This work presents a novel means for understanding learning dynamics and scaling relations in neural networks. We show that certain measures on the spectrum of the empirical neural tangent kernel, specifically entropy and trace, yield insight into the representations learned by a neural network and how these can be improved through architecture scaling. These results are demonstrated first on test cases before being shown on more complex networks, including transformers, auto-encoders, graph neural networks, and reinforcement learning studies. In testing on a wide range of architectures, we highlight the universal nature of training dynamics and further discuss how it can be used to understand the mechanisms behind learning in neural networks. We identify two such dominant mechanisms present throughout machine learning training. The first, information compression, is seen through a reduction in the entropy of the NTK spectrum during training, and occurs predominantly in small neural networks. The second, coined structure formation, is seen through an increasing entropy and thus, the creation of structure in the neural network representations beyond the prior established by the network at initialization. Due to the ubiquity of the latter in deep neural network architectures and its flexibility in the creation of feature-rich representations, we argue that this form of evolution of the network's entropy be considered the onset of a deep learning regime.

Entity Linking (EL) is the process of associating ambiguous textual mentions to specific entities in a knowledge base. Traditional EL methods heavily rely on large datasets to enhance their performance, a dependency that becomes problematic in the context of few-shot entity linking, where only a limited number of examples are available for training. To address this challenge, we present OneNet, an innovative framework that utilizes the few-shot learning capabilities of Large Language Models (LLMs) without the need for fine-tuning. To the best of our knowledge, this marks a pioneering approach to applying LLMs to few-shot entity linking tasks. OneNet is structured around three key components prompted by LLMs: (1) an entity reduction processor that simplifies inputs by summarizing and filtering out irrelevant entities, (2) a dual-perspective entity linker that combines contextual cues and prior knowledge for precise entity linking, and (3) an entity consensus judger that employs a unique consistency algorithm to alleviate the hallucination in the entity linking reasoning. Comprehensive evaluations across seven benchmark datasets reveal that OneNet outperforms current state-of-the-art entity linking methods.

--Decentralized Federated Learning has emerged as an alternative to centralized architectures due to its faster training, privacy preservation, and reduced communication overhead. In decentralized communication, the server aggregation phase in Centralized Federated Learning shifts to the client side, which means that clients connect with each other in a peer-to-peer manner . However, compared to the centralized mode, data heterogeneity in Decentralized Federated Learning will cause larger variances between aggregated models, which leads to slow convergence in training and poor generalization performance in tests. T o address these issues, we introduce Catalyst Acceleration and propose an acceleration Decentralized Federated Learning algorithm called DFedCata. It consists of two main components: the Moreau envelope function, which primarily addresses parameter inconsistencies among clients caused by data heterogeneity, and Nesterov's extrapolation step, which accelerates the aggregation phase. Theoretically, We prove the optimization error bound and generalization error bound of the algorithm, providing a further understanding of the nature of the algorithm and the theoretical perspectives on the hyperparameter choice. Empirically, we demonstrate the advantages of the proposed algorithm in both convergence speed and generalization performance on CIF AR10/100 with various non-iid data distributions. Furthermore, we also experimentally verify the theoretical properties of DFedCata. EDERA TED Learning (FL) is a new distributed machine learning paradigm that prioritizes privacy protection [1]- [3]. It enables multiple clients to collaborate on training models without sharing their raw data. Nowadays, much of the research [4]-[9] focus on Centralized Federated Learning (CFL), but the central server in CFL brings various challenges on communication burden, single point of failure [10], privacy breaches [11] and so on. In contrast, Decentralized Federated Learning (DFL) centralizes both the local update and aggregation steps on the client, which offers enhanced privacy protection [12], faster model training [13], and robustness to slow client devices [14]. Therefore, DFL has become a popular alternative solution [10], [13]. Qinglun Li, Miao Zhang, and Quanjun Yin are with the College of Systems Engineering, National University of Defense Technology. Yingqi Liu, Li Shen, and Xiaochun Cao are with the School of Cy-ber Science and Technology, Shenzhen Campus of Sun Y at-sen University, Shenzhen 518107, China. The optimization process diagrams for two clients under the DFedAvg and DFedCata algorithms are simulated. The primary improvements include two aspects.

Graphs and hypergraphs provide powerful abstractions for modeling interactions among a set of entities of interest and have been attracting a growing interest in the literature thanks to many successful applications in several fields. In particular, they are rapidly expanding in domains such as chemistry and biology, especially in the areas of drug discovery and molecule generation. One of the areas witnessing the fasted growth is the chemical reactions field, where chemical reactions can be naturally encoded as directed hyperedges of a hypergraph. In this paper, we address the chemical reaction classification problem by introducing the notation of a Directed Line Graph (DGL) associated with a given directed hypergraph. On top of it, we build the Directed Line Graph Network (DLGNet), the first spectral-based Graph Neural Network (GNN) expressly designed to operate on a hypergraph via its DLG transformation. The foundation of DLGNet is a novel Hermitian matrix, the Directed Line Graph Laplacian, which compactly encodes the directionality of the interactions taking place within the directed hyperedges of the hypergraph thanks to the DLG representation. The Directed Line Graph Laplacian enjoys many desirable properties, including admitting an eigenvalue decomposition and being positive semidefinite, which make it well-suited for its adoption within a spectral-based GNN. Through extensive experiments on chemical reaction datasets, we show that DGLNet significantly outperforms the existing approaches, achieving on a collection of real-world datasets an average relative-percentage-difference improvement of 33.01%, with a maximum improvement of 37.71%.

Understanding molecular structure and related knowledge is crucial for scientific research. Recent studies integrate molecular graphs with their textual descriptions to enhance molecular representation learning. However, they focus on the whole molecular graph and neglect frequently occurring subgraphs, known as motifs,which are essential for determining molecular properties. Without such fine-grained knowledge, these models struggle to generalize to unseen molecules and tasks that require motif-level insights. To bridge this gap, we propose FineMolTex, a novel Fine-grained Molecular graph-Text pre-training framework to jointly learn coarse-grained molecule-level knowledge and fine-grained motif-level knowledge. Specifically, FineMolTex consists of two pre-training tasks: a contrastive alignment task for coarse-grained matching and a masked multi-modal modeling task for fine-grained matching. In particular, the latter predicts the labels of masked motifs and words, leveraging insights from each other, thereby enabling FineMolTex to understand the fine-grained matching between motifs and words. Finally, we conduct extensive experiments across three downstream tasks, achieving up to 230% improvement in the text-based molecule editing task. Additionally, our case studies reveal that FineMolTex successfully captures fine-grained knowledge, potentially offering valuable insights for drug discovery and catalyst design.

Predicting the thermodynamic properties of mixtures is crucial for process design and optimization in chemical engineering. Machine learning (ML) methods are gaining increasing attention in this field, but experimental data for training are often scarce, which hampers their application. In this work, we introduce a novel generic approach for improving data-driven models: inspired by the ancient rule "similia similibus solvuntur", we lump components that behave similarly into chemical classes and model them jointly in the first step of a hierarchical approach. While the information on class affiliations can stem in principle from any source, we demonstrate how classes can reproducibly be defined based on mixture data alone by agglomerative clustering. The information from this clustering step is then used as an informed prior for fitting the individual data. We demonstrate the benefits of this approach by applying it in connection with a matrix completion method (MCM) for predicting isothermal activity coefficients at infinite dilution in binary mixtures. Using clustering leads to significantly improved predictions compared to an MCM without clustering. Furthermore, the chemical classes learned from the clustering give exciting insights into what matters on the molecular level for modeling given mixture properties.

Chemputation is the process of programming chemical robots to do experiments using a universal symbolic language, but the literature can be error prone and hard to read due to ambiguities. Large Language Models (LLMs) have demonstrated remarkable capabilities in various domains, including natural language processing, robotic control, and more recently, chemistry. Despite significant advancements in standardizing the reporting and collection of synthetic chemistry data, the automatic reproduction of reported syntheses remains a labour-intensive task. In this work, we introduce an LLM-based chemical research agent workflow designed for the automatic validation of synthetic literature procedures. Our workflow can autonomously extract synthetic procedures and analytical data from extensive documents, translate these procedures into universal XDL code, simulate the execution of the procedure in a hardware-specific setup, and ultimately execute the procedure on an XDL-controlled robotic system for synthetic chemistry. This demonstrates the potential of LLM-based workflows for autonomous chemical synthesis with Chemputers. Due to the abstraction of XDL this approach is safe, secure, and scalable since hallucinations will not be chemputable and the XDL can be both verified and encrypted. Unlike previous efforts, which either addressed only a limited portion of the workflow, relied on inflexible hard-coded rules, or lacked validation in physical systems, our approach provides four realistic examples of syntheses directly executed from synthetic literature. We anticipate that our workflow will significantly enhance automation in robotically driven synthetic chemistry research, streamline data extraction, improve the reproducibility, scalability, and safety of synthetic and experimental chemistry.

Electron density prediction stands as a cornerstone challenge in molecular systems, pivotal for various applications such as understanding molecular interactions and conducting precise quantum mechanical calculations. However, the scaling of density functional theory (DFT) calculations is prohibitively expensive. Machine learning methods provide an alternative, offering efficiency and accuracy. We introduce a novel SE(3)-equivariant architecture, drawing inspiration from Slater-Type Orbitals (STO), to learn representations of molecular electronic structures. Our approach offers an alternative functional form for learned orbital-like molecular representation. We showcase the effectiveness of our method by achieving SOTA prediction accuracy of molecular electron density with 30-70\% improvement over other work on Molecular Dynamics data.

Soft robots - due to their intrinsic flexibility of the body - can adaptively navigate unstructured environments. One of the most popular locomotion gaits that has been implemented in soft robots is undulation. The undulation motion in soft robots resembles the locomotion gait of stringy creatures such as snakes, eels, and C. Elegans. Typically, the implementation of undulation locomotion on a soft robot requires many actuators to control each segment of the stringy body. The added weight of multiple actuators limits the navigating performance of soft-bodied robots. In this paper, we propose a simple tendon-driven flexible beam with only one actuator (a DC motor) that can generate a mechanical traveling wave along the beam to support the undulation locomotion of soft robots. The beam will be precompressed along its axis by shortening the length of the two tendons to form an S-shape, thus pretensioning the tendons. The motor will wind and unwind the tendons to deform the flexible beam and generate traveling waves along the body of the robot. We experiment with different pre-tension to characterize the relationship between tendon pre-tension forces and the DC-motor winding/unwinding. Our proposal enables a simple implementation of undulation motion to support the locomotion of soft-bodied robots.

In a windowless shack on the far outskirts of Fresno, an ominious red glow illuminates a lab filled with X-ray machines, shelves of glowing boxes, a quietly humming incubator and a miniature wind tunnel. While the scene looks like something straight out of a sci-fi movie, its actually part of an experimental program to prevent a damaging almond pest from successfully mating. With California almond growers reeling from dropping nut prices and rising costs, the pests have only added to their woes. Every year, the navel orangeworm eats through roughly 2% of California's almonds before they can make it to grocery store shelves. Last year, it was almost double that.