A neural network (cf. Figure 1) can be thought of as a directed acyclic network consisting of

The high-level question in this work is: If we learn a task using a sufficiently deep NN, how can we uncover the underlying hierarchical organization of sub-functions in that task?

This study investigates the limitations of applying Markov Chain Monte Carlo (MCMC) methods to arbitrary objective functions, focusing on a two-block MCMC framework which alternates between Metropolis-Hastings and Gibbs sampling. While such approaches are often considered advantageous for enabling data-driven regularization, we show that their performance critically depends on the sharpness of the employed likelihood form. By introducing a sharpness parameter and exploring alternative likelihood formulations proportional to the target objective function, we demonstrate how likelihood curvature governs both in-sample performance and the degree of regularization inferred by the training data. Empirical applications are conducted on reinforcement learning tasks: including a navigation problem and the game of tic-tac-toe. The study concludes with a separate analysis examining the implications of extreme likelihood sharpness on arbitrary objective functions stemming from the classic game of blackjack, where the first block of the two-block MCMC framework is replaced with an iterative optimization step. The resulting hybrid approach achieves performance nearly identical to the original MCMC framework, indicating that excessive likelihood sharpness effectively collapses posterior mass onto a single dominant mode.

Cellular reprogramming, the artificial transformation of one cell type into another, has been attracting increasing research attention due to its therapeutic potential for complex diseases. However, identifying effective reprogramming strategies through classical wet-lab experiments is hindered by lengthy time commitments and high costs. In this study, we explore the use of deep reinforcement learning (DRL) to control Boolean network models of complex biological systems, such as gene regulatory and signalling pathway networks. We formulate a novel control problem for Boolean network models under the asynchronous update mode, specifically in the context of cellular reprogramming. To solve it, we devise GATTACA, a scalable computational framework. To facilitate scalability of our framework, we consider previously introduced concept of a pseudo-attractor and improve the procedure for effective identification of pseudo-attractor states. We then incorporate graph neural networks with graph convolution operations into the artificial neural network approximator of the DRL agent's action-value function. This allows us to leverage the available knowledge on the structure of a biological system and to indirectly, yet effectively, encode the system's modelled dynamics into a latent representation. Experiments on several large-scale, real-world biological networks from the literature demonstrate the scalability and effectiveness of our approach.

A neural network (cf. Figure 1) can be thought of as a directed acyclic network consisting of

Probabilistic Circuits (PCs) offer a computationally scalable framework for generative modeling, supporting exact and efficient inference of a wide range of probabilistic queries. While recent advances have significantly improved the expressiveness and scalability of PCs, effectively training their parameters remains a challenge. In particular, a widely used optimization method, full-batch Expectation-Maximization (EM), requires processing the entire dataset before performing a single update, making it ineffective for large datasets. Although empirical extensions to the mini-batch setting, as well as gradient-based mini-batch algorithms, converge faster than full-batch EM, they generally underperform in terms of final likelihood. We investigate this gap by establishing a novel theoretical connection between these practical algorithms and the general EM objective. Our analysis reveals a fundamental issue that existing mini-batch EM and gradient-based methods fail to properly regularize distribution changes, causing each update to effectively ``overfit'' the current mini-batch. Motivated by this insight, we introduce anemone, a new mini-batch EM algorithm for PCs. Anemone applies an implicit adaptive learning rate to each parameter, scaled by how much it contributes to the likelihood of the current batch. Across extensive experiments on language, image, and DNA datasets, anemone consistently outperforms existing optimizers in both convergence speed and final performance.

Thanks for the comments and we will reorganize the paper according to your suggestions. R1 may think NA T as a NAS method. How to get skip connections in VGG? Then, NA T can add skip connections into VGG by replacing the null connections (see more discussions in Section 4.5). Why the generated networks have two inputs "-2" and "-1": "-1" represent the outputs of the second nearest and the most nearest cell in front of the current one, respectively.