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Efficient sampling of the Boltzmann distribution of molecular systems is a long-standing challenge. Recently, instead of generating long molecular dynamics simulations, generative machine learning methods such as normalizing flows have been used to learn the Boltzmann distribution directly, without samples. However, this approach is susceptible to mode collapse and thus often does not explore the full configurational space. In this work, we address this challenge by separating the problem into two levels, the fine-grained and coarse-grained degrees of freedom. A normalizing flow conditioned on the coarse-grained space yields a probabilistic connection between the two levels. To explore the configurational space, we employ coarse-grained simulations with active learning which allows us to update the flow and make all-atom potential energy evaluations only when necessary. Using alanine dipeptide as an example, we show that our methods obtain a speedup to molecular dynamics simulations of approximately 15.9 to 216.2 compared to the speedup of 4.5 of the current state-of-the-art machine learning approach.

Accurate, detailed, and high-frequent bathymetry, coupled with complex semantic content, is crucial for the undermapped shallow seabed areas facing intense climatological and anthropogenic pressures. Current methods exploiting remote sensing images to derive bathymetry or seabed classes mainly exploit non-open data. This lack of openly accessible benchmark archives prevents the wider use of deep learning methods in such applications. To address this issue, in this paper we present the MagicBathyNet, which is a benchmark dataset made up of image patches of Sentinel2, SPOT-6 and aerial imagery, bathymetry in raster format and annotations of seabed classes. MagicBathyNet is then exploited to benchmark state-of-the-art methods in learning-based bathymetry and pixel-based classification. Dataset, pre-trained weights, and code are publicly available at www.magicbathy.eu/magicbathynet.html.

Go-Explore is a powerful family of algorithms designed to solve hard-exploration problems, built on the principle of archiving discovered states, and iteratively returning to and exploring from the most promising states. This approach has led to superhuman performance across a wide variety of challenging problems including Atari games and robotic control, but requires manually designing heuristics to guide exploration, which is time-consuming and infeasible in general. To resolve this, we propose Intelligent Go-Explore (IGE) which greatly extends the scope of the original Go-Explore by replacing these heuristics with the intelligence and internalized human notions of interestingness captured by giant foundation models (FMs). This provides IGE with a human-like ability to instinctively identify how interesting or promising any new state is (e.g. discovering new objects, locations, or behaviors), even in complex environments where heuristics are hard to define. Moreover, IGE offers the exciting and previously impossible opportunity to recognize and capitalize on serendipitous discoveries that cannot be predicted ahead of time. We evaluate IGE on a range of language-based tasks that require search and exploration. In Game of 24, a multistep mathematical reasoning problem, IGE reaches 100% success rate 70.8% faster than the best classic graph search baseline. Next, in BabyAI-Text, a challenging partially observable gridworld, IGE exceeds the previous SOTA with orders of magnitude fewer online samples. Finally, in TextWorld, we show the unique ability of IGE to succeed in settings requiring long-horizon exploration where prior SOTA FM agents like Reflexion completely fail. Overall, IGE combines the tremendous strengths of FMs and the powerful Go-Explore algorithm, opening up a new frontier of research into creating more generally capable agents with impressive exploration capabilities.

Multiplex graphs, characterised by their layered structure, exhibit informative interdependencies within layers that are crucial for understanding complex network dynamics. Quantifying the interaction and shared information among these layers is challenging due to the non-Euclidean structure of graphs. Our paper introduces a comprehensive theory of multivariate information measures for multiplex graphs. We introduce graphon mutual information for pairs of graphs and expand this to graphon interaction information for three or more graphs, including their conditional variants. We then define graphon total correlation and graphon dual total correlation, along with their conditional forms, and introduce graphon $O-$information. We discuss and quantify the concepts of synergy and redundancy in graphs for the first time, introduce consistent nonparametric estimators for these multivariate graphon information--theoretic measures, and provide their convergence rates. We also conduct a simulation study to illustrate our theoretical findings and demonstrate the relationship between the introduced measures, multiplex graph structure, and higher--order interdependecies. Real-world applications further show the utility of our estimators in revealing shared information and dependence structures in real-world multiplex graphs. This work not only answers fundamental questions about information sharing across multiple graphs but also sets the stage for advanced pattern analysis in complex networks.

Existing genetic programming (GP) methods are typically designed based on a certain representation, such as tree-based or linear representations. These representations show various pros and cons in different domains. However, due to the complicated relationships among representation and fitness landscapes of GP, it is hard to intuitively determine which GP representation is the most suitable for solving a certain problem. Evolving programs (or models) with multiple representations simultaneously can alternatively search on different fitness landscapes since representations are highly related to the search space that essentially defines the fitness landscape. Fully using the latent synergies among different GP individual representations might be helpful for GP to search for better solutions. However, existing GP literature rarely investigates the simultaneous effective use of evolving multiple representations. To fill this gap, this paper proposes a multi-representation GP algorithm based on tree-based and linear representations, which are two commonly used GP representations. In addition, we develop a new cross-representation crossover operator to harness the interplay between tree-based and linear representations. Empirical results show that navigating the learned knowledge between basic tree-based and linear representations successfully improves the effectiveness of GP with solely tree-based or linear representation in solving symbolic regression and dynamic job shop scheduling problems.

Graph generation has been dominated by autoregressive models due to their simplicity and effectiveness, despite their sensitivity to ordering. Yet diffusion models have garnered increasing attention, as they offer comparable performance while being permutation-invariant. Current graph diffusion models generate graphs in a one-shot fashion, but they require extra features and thousands of denoising steps to achieve optimal performance. We introduce PARD, a Permutation-invariant Auto Regressive Diffusion model that integrates diffusion models with autoregressive methods. PARD harnesses the effectiveness and efficiency of the autoregressive model while maintaining permutation invariance without ordering sensitivity. Specifically, we show that contrary to sets, elements in a graph are not entirely unordered and there is a unique partial order for nodes and edges. With this partial order, PARD generates a graph in a block-by-block, autoregressive fashion, where each block's probability is conditionally modeled by a shared diffusion model with an equivariant network. To ensure efficiency while being expressive, we further propose a higher-order graph transformer, which integrates transformer with PPGN. Like GPT, we extend the higher-order graph transformer to support parallel training of all blocks. Without any extra features, PARD achieves state-of-the-art performance on molecular and non-molecular datasets, and scales to large datasets like MOSES containing 1.9M molecules. Pard is open-sourced at //github.com/LingxiaoShawn/Pard.

The existence of representative datasets is a prerequisite of many successful artificial intelligence and machine learning models. However, the subsequent application of these models often involves scenarios that are inadequately represented in the data used for training. The reasons for this are manifold and range from time and cost constraints to ethical considerations. As a consequence, the reliable use of these models, especially in safety-critical applications, is a huge challenge. Leveraging additional, already existing sources of knowledge is key to overcome the limitations of purely data-driven approaches, and eventually to increase the generalization capability of these models. Furthermore, predictions that conform with knowledge are crucial for making trustworthy and safe decisions even in underrepresented scenarios. This work provides an overview of existing techniques and methods in the literature that combine data-based models with existing knowledge. The identified approaches are structured according to the categories integration, extraction and conformity. Special attention is given to applications in the field of autonomous driving.

Most existing knowledge graphs suffer from incompleteness, which can be alleviated by inferring missing links based on known facts. One popular way to accomplish this is to generate low-dimensional embeddings of entities and relations, and use these to make inferences. ConvE, a recently proposed approach, applies convolutional filters on 2D reshapings of entity and relation embeddings in order to capture rich interactions between their components. However, the number of interactions that ConvE can capture is limited. In this paper, we analyze how increasing the number of these interactions affects link prediction performance, and utilize our observations to propose InteractE. InteractE is based on three key ideas -- feature permutation, a novel feature reshaping, and circular convolution. Through extensive experiments, we find that InteractE outperforms state-of-the-art convolutional link prediction baselines on FB15k-237. Further, InteractE achieves an MRR score that is 9%, 7.5%, and 23% better than ConvE on the FB15k-237, WN18RR and YAGO3-10 datasets respectively. The results validate our central hypothesis -- that increasing feature interaction is beneficial to link prediction performance. We make the source code of InteractE available to encourage reproducible research.

We propose a novel attention gate (AG) model for medical imaging that automatically learns to focus on target structures of varying shapes and sizes. Models trained with AGs implicitly learn to suppress irrelevant regions in an input image while highlighting salient features useful for a specific task. This enables us to eliminate the necessity of using explicit external tissue/organ localisation modules of cascaded convolutional neural networks (CNNs). AGs can be easily integrated into standard CNN architectures such as the U-Net model with minimal computational overhead while increasing the model sensitivity and prediction accuracy. The proposed Attention U-Net architecture is evaluated on two large CT abdominal datasets for multi-class image segmentation. Experimental results show that AGs consistently improve the prediction performance of U-Net across different datasets and training sizes while preserving computational efficiency. The code for the proposed architecture is publicly available.