Despite significant progress in static protein structure collection and prediction, the dynamic behavior of proteins, one of their most vital characteristics, has been largely overlooked in prior research. This oversight can be attributed to the limited availability, diversity, and heterogeneity of dynamic protein datasets. To address this gap, we propose to enhance existing prestigious static 3D protein structural databases, such as the Protein Data Bank (PDB), by integrating dynamic data and additional physical properties. Specifically, we introduce a large-scale dataset, Dynamic PDB, encompassing approximately 12.6K proteins, each subjected to all-atom molecular dynamics (MD) simulations lasting 1 microsecond to capture conformational changes. Furthermore, we provide a comprehensive suite of physical properties, including atomic velocities and forces, potential and kinetic energies of proteins, and the temperature of the simulation environment, recorded at 1 picosecond intervals throughout the simulations. For benchmarking purposes, we evaluate state-of-the-art methods on the proposed dataset for the task of trajectory prediction. To demonstrate the value of integrating richer physical properties in the study of protein dynamics and related model design, we base our approach on the SE(3) diffusion model and incorporate these physical properties into the trajectory prediction process. Preliminary results indicate that this straightforward extension of the SE(3) model yields improved accuracy, as measured by MAE and RMSD, when the proposed physical properties are taken into consideration. https://fudan-generative-vision.github.io/dynamicPDB/ .

Relational representation learning transforms relational data into continuous and low-dimensional vector representations. However, vector-based representations fall short in capturing crucial properties of relational data that are complex and symbolic. We propose geometric relational embeddings, a paradigm of relational embeddings that respect the underlying symbolic structures. Specifically, this dissertation introduces various geometric relational embedding models capable of capturing: 1) complex structured patterns like hierarchies and cycles in networks and knowledge graphs; 2) logical structures in ontologies and logical constraints applicable for constraining machine learning model outputs; and 3) high-order structures between entities and relations. Our results obtained from benchmark and real-world datasets demonstrate the efficacy of geometric relational embeddings in adeptly capturing these discrete, symbolic, and structured properties inherent in relational data.

Two people have been arrested on suspicion of murder after a baby died in Stoke-on-Trent. Police and the ambulance service were called to Sherwin Road, Burslem, shortly after 09:00 BST on 27 August following the death of a baby boy. A woman, 26, and man, 25, were arrested on 30 August on suspicion of causing or allowing the death of a child. The pair, from Stoke-on-Trent, were further arrested on suspicion of murder on Tuesday, Staffordshire Police said. A spokesperson for the force said specialist officers were supporting the baby's family.

Inventor and futurist Ray Kurzweil, researcher and Brookings Institution fellow Chinasa T. Okolo, director of the U.S. Artificial Safety Institute (AISI) Elizabeth Kelly, and Cognizant CEO Ravi Kumar S, discussed the transformative power of AI during a panel at a TIME100 Impact Dinner in San Francisco on Monday. During the discussion, which was moderated by TIME's editor-in-chief Sam Jacobs, Kurzweil predicted that we will achieve Artificial General Intelligence (AGI), a type of AI that might be smarter than humans, by 2029. "Nobody really took it seriously until now," Kurzweil said about AI. "People are convinced it's going to either endow us with things we'd never had before, or it's going to kill us." Cognizant sponsored Monday's event, which celebrated the 100 most influential people leading change in AI. Jacobs probed the four panelists--three of whom were named to the 2024 list--about the opportunities and challenges presented by AI's rapid advancement.

Quantum computers represent a transformative frontier in computational technology, promising exponential speedups beyond classical computing limits. IBM Quantum has led significant advancements in both hardware and software, providing access to quantum hardware via IBM Cloud since 2016, achieving a milestone with the world's first accessible quantum computer. This article explores IBM's quantum computing journey, focusing on the development of practical quantum computers. We summarize the evolution and advancements of IBM Quantum's processors across generations, including their recent breakthrough surpassing the 1,000-qubit barrier. The paper reviews detailed performance metrics across various hardware, tracing their evolution over time and highlighting IBM Quantum's transition from the noisy intermediate-scale quantum (NISQ) computing era towards fault-tolerant quantum computing capabilities.

Graph neural networks (GNNs) are a type of neural network capable of learning on graph-structured data. However, training GNNs on large-scale graphs is challenging due to iterative aggregations of high-dimensional features from neighboring vertices within sparse graph structures combined with neural network operations. The sparsity of graphs frequently results in suboptimal memory access patterns and longer training time. Graph reordering is an optimization strategy aiming to improve the graph data layout. It has shown to be effective to speed up graph analytics workloads, but its effect on the performance of GNN training has not been investigated yet. The generalization of reordering to GNN performance is nontrivial, as multiple aspects must be considered: GNN hyper-parameters such as the number of layers, the number of hidden dimensions, and the feature size used in the GNN model, neural network operations, large intermediate vertex states, and GPU acceleration. In our work, we close this gap by performing an empirical evaluation of 12 reordering strategies in two state-of-the-art GNN systems, PyTorch Geometric and Deep Graph Library. Our results show that graph reordering is effective in reducing training time for CPU- and GPU-based training, respectively. Further, we find that GNN hyper-parameters influence the effectiveness of reordering, that reordering metrics play an important role in selecting a reordering strategy, that lightweight reordering performs better for GPU-based than for CPU-based training, and that invested reordering time can in many cases be amortized.

Next-token prediction serves as the dominant component in current neural language models. During the training phase, the model employs teacher forcing, which predicts tokens based on all preceding ground truth tokens. However, this approach has been found to create shortcuts, utilizing the revealed prefix to spuriously fit future tokens, potentially compromising the accuracy of the next-token predictor. In this paper, we introduce Semformer, a novel method of training a Transformer language model that explicitly models the semantic planning of response. Specifically, we incorporate a sequence of planning tokens into the prefix, guiding the planning token representations to predict the latent semantic representations of the response, which are induced by an autoencoder. In a minimal planning task (i.e., graph path-finding), our model exhibits near-perfect performance and effectively mitigates shortcut learning, a feat that standard training methods and baseline models have been unable to accomplish. Furthermore, we pretrain Semformer from scratch with 125M parameters, demonstrating its efficacy through measures of perplexity, in-context learning, and fine-tuning on summarization tasks.

The modern theory of classical mechanics, developed by Lagrange, Hamilton and Noether, attempts to cast all of classical motion in the form of an optimization problem, based on an energy functional called the classical action. The most important advantage of this formalism is the ability to manifestly incorporate and exploit symmetries and conservation laws. This reformulation succeeded for unconstrained and holonomic systems that at most obey position equality constraints. Non-holonomic systems, which obey velocity dependent constraints or position inequality constraints, are abundant in nature and of central relevance for science, engineering and industry. All attempts so far to solve non-holonomic dynamics as a classical action optimization problem have failed. Here we utilize the classical limit of a quantum field theory action principle to construct a novel classical action for non-holonomic systems. We therefore put to rest the 190 year old question of whether classical mechanics is variational, answering in the affirmative. We illustrate and validate our approach by solving three canonical model problems by direct numerical optimization of our new action. The formalism developed in this work significantly extends the reach of action principles to a large class of relevant mechanical systems, opening new avenues for their analysis and control both analytically and numerically.

The ability of message-passing neural networks (MPNNs) to fit complex functions over graphs is limited each iteration of message-passing over a simple makes representations more similar, a phenomenon known as rank collapse, and over-smoothing as a special case. Most approaches to mitigate over-smoothing extend common message-passing schemes, e.g., the graph convolutional network, by utilizing residual connections, gating mechanisms, normalization, or regularization techniques. Our work contrarily proposes to directly tackle the cause of this issue by modifying the message-passing scheme and exchanging different types of messages using multi-relational graphs. We identify the necessary and sufficient condition to ensure linearly independent node representations. As one instantion, we show that operating on multiple directed acyclic graphs always satisfies our condition and propose to obtain these by defining a strict partial ordering of the nodes. We conduct comprehensive experiments that confirm the benefits of operating on multi-relational graphs to achieve more informative node representations.

The integration of tools in LLM-based agents overcame the difficulties of standalone LLMs and traditional agents' limited capabilities. However, the conjunction of these technologies and the proposed enhancements in several state-of-the-art works followed a non-unified software architecture resulting in a lack of modularity. Indeed, they focused mainly on functionalities and overlooked the definition of the component's boundaries within the agent. This caused terminological and architectural ambiguities between researchers which we addressed in this paper by proposing a unified framework that establishes a clear foundation for LLM-based agents' development from both functional and software architectural perspectives. Our framework, LLM-Agent-UMF (LLM-based Agent Unified Modeling Framework), clearly distinguishes between the different components of an agent, setting LLMs, and tools apart from a newly introduced element: the core-agent, playing the role of the central coordinator of the agent which comprises five modules: planning, memory, profile, action, and security, the latter often neglected in previous works. Differences in the internal structure of core-agents led us to classify them into a taxonomy of passive and active types. Based on this, we proposed different multi-core agent architectures combining unique characteristics of various individual agents. For evaluation purposes, we applied this framework to a selection of state-of-the-art agents, thereby demonstrating its alignment with their functionalities and clarifying the overlooked architectural aspects. Moreover, we thoroughly assessed four of our proposed architectures by integrating distinctive agents into hybrid active/passive core-agents' systems. This analysis provided clear insights into potential improvements and highlighted the challenges involved in the combination of specific agents.