Time-varying linear state-space models are powerful tools for obtaining mathematically interpretable representations of neural signals. For example, switching and decomposed models describe complex systems using latent variables that evolve according to simple locally linear dynamics. However, existing methods for latent variable estimation are not robust to dynamical noise and system nonlinearity due to noise-sensitive inference procedures and limited model formulations. This can lead to inconsistent results on signals with similar dynamics, limiting the model's ability to provide scientific insight. In this work, we address these limitations and propose a probabilistic approach to latent variable estimation in decomposed models that improves robustness against dynamical noise. Additionally, we introduce an extended latent dynamics model to improve robustness against system nonlinearities. We evaluate our approach on several synthetic dynamical systems, including an empirically-derived brain-computer interface experiment, and demonstrate more accurate latent variable inference in nonlinear systems with diverse noise conditions. Furthermore, we apply our method to a real-world clinical neurophysiology dataset, illustrating the ability to identify interpretable and coherent structure where previous models cannot.

Breast cancer is one of the two cancers responsible for the most deaths in women, with about 42,000 deaths each year in the US. That there are over 300,000 breast cancers newly diagnosed each year suggests that only a fraction of the cancers result in mortality. Thus, most of the women undergo seemingly curative treatment for localized cancers, but a significant later succumb to metastatic disease for which current treatments are only temporizing for the vast majority. The current prognostic metrics are of little actionable value for 4 of the 5 women seemingly cured after local treatment, and many women are exposed to morbid and even mortal adjuvant therapies unnecessarily, with these adjuvant therapies reducing metastatic recurrence by only a third. Thus, there is a need for better prognostics to target aggressive treatment at those who are likely to relapse and spare those who were actually cured. While there is a plethora of molecular and tumor-marker assays in use and under-development to detect recurrence early, these are time consuming, expensive and still often un-validated as to actionable prognostic utility. A different approach would use large data techniques to determine clinical and histopathological parameters that would provide accurate prognostics using existing data. Herein, we report on machine learning, together with grid search and Bayesian Networks to develop algorithms that present a AUC of up to 0.9 in ROC analyses, using only extant data. Such algorithms could be rapidly translated to clinical management as they do not require testing beyond routine tumor evaluations.

Variational continual learning (VCL) is a turn-key learning algorithm that has state-of-the-art performance among the best continual learning models. In our work, we explore an extension of the generalized variational continual learning (GVCL) model, named AutoVCL, which combines task heuristics for informed learning and model optimization. We demonstrate that our model outperforms the standard GVCL with fixed hyperparameters, benefiting from the automatic adjustment of the hyperparameter based on the difficulty and similarity of the incoming task compared to the previous tasks.

Learning a transition model via Maximum Likelihood Estimation (MLE) followed by planning inside the learned model is perhaps the most standard and simplest Model-based Reinforcement Learning (RL) framework. In this work, we show that such a simple Model-based RL scheme, when equipped with optimistic and pessimistic planning procedures, achieves strong regret and sample complexity bounds in online and offline RL settings. Particularly, we demonstrate that under the conditions where the trajectory-wise reward is normalized between zero and one and the transition is time-homogenous, it achieves horizon-free and second-order bounds. Horizon-free means that our bounds have no polynomial dependence on the horizon of the Markov Decision Process. A second-order bound is a type of instance-dependent bound that scales with respect to the variances of the returns of the policies which can be small when the system is nearly deterministic and (or) the optimal policy has small values. We highlight that our algorithms are simple, fairly standard, and indeed have been extensively studied in the RL literature: they learn a model via MLE, build a version space around the MLE solution, and perform optimistic or pessimistic planning depending on whether operating in the online or offline mode. These algorithms do not rely on additional specialized algorithmic designs such as learning variances and performing variance-weighted learning and thus can leverage rich function approximations that are significantly beyond linear or tabular structures. The simplicity of the algorithms also implies that our horizon-free and second-order regret analysis is actually standard and mainly follows the general framework of optimism/pessimism in the face of uncertainty.

Neural Networks (NNs) are promising models for refining the accuracy of molecular dynamics, potentially opening up new fields of application. Typically trained bottom-up, atomistic NN potential models can reach first-principle accuracy, while coarse-grained implicit solvent NN potentials surpass classical continuum solvent models. However, overcoming the limitations of costly generation of accurate reference data and data inefficiency of common bottom-up training demands efficient incorporation of data from many sources. This paper introduces the framework chemtrain to learn sophisticated NN potential models through customizable training routines and advanced training algorithms. These routines can combine multiple top-down and bottom-up algorithms, e.g., to incorporate both experimental and simulation data or pre-train potentials with less costly algorithms. chemtrain provides an object-oriented high-level interface to simplify the creation of custom routines. On the lower level, chemtrain relies on JAX to compute gradients and scale the computations to use available resources. We demonstrate the simplicity and importance of combining multiple algorithms in the examples of parametrizing an all-atomistic model of titanium and a coarse-grained implicit solvent model of alanine dipeptide.

Generative Flow Networks (GFlowNets) are a class of generative models that sample objects in proportion to a specified reward function through a learned policy. They can be trained either on-policy or off-policy, needing a balance between exploration and exploitation for fast convergence to a target distribution. While exploration strategies for discrete GFlowNets have been studied, exploration in the continuous case remains to be investigated, despite the potential for novel exploration algorithms due to the local connectedness of continuous domains. Here, we introduce Adapted Metadynamics, a variant of metadynamics that can be applied to arbitrary black-box reward functions on continuous domains. We use Adapted Metadynamics as an exploration strategy for continuous GFlowNets. We show three continuous domains where the resulting algorithm, MetaGFN, accelerates convergence to the target distribution and discovers more distant reward modes than previous off-policy exploration strategies used for GFlowNets.

The optimization of atomic structures plays a pivotal role in understanding and designing materials with desired properties. However, conventional methods often struggle with the formidable task of navigating the vast potential energy surface, especially in high-dimensional spaces with numerous local minima. Recent advancements in machine learning-driven surrogate models offer a promising avenue for alleviating this computational burden. In this study, we propose a novel approach that combines the strengths of universal machine learning potentials with a Bayesian approach of the GOFEE/BEACON framework. By leveraging the comprehensive chemical knowledge encoded in pretrained universal machine learning potentials as a prior estimate of energy and forces, we enable the Gaussian process to focus solely on capturing the intricate nuances of the potential energy surface. We demonstrate the efficacy of our approach through comparative analyses across diverse systems, including periodic bulk materials, surface structures, and a cluster.

In this paper, we investigate the use of probabilistic graphical models, specifically stochastic blockmodels, for the purpose of hierarchical entity clustering on knowledge graphs. These models, seldom used in the Semantic Web community, decompose a graph into a set of probability distributions. The parameters of these distributions are then inferred allowing for their subsequent sampling to generate a random graph. In a non-parametric setting, this allows for the induction of hierarchical clusterings without prior constraints on the hierarchy's structure. Specifically, this is achieved by the integration of the Nested Chinese Restaurant Process and the Stick Breaking Process into the generative model. In this regard, we propose a model leveraging such integration and derive a collapsed Gibbs sampling scheme for its inference. To aid in understanding, we describe the steps in this derivation and provide an implementation for the sampler. We evaluate our model on synthetic and real-world datasets and quantitatively compare against benchmark models. We further evaluate our results qualitatively and find that our model is capable of inducing coherent cluster hierarchies in small scale settings. The work presented in this paper provides the first step for the further application of stochastic blockmodels for knowledge graphs on a larger scale. We conclude the paper with potential avenues for future work on more scalable inference schemes.

Generative Bayesian Computation (GBC) methods are developed to provide an efficient computational solution for maximum expected utility (MEU). We propose a density-free generative method based on quantiles that naturally calculates expected utility as a marginal of quantiles. Our approach uses a deep quantile neural estimator to directly estimate distributional utilities. Generative methods assume only the ability to simulate from the model and parameters and as such are likelihood-free. A large training dataset is generated from parameters and output together with a base distribution. Our method a number of computational advantages primarily being density-free with an efficient estimator of expected utility. A link with the dual theory of expected utility and risk taking is also discussed. To illustrate our methodology, we solve an optimal portfolio allocation problem with Bayesian learning and a power utility (a.k.a. fractional Kelly criterion). Finally, we conclude with directions for future research.

The detection of cyber-attacks in computer networks is a crucial and ongoing research challenge. Machine learning-based attack classification offers a promising solution, as these models can be continuously updated with new data, enhancing the effectiveness of network intrusion detection systems (NIDS). Unlike binary classification models that simply indicate the presence of an attack, multi-class models can identify specific types of attacks, allowing for more targeted and effective incident responses. However, a significant drawback of these classification models is their sensitivity to imbalanced training data. Recent advances suggest that generative models can assist in data augmentation, claiming to offer superior solutions for imbalanced datasets. Classical balancing methods, although less novel, also provide potential remedies for this issue. Despite these claims, a comprehensive comparison of these methods within the NIDS domain is lacking. Most existing studies focus narrowly on individual methods, making it difficult to compare results due to varying experimental setups. To close this gap, we designed a systematic framework to compare classical and generative resampling methods for class balancing across multiple popular classification models in the NIDS domain, evaluated on several NIDS benchmark datasets. Our experiments indicate that resampling methods for balancing training data do not reliably improve classification performance. Although some instances show performance improvements, the majority of results indicate decreased performance, with no consistent trend in favor of a specific resampling technique enhancing a particular classifier.