Structure-based drug design (SBDD) is a critical task in drug discovery, requiring the generation of molecular information across two distinct modalities: discrete molecular graphs and continuous 3D coordinates. However, existing SBDD methods often overlook two key challenges: (1) the multi-modal nature of this task and (2) the causal relationship between these modalities, limiting their plausibility and performance. To address both challenges, we propose TransDiffSBDD, an integrated framework combining autoregressive transformers and diffusion models for SBDD. Specifically, the autoregressive transformer models discrete molecular information, while the diffusion model samples continuous distributions, effectively resolving the first challenge. To address the second challenge, we design a hybrid-modal sequence for protein-ligand complexes that explicitly respects the causality between modalities. Experiments on the CrossDocked2020 benchmark demonstrate that TransDiffSBDD outperforms existing baselines.

Traditional supervised fine-tuning (SFT) strategies for sequence-to-sequence tasks often train models to directly generate the target output. Recent work has shown that guiding models with intermediate steps, such as keywords, outlines, or reasoning chains, can significantly improve performance, coherence, and interpretability. However, these methods often depend on predefined intermediate formats and annotated data, limiting their scalability and generalizability. In this work, we introduce a task-agnostic framework that enables models to generate intermediate "warmup" sequences. These warmup sequences, serving as an initial state for subsequent generation, are optimized to enhance the probability of generating the target sequence without relying on external supervision or human-designed structures. Drawing inspiration from reinforcement learning principles, our method iteratively refines these intermediate steps to maximize their contribution to the final output, similar to reward-driven optimization in reinforcement learning with human feedback. Experimental results across tasks such as translation, summarization, and multi-choice question answering for logical reasoning show that our approach outperforms traditional SFT methods, and offers a scalable and flexible solution for sequence-to-sequence tasks.

Structure-based drug discovery, encompassing the tasks of protein-ligand docking and pocket-aware 3D drug design, represents a core challenge in drug discovery. However, no existing work can deal with both tasks to effectively leverage the duality between them, and current methods for each task are hindered by challenges in modeling 3D information and the limitations of available data. To address these issues, we propose 3DMolFormer, a unified dual-channel transformerbased framework applicable to both docking and 3D drug design tasks, which exploits their duality by utilizing docking functionalities within the drug design process. Specifically, we represent 3D pocket-ligand complexes using parallel sequences of discrete tokens and continuous numbers, and we design a corresponding dual-channel transformer model to handle this format, thereby overcoming the challenges of 3D information modeling. Additionally, we alleviate data limitations through large-scale pre-training on a mixed dataset, followed by supervised and reinforcement learning fine-tuning techniques respectively tailored for the two tasks. Experimental results demonstrate that 3DMolFormer outperforms previous approaches in both protein-ligand docking and pocket-aware 3D drug design, highlighting its promising application in structure-based drug discovery. These developments hold the promise of dramatically enhancing the efficiency of drug development processes (Blanco-Gonzalez et al., 2023). Structure-based drug discovery (SBDD) is one of the most critical strategies in drug discovery practices, relying on theories of drug-receptor interactions to study the complexes formed between protein pockets and small molecule ligands (Van Montfort & Workman, 2017). SBDD encompasses two core tasks: (1) protein-ligand binding pose prediction (docking), which involves predicting the 3D binding conformation of a ligand given the 3D structure of a protein and the 2D representation of the ligand (Yang et al., 2022), and (2) pocket-aware 3D drug design, which entails designing 3D drug molecules that bind well (with low binding energy) to a given pocket target on a protein These two tasks are inherently dual, and one is predictive, while the other is generative. However, as of now, the application of machine learning in these two SBDD tasks remains widely recognized as a challenge (Pala & Clark, 2024).

Multivariate time series data is ubiquitous, and forecasting it has important applications in many domains. However, its complex spatial dependencies and non-linear temporal dynamics can be challenging for traditional techniques. Existing methods tackle these challenges by learning the two dimensions separately. Here, we introduce Temporal Graphormer (T-Graphormer), a Transformer-based approach capable of modelling spatiotemporal correlations simultaneously. By incorporating temporal dynamics in the Graphormer architecture, each node attends to all other nodes within the graph sequence. Our design enables the model to capture rich spatiotemporal patterns with minimal reliance on predefined spacetime inductive biases. We validate the effectiveness of T-Graphormer on real-world traffic prediction benchmark datasets. Compared to state-of-the-art methods, T-Graphormer reduces root mean squared error (RMSE) and mean absolute percentage error (MAPE) by up to 10%.

Blockchain technology, with implications in the financial domain, offers data in the form of large-scale transaction networks. Analyzing transaction networks facilitates fraud detection, market analysis, and supports government regulation. Despite many graph representation learning methods for transaction network analysis, we pinpoint two salient limitations that merit more investigation. Existing methods predominantly focus on the snapshots of transaction networks, sidelining the evolving nature of blockchain transaction networks. Existing methodologies may not sufficiently emphasize efficient, incremental learning capabilities, which are essential for addressing the scalability challenges in ever-expanding large-scale transaction networks. To address these challenges, we employed an incremental approach for random walk-based node representation learning in transaction networks. Further, we proposed a Metropolis-Hastings-based random walk mechanism for improved efficiency. The empirical evaluation conducted on blockchain transaction datasets reveals comparable performance in node classification tasks while reducing computational overhead. Potential applications include transaction network monitoring, the efficient classification of blockchain addresses for fraud detection or the identification of specialized address types within the network.

Offline black-box optimization aims to maximize a black-box function using an offline dataset of designs and their measured properties. Two main approaches have emerged: the forward approach, which learns a mapping from input to its value, thereby acting as a proxy to guide optimization, and the inverse approach, which learns a mapping from value to input for conditional generation. (a) Although proxy-free~(classifier-free) diffusion shows promise in robustly modeling the inverse mapping, it lacks explicit guidance from proxies, essential for generating high-performance samples beyond the training distribution. Therefore, we propose \textit{proxy-enhanced sampling} which utilizes the explicit guidance from a trained proxy to bolster proxy-free diffusion with enhanced sampling control. (b) Yet, the trained proxy is susceptible to out-of-distribution issues. To address this, we devise the module \textit{diffusion-based proxy refinement}, which seamlessly integrates insights from proxy-free diffusion back into the proxy for refinement. To sum up, we propose \textit{\textbf{R}obust \textbf{G}uided \textbf{D}iffusion for Offline Black-box Optimization}~(\textbf{RGD}), combining the advantages of proxy~(explicit guidance) and proxy-free diffusion~(robustness) for effective conditional generation. RGD achieves state-of-the-art results on various design-bench tasks, underscoring its efficacy. Our code is at https://github.com/GGchen1997/RGD.

Large language models (LLMs) have received considerable interest recently due to their outstanding reasoning and comprehension capabilities. This work explores applying LLMs to vehicular networks, aiming to jointly optimize vehicle-to-infrastructure (V2I) communications and autonomous driving (AD) policies. We deploy LLMs for AD decision-making to maximize traffic flow and avoid collisions for road safety, and a double deep Q-learning algorithm (DDQN) is used for V2I optimization to maximize the received data rate and reduce frequent handovers. In particular, for LLM-enabled AD, we employ the Euclidean distance to identify previously explored AD experiences, and then LLMs can learn from past good and bad decisions for further improvement. Then, LLM-based AD decisions will become part of states in V2I problems, and DDQN will optimize the V2I decisions accordingly. After that, the AD and V2I decisions are iteratively optimized until convergence. Such an iterative optimization approach can better explore the interactions between LLMs and conventional reinforcement learning techniques, revealing the potential of using LLMs for network optimization and management. Finally, the simulations demonstrate that our proposed hybrid LLM-DDQN approach outperforms the conventional DDQN algorithm, showing faster convergence and higher average rewards.

Edge Intelligence (EI) has been instrumental in delivering real-time, localized services by leveraging the computational capabilities of edge networks. The integration of Large Language Models (LLMs) empowers EI to evolve into the next stage: Edge General Intelligence (EGI), enabling more adaptive and versatile applications that require advanced understanding and reasoning capabilities. However, systematic exploration in this area remains insufficient. This survey delineates the distinctions between EGI and traditional EI, categorizing LLM-empowered EGI into three conceptual systems: centralized, hybrid, and decentralized. For each system, we detail the framework designs and review existing implementations. Furthermore, we evaluate the performance and throughput of various Small Language Models (SLMs) that are more suitable for development on edge devices. This survey provides researchers with a comprehensive vision of EGI, offering insights into its vast potential and establishing a foundation for future advancements in this rapidly evolving field.

In offline multi-objective optimization (MOO), we leverage an offline dataset of designs and their associated labels to simultaneously minimize multiple objectives. This setting more closely mirrors complex real-world problems compared to single-objective optimization. Recent works mainly employ evolutionary algorithms and Bayesian optimization, with limited attention given to the generative modeling capabilities inherent in such data. In this study, we explore generative modeling in offline MOO through flow matching, noted for its effectiveness and efficiency. We introduce ParetoFlow, specifically designed to guide flow sampling to approximate the Pareto front. Traditional predictor (classifier) guidance is inadequate for this purpose because it models only a single objective. In response, we propose a multi-objective predictor guidance module that assigns each sample a weight vector, representing a weighted distribution across multiple objective predictions. A local filtering scheme is introduced to address non-convex Pareto fronts. These weights uniformly cover the entire objective space, effectively directing sample generation towards the Pareto front. Since distributions with similar weights tend to generate similar samples, we introduce a neighboring evolution module to foster knowledge sharing among neighboring distributions. This module generates offspring from these distributions, and selects the most promising one for the next iteration. Our method achieves state-of-the-art performance across various tasks.

The evolution of previous Click-Through Rate (CTR) models has mainly been driven by proposing complex components, whether shallow or deep, that are adept at modeling feature interactions. However, there has been less focus on improving fusion design. Instead, two naive solutions, stacked and parallel fusion, are commonly used. Both solutions rely on pre-determined fusion connections and fixed fusion operations. It has been repetitively observed that changes in fusion design may result in different performances, highlighting the critical role that fusion plays in CTR models. While there have been attempts to refine these basic fusion strategies, these efforts have often been constrained to specific settings or dependent on specific components. Neural architecture search has also been introduced to partially deal with fusion design, but it comes with limitations. The complexity of the search space can lead to inefficient and ineffective results. To bridge this gap, we introduce OptFusion, a method that automates the learning of fusion, encompassing both the connection learning and the operation selection. We have proposed a one-shot learning algorithm tackling these tasks concurrently. Our experiments are conducted over three large-scale datasets. Extensive experiments prove both the effectiveness and efficiency of OptFusion in improving CTR model performance. Our code implementation is available here\url{https://github.com/kexin-kxzhang/OptFusion}.