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Yu Kang

Publications and source records attributed to Yu Kang.

At least 73 records · Page 4Linked to original sources
arXiv2024

Token-Mol 1.0: Tokenized drug design with large language model

Significant interests have recently risen in leveraging sequence-based large language models (LLMs) for drug design. However, most current applications of LLMs in drug discovery lack the ability to comprehend three-dimensional (3D) structures, thereby limiting their effectiveness in tasks that explicitly involve molecular conformations. In this study, we introduced Token-Mol, a token-only 3D drug design model. This model encodes all molecular information, including 2D and 3D structures, as well as molecular property data, into tokens, which transforms classification and regression tasks in drug discovery into probabilistic prediction problems, thereby enabling learning through a unified paradigm. Token-Mol is built on the transformer decoder architecture and trained using random causal masking techniques. Additionally, we proposed the Gaussian cross-entropy (GCE) loss function to overcome the challenges in regression tasks, significantly enhancing the capacity of LLMs to learn continuous numerical values. Through a combination of fine-tuning and reinforcement learning (RL), Token-Mol achieves performance comparable to or surpassing existing task-specific methods across various downstream tasks, including pocket-based molecular generation, conformation generation, and molecular property prediction. Compared to existing molecular pre-trained models, Token-Mol exhibits superior proficiency in handling a wider range of downstream tasks essential for drug design. Notably, our approach improves regression task accuracy by approximately 30% compared to similar token-only methods. Token-Mol overcomes the precision limitations of token-only models and has the potential to integrate seamlessly with general models such as ChatGPT, paving the way for the development of a universal artificial intelligence drug design model that facilitates rapid and high-quality drug design by experts.

q-bio.BM↗
arXiv2024

Improving embedding with contrastive fine-tuning on small datasets with expert-augmented scores

This paper presents an approach to improve text embedding models through contrastive fine-tuning on small datasets augmented with expert scores. It focuses on enhancing semantic textual similarity tasks and addressing text retrieval problems. The proposed method uses soft labels derived from expert-augmented scores to fine-tune embedding models, preserving their versatility and ensuring retrieval capability is improved. The paper evaluates the method using a Q\&A dataset from an online shopping website and eight expert models. Results show improved performance over a benchmark model across multiple metrics on various retrieval tasks from the massive text embedding benchmark (MTEB). The method is cost-effective and practical for real-world applications, especially when labeled data is scarce.

cs.CL↗
arXiv2024

PEAR: Phrase-Based Hand-Object Interaction Anticipation

First-person hand-object interaction anticipation aims to predict the interaction process over a forthcoming period based on current scenes and prompts. This capability is crucial for embodied intelligence and human-robot collaboration. The complete interaction process involves both pre-contact interaction intention (i.e., hand motion trends and interaction hotspots) and post-contact interaction manipulation (i.e., manipulation trajectories and hand poses with contact). Existing research typically anticipates only interaction intention while neglecting manipulation, resulting in incomplete predictions and an increased likelihood of intention errors due to the lack of manipulation constraints. To address this, we propose a novel model, PEAR (Phrase-Based Hand-Object Interaction Anticipation), which jointly anticipates interaction intention and manipulation. To handle uncertainties in the interaction process, we employ a twofold approach. Firstly, we perform cross-alignment of verbs, nouns, and images to reduce the diversity of hand movement patterns and object functional attributes, thereby mitigating intention uncertainty. Secondly, we establish bidirectional constraints between intention and manipulation using dynamic integration and residual connections, ensuring consistency among elements and thus overcoming manipulation uncertainty. To rigorously evaluate the performance of the proposed model, we collect a new task-relevant dataset, EGO-HOIP, with comprehensive annotations. Extensive experimental results demonstrate the superiority of our method.

cs.CV↗
arXiv2024

FMamba: Mamba based on Fast-attention for Multivariate Time-series Forecasting

In multivariate time-series forecasting (MTSF), extracting the temporal correlations of the input sequences is crucial. While popular Transformer-based predictive models can perform well, their quadratic computational complexity results in inefficiency and high overhead. The recently emerged Mamba, a selective state space model, has shown promising results in many fields due to its strong temporal feature extraction capabilities and linear computational complexity. However, due to the unilateral nature of Mamba, channel-independent predictive models based on Mamba cannot attend to the relationships among all variables in the manner of Transformer-based models. To address this issue, we combine fast-attention with Mamba to introduce a novel framework named FMamba for MTSF. Technically, we first extract the temporal features of the input variables through an embedding layer, then compute the dependencies among input variables via the fast-attention module. Subsequently, we use Mamba to selectively deal with the input features and further extract the temporal dependencies of the variables through the multi-layer perceptron block (MLP-block). Finally, FMamba obtains the predictive results through the projector, a linear layer. Experimental results on eight public datasets demonstrate that FMamba can achieve state-of-the-art performance while maintaining low computational overhead.

cs.LG↗
arXiv2024

TaskWeaver: A Code-First Agent Framework

Large Language Models (LLMs) have shown impressive abilities in natural language understanding and generation, leading to their widespread use in applications such as chatbots and virtual assistants. However, existing LLM frameworks face limitations in handling domain-specific data analytics tasks with rich data structures. Moreover, they struggle with flexibility to meet diverse user requirements. To address these issues, TaskWeaver is proposed as a code-first framework for building LLM-powered autonomous agents. It converts user requests into executable code and treats user-defined plugins as callable functions. TaskWeaver provides support for rich data structures, flexible plugin usage, and dynamic plugin selection, and leverages LLM coding capabilities for complex logic. It also incorporates domain-specific knowledge through examples and ensures the secure execution of generated code. TaskWeaver offers a powerful and flexible framework for creating intelligent conversational agents that can handle complex tasks and adapt to domain-specific scenarios. The code is open sourced at https://github.com/microsoft/TaskWeaver/.

cs.AI↗
arXiv2024

UFO: A UI-Focused Agent for Windows OS Interaction

We introduce UFO, an innovative UI-Focused agent to fulfill user requests tailored to applications on Windows OS, harnessing the capabilities of GPT-Vision. UFO employs a dual-agent framework to meticulously observe and analyze the graphical user interface (GUI) and control information of Windows applications. This enables the agent to seamlessly navigate and operate within individual applications and across them to fulfill user requests, even when spanning multiple applications. The framework incorporates a control interaction module, facilitating action grounding without human intervention and enabling fully automated execution. Consequently, UFO transforms arduous and time-consuming processes into simple tasks achievable solely through natural language commands. We conducted testing of UFO across 9 popular Windows applications, encompassing a variety of scenarios reflective of users' daily usage. The results, derived from both quantitative metrics and real-case studies, underscore the superior effectiveness of UFO in fulfilling user requests. To the best of our knowledge, UFO stands as the first UI agent specifically tailored for task completion within the Windows OS environment. The open-source code for UFO is available on https://github.com/microsoft/UFO.

cs.HC↗
arXiv2024

Nissist: An Incident Mitigation Copilot based on Troubleshooting Guides

Effective incident management is pivotal for the smooth operation of enterprises-level cloud services. In order to expedite incident mitigation, service teams compile troubleshooting knowledge into Troubleshooting Guides (TSGs) accessible to on-call engineers (OCEs). While automated pipelines are enabled to resolve the most frequent and easy incidents, there still exist complex incidents that require OCEs' intervention. However, TSGs are often unstructured and incomplete, which requires manual interpretation by OCEs, leading to on-call fatigue and decreased productivity, especially among new-hire OCEs. In this work, we propose Nissist which leverages TSGs and incident mitigation histories to provide proactive suggestions, reducing human intervention. Leveraging Large Language Models (LLM), Nissist extracts insights from unstructured TSGs and historical incident mitigation discussions, forming a comprehensive knowledge base. Its multi-agent system design enhances proficiency in precisely discerning user queries, retrieving relevant information, and delivering systematic plans consecutively. Through our user case and experiment, we demonstrate that Nissist significant reduce Time to Mitigate (TTM) in incident mitigation, alleviating operational burdens on OCEs and improving service reliability. Our demo is available at https://aka.ms/nissist_demo.

cs.SE↗
arXiv2024

Bidirectional Progressive Transformer for Interaction Intention Anticipation

Interaction intention anticipation aims to jointly predict future hand trajectories and interaction hotspots. Existing research often treated trajectory forecasting and interaction hotspots prediction as separate tasks or solely considered the impact of trajectories on interaction hotspots, which led to the accumulation of prediction errors over time. However, a deeper inherent connection exists between hand trajectories and interaction hotspots, which allows for continuous mutual correction between them. Building upon this relationship, a novel Bidirectional prOgressive Transformer (BOT), which introduces a Bidirectional Progressive mechanism into the anticipation of interaction intention is established. Initially, BOT maximizes the utilization of spatial information from the last observation frame through the Spatial-Temporal Reconstruction Module, mitigating conflicts arising from changes of view in first-person videos. Subsequently, based on two independent prediction branches, a Bidirectional Progressive Enhancement Module is introduced to mutually improve the prediction of hand trajectories and interaction hotspots over time to minimize error accumulation. Finally, acknowledging the intrinsic randomness in human natural behavior, we employ a Trajectory Stochastic Unit and a C-VAE to introduce appropriate uncertainty to trajectories and interaction hotspots, respectively. Our method achieves state-of-the-art results on three benchmark datasets Epic-Kitchens-100, EGO4D, and EGTEA Gaze+, demonstrating superior in complex scenarios.

cs.CV↗
arXiv2024

AllHands: Ask Me Anything on Large-scale Verbatim Feedback via Large Language Models

Verbatim feedback constitutes a valuable repository of user experiences, opinions, and requirements essential for software development. Effectively and efficiently extracting valuable insights from such data poses a challenging task. This paper introduces Allhands , an innovative analytic framework designed for large-scale feedback analysis through a natural language interface, leveraging large language models (LLMs). Allhands adheres to a conventional feedback analytic workflow, initially conducting classification and topic modeling on the feedback to convert them into a structurally augmented format, incorporating LLMs to enhance accuracy, robustness, generalization, and user-friendliness. Subsequently, an LLM agent is employed to interpret users' diverse questions in natural language on feedback, translating them into Python code for execution, and delivering comprehensive multi-modal responses, including text, code, tables, and images. We evaluate Allhands across three diverse feedback datasets. The experiments demonstrate that Allhands achieves superior efficacy at all stages of analysis, including classification and topic modeling, eventually providing users with an "ask me anything" experience with comprehensive, correct and human-readable response. To the best of our knowledge, Allhands stands as the first comprehensive feedback analysis framework that supports diverse and customized requirements for insight extraction through a natural language interface.

cs.SE↗
arXiv2024

Deep Geometry Handling and Fragment-wise Molecular 3D Graph Generation

Most earlier 3D structure-based molecular generation approaches follow an atom-wise paradigm, incrementally adding atoms to a partially built molecular fragment within protein pockets. These methods, while effective in designing tightly bound ligands, often overlook other essential properties such as synthesizability. The fragment-wise generation paradigm offers a promising solution. However, a common challenge across both atom-wise and fragment-wise methods lies in their limited ability to co-design plausible chemical and geometrical structures, resulting in distorted conformations. In response to this challenge, we introduce the Deep Geometry Handling protocol, a more abstract design that extends the design focus beyond the model architecture. Through a comprehensive review of existing geometry-related models and their protocols, we propose a novel hybrid strategy, culminating in the development of FragGen - a geometry-reliable, fragment-wise molecular generation method. FragGen marks a significant leap forward in the quality of generated geometry and the synthesis accessibility of molecules. The efficacy of FragGen is further validated by its successful application in designing type II kinase inhibitors at the nanomolar level.

physics.chem-ph↗
arXiv2024

Exponential Cluster Synchronization in Fast Switching Network Topologies: A Pinning Control Approach with Necessary and Sufficient Conditions

This research investigates the intricate domain of synchronization problem among multiple agents operating within a dynamic fast switching network topology. We concentrate on cluster synchronization within coupled linear system under pinning control, providing both necessary and sufficient conditions. As a pivotal aspect, this paper aim to president the weakest possible conditions to make the coupled linear system realize cluster synchronization exponentially. Within the context of fast switching framework, we initially examine the necessary conditions, commencing with the transformation of the consensus problem into a stability problem, introducing a new variable to make the coupled system achieve cluster synchronization if the system is controllable; communication topology switching fast enough and the coupling strength should be sufficiently robust. Then, by using the Lyapunov theorem, we also present that the state matrix controllable is necessary for cluster synchronization. Furthermore, this paper culminating in the incorporation of contraction theory and an invariant manifold, demonstrating that the switching topology has an average is imperative for achieving cluster synchronization. Finally, we introduce three simulations to validate the efficacy of the proposed approach.

eess.SY↗
arXiv2024

Automated Root Causing of Cloud Incidents using In-Context Learning with GPT-4

Root Cause Analysis (RCA) plays a pivotal role in the incident diagnosis process for cloud services, requiring on-call engineers to identify the primary issues and implement corrective actions to prevent future recurrences. Improving the incident RCA process is vital for minimizing service downtime, customer impact and manual toil. Recent advances in artificial intelligence have introduced state-of-the-art Large Language Models (LLMs) like GPT-4, which have proven effective in tackling various AIOps problems, ranging from code authoring to incident management. Nonetheless, the GPT-4 model's immense size presents challenges when trying to fine-tune it on user data because of the significant GPU resource demand and the necessity for continuous model fine-tuning with the emergence of new data. To address the high cost of fine-tuning LLM, we propose an in-context learning approach for automated root causing, which eliminates the need for fine-tuning. We conduct extensive study over 100,000 production incidents, comparing several large language models using multiple metrics. The results reveal that our in-context learning approach outperforms the previous fine-tuned large language models such as GPT-3 by an average of 24.8\% across all metrics, with an impressive 49.7\% improvement over the zero-shot model. Moreover, human evaluation involving actual incident owners demonstrates its superiority over the fine-tuned model, achieving a 43.5\% improvement in correctness and an 8.7\% enhancement in readability. The impressive results demonstrate the viability of utilizing a vanilla GPT model for the RCA task, thereby avoiding the high computational and maintenance costs associated with a fine-tuned model.

cs.CL↗
arXiv2023

Xpert: Empowering Incident Management with Query Recommendations via Large Language Models

Large-scale cloud systems play a pivotal role in modern IT infrastructure. However, incidents occurring within these systems can lead to service disruptions and adversely affect user experience. To swiftly resolve such incidents, on-call engineers depend on crafting domain-specific language (DSL) queries to analyze telemetry data. However, writing these queries can be challenging and time-consuming. This paper presents a thorough empirical study on the utilization of queries of KQL, a DSL employed for incident management in a large-scale cloud management system at Microsoft. The findings obtained underscore the importance and viability of KQL queries recommendation to enhance incident management. Building upon these valuable insights, we introduce Xpert, an end-to-end machine learning framework that automates KQL recommendation process. By leveraging historical incident data and large language models, Xpert generates customized KQL queries tailored to new incidents. Furthermore, Xpert incorporates a novel performance metric called Xcore, enabling a thorough evaluation of query quality from three comprehensive perspectives. We conduct extensive evaluations of Xpert, demonstrating its effectiveness in offline settings. Notably, we deploy Xpert in the real production environment of a large-scale incident management system in Microsoft, validating its efficiency in supporting incident management. To the best of our knowledge, this paper represents the first empirical study of its kind, and Xpert stands as a pioneering DSL query recommendation framework designed for incident management.

cs.SE↗
arXiv2023

Automatic Root Cause Analysis via Large Language Models for Cloud Incidents

Ensuring the reliability and availability of cloud services necessitates efficient root cause analysis (RCA) for cloud incidents. Traditional RCA methods, which rely on manual investigations of data sources such as logs and traces, are often laborious, error-prone, and challenging for on-call engineers. In this paper, we introduce RCACopilot, an innovative on-call system empowered by the large language model for automating RCA of cloud incidents. RCACopilot matches incoming incidents to corresponding incident handlers based on their alert types, aggregates the critical runtime diagnostic information, predicts the incident's root cause category, and provides an explanatory narrative. We evaluate RCACopilot using a real-world dataset consisting of a year's worth of incidents from Microsoft. Our evaluation demonstrates that RCACopilot achieves RCA accuracy up to 0.766. Furthermore, the diagnostic information collection component of RCACopilot has been successfully in use at Microsoft for over four years.

cs.SE↗
arXiv2023

Delete: Deep Lead Optimization Enveloped in Protein Pocket through Unified Deleting Strategies and a Structure-aware Network

Drug discovery is a highly complicated process, and it is unfeasible to fully commit it to the recently developed molecular generation methods. Deep learning-based lead optimization takes expert knowledge as a starting point, learning from numerous historical cases about how to modify the structure for better drug-forming properties. However, compared with the more established de novo generation schemes, lead optimization is still an area that requires further exploration. Previously developed models are often limited to resolving one (or few) certain subtask(s) of lead optimization, and most of them can only generate the two-dimensional structures of molecules while disregarding the vital protein-ligand interactions based on the three-dimensional binding poses. To address these challenges, we present a novel tool for lead optimization, named Delete (Deep lead optimization enveloped in protein pocket). Our model can handle all subtasks of lead optimization involving fragment growing, linking, and replacement through a unified deleting (masking) strategy, and is aware of the intricate pocket-ligand interactions through the geometric design of networks. Statistical evaluations and case studies conducted on individual subtasks demonstrate that Delete has a significant ability to produce molecules with superior binding affinities to protein targets and reasonable drug-likeness from given fragments or atoms. This feature may assist medicinal chemists in developing not only me-too/me-better products from existing drugs but also hit-to-lead for first-in-class drugs in a highly efficient manner.

q-bio.BM↗
arXiv2023

Highly accurate and efficient deep learning paradigm for full-atom protein loop modeling with KarmaLoop

Protein loop modeling is the most challenging yet highly non-trivial task in protein structure prediction. Despite recent progress, existing methods including knowledge-based, ab initio, hybrid and deep learning (DL) methods fall significantly short of either atomic accuracy or computational efficiency. Moreover, an overarching focus on backbone atoms has resulted in a dearth of attention given to side-chain conformation, a critical aspect in a host of downstream applications including ligand docking, molecular dynamics simulation and drug design. To overcome these limitations, we present KarmaLoop, a novel paradigm that distinguishes itself as the first DL method centered on full-atom (encompassing both backbone and side-chain heavy atoms) protein loop modeling. Our results demonstrate that KarmaLoop considerably outperforms conventional and DL-based methods of loop modeling in terms of both accuracy and efficiency, with the average RMSD improved by over two-fold compared to the second-best baseline method across different tasks, and manifests at least two orders of magnitude speedup in general. Consequently, our comprehensive evaluations indicate that KarmaLoop provides a state-of-the-art DL solution for protein loop modeling, with the potential to hasten the advancement of protein engineering, antibody-antigen recognition, and drug design.

q-bio.BM↗
arXiv2023

Assess and Summarize: Improve Outage Understanding with Large Language Models

Cloud systems have become increasingly popular in recent years due to their flexibility and scalability. Each time cloud computing applications and services hosted on the cloud are affected by a cloud outage, users can experience slow response times, connection issues or total service disruption, resulting in a significant negative business impact. Outages are usually comprised of several concurring events/source causes, and therefore understanding the context of outages is a very challenging yet crucial first step toward mitigating and resolving outages. In current practice, on-call engineers with in-depth domain knowledge, have to manually assess and summarize outages when they happen, which is time-consuming and labor-intensive. In this paper, we first present a large-scale empirical study investigating the way on-call engineers currently deal with cloud outages at Microsoft, and then present and empirically validate a novel approach (dubbed Oasis) to help the engineers in this task. Oasis is able to automatically assess the impact scope of outages as well as to produce human-readable summarization. Specifically, Oasis first assesses the impact scope of an outage by aggregating relevant incidents via multiple techniques. Then, it generates a human-readable summary by leveraging fine-tuned large language models like GPT-3.x. The impact assessment component of Oasis was introduced in Microsoft over three years ago, and it is now widely adopted, while the outage summarization component has been recently introduced, and in this article we present the results of an empirical evaluation we carried out on 18 real-world cloud systems as well as a human-based evaluation with outage owners. The results show that Oasis can effectively and efficiently summarize outages, and lead Microsoft to deploy its first prototype which is currently under experimental adoption by some of the incident teams.

cs.SE↗
arXiv2023

E-MLB: Multilevel Benchmark for Event-Based Camera Denoising

Event cameras, such as dynamic vision sensors (DVS), are biologically inspired vision sensors that have advanced over conventional cameras in high dynamic range, low latency and low power consumption, showing great application potential in many fields. Event cameras are more sensitive to junction leakage current and photocurrent as they output differential signals, losing the smoothing function of the integral imaging process in the RGB camera. The logarithmic conversion further amplifies noise, especially in low-contrast conditions. Recently, researchers proposed a series of datasets and evaluation metrics but limitations remain: 1) the existing datasets are small in scale and insufficient in noise diversity, which cannot reflect the authentic working environments of event cameras; and 2) the existing denoising evaluation metrics are mostly referenced evaluation metrics, relying on APS information or manual annotation. To address the above issues, we construct a large-scale event denoising dataset (multilevel benchmark for event denoising, E-MLB) for the first time, which consists of 100 scenes, each with four noise levels, that is 12 times larger than the largest existing denoising dataset. We also propose the first nonreference event denoising metric, the event structural ratio (ESR), which measures the structural intensity of given events. ESR is inspired by the contrast metric, but is independent of the number of events and projection direction. Based on the proposed benchmark and ESR, we evaluate the most representative denoising algorithms, including classic and SOTA, and provide denoising baselines under various scenes and noise levels. The corresponding results and codes are available at https://github.com/KugaMaxx/cuke-emlb.

cs.CV↗