independent topics for each category incrementally and to adapt to the environment in time. Hierarchical Bayesian approaches like Latent Dirichlet Allocation (LDA) can transform low-level features to high-level conceptual topics for 3D object categorization. However, the efficiency and accuracy of LDA-based approaches depend on the number of topics that is chosen manually. Moreover, fixing the number of topics for all categories can lead to overfitting or underfitting of the model. In contrast, the proposed Local-HDP can autonomously determine the number of topics for each category. Furthermore, an inference method is proposed that results in a fast posterior approximation. Experiments show that Local-HDP outperforms other state-of-the-art approaches in terms of accuracy, scalability, and memory efficiency with a large margin.

Out-of-training-distribution (OOD) scenarios are a common challenge of learning agents at deployment, typically leading to arbitrary deductions and poorly-informed decisions. In principle, detection of and adaptation to OOD scenes can mitigate their adverse effects. In this paper, we highlight the limitations of current approaches to novel driving scenes and propose an epistemic uncertainty-aware planning method, called \emph{robust imitative planning} (RIP). Our method can detect and recover from some distribution shifts, reducing the overconfident and catastrophic extrapolations in OOD scenes. If the model's uncertainty is too great to suggest a safe course of action, the model can instead query the expert driver for feedback, enabling sample-efficient online adaptation, a variant of our method we term \emph{adaptive robust imitative planning} (AdaRIP). Our methods outperform current state-of-the-art approaches in the nuScenes \emph{prediction} challenge, but since no benchmark evaluating OOD detection and adaption currently exists to assess \emph{control}, we introduce an autonomous car novel-scene benchmark, \texttt{CARNOVEL}, to evaluate the robustness of driving agents to a suite of tasks with distribution shifts.