Proteins are sequences of amino acids that serve as the basic building blocks of living organisms. Despite rapidly growing databases documenting structural and functional information for various protein sequences, our understanding of proteins remains limited because of the large possible sequence space and the complex inter- and intra-molecular forces. Deep learning, which is characterized by its ability to learn relevant features directly from large datasets, has demonstrated remarkable performance in fields such as computer vision and natural language processing. It has also been increasingly applied in recent years to the data-rich domain of protein sequences with great success, most notably with Alphafold2's breakout performance in the protein structure prediction. The performance improvements achieved by deep learning unlocks new possibilities in the field of protein bioinformatics, including protein design, one of the most difficult but useful tasks. In this paper, we broadly categorize problems in protein bioinformatics into three main categories: 1) structural prediction, 2) functional prediction, and 3) protein design, and review the progress achieved from using deep learning methodologies in each of them. We expand on the main challenges of the protein design problem and highlight how advances in structural and functional prediction have directly contributed to design tasks. Finally, we conclude by identifying important topics and future research directions.

Integrating Large Language Models (LLMs) in healthcare diagnosis demands systematic frameworks that can handle complex medical scenarios while maintaining specialized expertise. We present KG4Diagnosis, a novel hierarchical multi-agent framework that combines LLMs with automated knowledge graph construction, encompassing 362 common diseases across medical specialties. Our framework mirrors real-world medical systems through a two-tier architecture: a general practitioner (GP) agent for initial assessment and triage, coordinating with specialized agents for in-depth diagnosis in specific domains. The core innovation lies in our end-to-end knowledge graph generation methodology, incorporating: (1) semantic-driven entity and relation extraction optimized for medical terminology, (2) multi-dimensional decision relationship reconstruction from unstructured medical texts, and (3) human-guided reasoning for knowledge expansion. KG4Diagnosis serves as an extensible foundation for specialized medical diagnosis systems, with capabilities to incorporate new diseases and medical knowledge. The framework's modular design enables seamless integration of domain-specific enhancements, making it valuable for developing targeted medical diagnosis systems. We provide architectural guidelines and protocols to facilitate adoption across medical contexts.

In the many years since the inception of wearable sensor-based Human Activity Recognition (HAR), a wide variety of methods have been introduced and evaluated for their ability to recognize activities. Substantial gains have been made since the days of hand-crafting heuristics as features, yet, progress has seemingly stalled on many popular benchmarks, with performance falling short of what may be considered 'sufficient'-- despite the increase in computational power and scale of sensor data, as well as rising complexity in techniques being employed. The HAR community approaches a new paradigm shift, this time incorporating world knowledge from foundational models. In this paper, we take stock of sensor-based HAR -- surveying it from its beginnings to the current state of the field, and charting its future. This is accompanied by a hands-on tutorial, through which we guide practitioners in developing HAR systems for real-world application scenarios. We provide a compendium for novices and experts alike, of methods that aim at finally solving the activity recognition problem.

Post-alignment of large language models (LLMs) is critical in improving their utility, safety, and alignment with human intentions. Direct preference optimisation (DPO) has become one of the most widely used algorithms for achieving this alignment, given its ability to optimise models based on human feedback directly. However, the vast number of DPO variants in the literature has made it increasingly difficult for researchers to navigate and fully grasp the connections between these approaches. This paper introduces a unifying framework inspired by mutual information, which proposes a new loss function with flexible priors. By carefully specifying these priors, we demonstrate that many existing algorithms, such as SimPO, TDPO, SparsePO, and others, can be derived from our framework. This unification offers a clearer and more structured approach, allowing researchers to understand the relationships between different DPO variants better. We aim to simplify the landscape of DPO algorithms, making it easier for the research community to gain insights and foster further advancements in LLM alignment. Ultimately, we hope our framework can be a foundation for developing more robust and interpretable alignment techniques.

Cloud computing has revolutionized the provisioning of computing resources, offering scalable, flexible, and on-demand services to meet the diverse requirements of modern applications. At the heart of efficient cloud operations are job scheduling and resource management, which are critical for optimizing system performance and ensuring timely and cost-effective service delivery. However, the dynamic and heterogeneous nature of cloud environments presents significant challenges for these tasks, as workloads and resource availability can fluctuate unpredictably. Traditional approaches, including heuristic and meta-heuristic algorithms, often struggle to adapt to these real-time changes due to their reliance on static models or predefined rules. Deep Reinforcement Learning (DRL) has emerged as a promising solution to these challenges by enabling systems to learn and adapt policies based on continuous observations of the environment, facilitating intelligent and responsive decision-making. This survey provides a comprehensive review of DRL-based algorithms for job scheduling and resource management in cloud computing, analyzing their methodologies, performance metrics, and practical applications. We also highlight emerging trends and future research directions, offering valuable insights into leveraging DRL to advance both job scheduling and resource management in cloud computing.

Reasoning is fundamental to human intelligence, and critical for problem-solving, decision-making, and critical thinking. Reasoning refers to drawing new conclusions based on existing knowledge, which can support various applications like clinical diagnosis, basic education, and financial analysis. Though a good number of surveys have been proposed for reviewing reasoning-related methods, none of them has systematically investigated these methods from the viewpoint of their dependent knowledge base. Both the scenarios to which the knowledge bases are applied and their storage formats are significantly different. Hence, investigating reasoning methods from the knowledge base perspective helps us better understand the challenges and future directions. To fill this gap, this paper first classifies the knowledge base into symbolic and parametric ones. The former explicitly stores information in human-readable symbols, and the latter implicitly encodes knowledge within parameters. Then, we provide a comprehensive overview of reasoning methods using symbolic knowledge bases, parametric knowledge bases, and both of them. Finally, we identify the future direction toward enhancing reasoning capabilities to bridge the gap between human and machine intelligence.

Efforts towards endowing robots with the ability to speak have benefited from recent advancements in NLP, in particular large language models. However, as powerful as current models have become, they still operate on sentence or multi-sentence level input, not on the word-by-word input that humans operate on, affecting the degree of responsiveness that they offer, which is critical in situations where humans interact with robots using speech. In this paper, we review the literature on interactive systems that operate incrementally (i.e., at the word level or below it). We motivate the need for incremental systems, survey incremental modeling of important aspects of dialogue like speech recognition and language generation. Primary focus is on the part of the system that makes decisions, known as the dialogue manager. We find that there is very little research on incremental dialogue management, offer some requirements for practical incremental dialogue management, and the implications of incremental dialogue for embodied, robotic platforms.

Large Language Models (LLMs) have revolutionized a wide range of domains such as natural language processing, computer vision, and multi-modal tasks due to their ability to comprehend context and perform logical reasoning. However, the computational and memory demands of LLMs, particularly during inference, pose significant challenges when scaling them to real-world, long-context, and real-time applications. Key-Value (KV) cache management has emerged as a critical optimization technique for accelerating LLM inference by reducing redundant computations and improving memory utilization. This survey provides a comprehensive overview of KV cache management strategies for LLM acceleration, categorizing them into token-level, model-level, and system-level optimizations. Token-level strategies include KV cache selection, budget allocation, merging, quantization, and low-rank decomposition, while model-level optimizations focus on architectural innovations and attention mechanisms to enhance KV reuse. System-level approaches address memory management, scheduling, and hardware-aware designs to improve efficiency across diverse computing environments. Additionally, the survey provides an overview of both text and multimodal datasets and benchmarks used to evaluate these strategies. By presenting detailed taxonomies and comparative analyses, this work aims to offer useful insights for researchers and practitioners to support the development of efficient and scalable KV cache management techniques, contributing to the practical deployment of LLMs in real-world applications. The curated paper list for KV cache management is in: \href{https://github.com/TreeAI-Lab/Awesome-KV-Cache-Management}{https://github.com/TreeAI-Lab/Awesome-KV-Cache-Management}.

Recently, the remarkable success of ChatGPT has sparked a renewed wave of interest in artificial intelligence (AI), and the advancements in visual language models (VLMs) have pushed this enthusiasm to new heights. Differring from previous AI approaches that generally formulated different tasks as discriminative models, VLMs frame tasks as generative models and align language with visual information, enabling the handling of more challenging problems. The remote sensing (RS) field, a highly practical domain, has also embraced this new trend and introduced several VLM-based RS methods that have demonstrated promising performance and enormous potential. In this paper, we first review the fundamental theories related to VLM, then summarize the datasets constructed for VLMs in remote sensing and the various tasks they addressed. Finally, we categorize the improvement methods into three main parts according to the core components of VLMs and provide a detailed introduction and comparison of these methods. A project associated with this review has been created at https://github.com/taolijie11111/VLMs-in-RS-review.

Augmented Reality assistance are increasingly popular for supporting users with tasks like assembly and cooking. However, current practice typically provide reactive responses initialized from user requests, lacking consideration of rich contextual and user-specific information. To address this limitation, we propose a novel AR assistance system, Satori, that models both user states and environmental contexts to deliver proactive guidance. Our system combines the Belief-Desire-Intention (BDI) model with a state-of-the-art multi-modal large language model (LLM) to infer contextually appropriate guidance. The design is informed by two formative studies involving twelve experts. A sixteen within-subject study find that Satori achieves performance comparable to an designer-created Wizard-of-Oz (WoZ) system without relying on manual configurations or heuristics, thereby enhancing generalizability, reusability and opening up new possibilities for AR assistance.