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Add to EdgePost-Fair Federated Learning: Achieving Group and Community Fairness in Federated Learning via Post-processing
May 28, 2024
Federated Learning (FL) is a distributed machine learning framework in which a set of local communities collaboratively learn a shared global model while retaining all training data locally within each community. Two notions of fairness have recently emerged as important issues for federated learning: group fairness and community fairness. Group fairness requires that a model's decisions do not favor any particular group based on a set of legally protected attributes such as race or gender. Community fairness requires that global models exhibit similar levels of performance (accuracy) across all collaborating communities. Both fairness concepts can coexist within an FL framework, but the existing literature has focused on either one concept or the other. This paper proposes and analyzes a post-processing fair federated learning (FFL) framework called post-FFL. Post-FFL uses a linear program to simultaneously enforce group and community fairness while maximizing the utility of the global model. Because Post-FFL is a post-processing approach, it can be used with existing FL training pipelines whose convergence properties are well understood. This paper uses post-FFL on real-world datasets to mimic how hospital networks, for example, use federated learning to deliver community health care. Theoretical results bound the accuracy lost when post-FFL enforces both notion of fairness. Experimental results illustrate that post-FFL simultaneously improves both group and community fairness in FL. Moreover, post-FFL outperforms the existing in-processing fair federated learning in terms of improving both notions of fairness, communication efficiency and computation cost.
Learning to Predict Mutation Effects of Protein-Protein Interactions by Microenvironment-aware Hierarchical Prompt Learning
May 16, 2024Protein-protein bindings play a key role in a variety of fundamental biological processes, and thus predicting the effects of amino acid mutations on protein-protein binding is crucial. To tackle the scarcity of annotated mutation data, pre-training with massive unlabeled data has emerged as a promising solution. However, this process faces a series of challenges: (1) complex higher-order dependencies among multiple (more than paired) structural scales have not yet been fully captured; (2) it is rarely explored how mutations alter the local conformation of the surrounding microenvironment; (3) pre-training is costly, both in data size and computational burden. In this paper, we first construct a hierarchical prompt codebook to record common microenvironmental patterns at different structural scales independently. Then, we develop a novel codebook pre-training task, namely masked microenvironment modeling, to model the joint distribution of each mutation with their residue types, angular statistics, and local conformational changes in the microenvironment. With the constructed prompt codebook, we encode the microenvironment around each mutation into multiple hierarchical prompts and combine them to flexibly provide information to wild-type and mutated protein complexes about their microenvironmental differences. Such a hierarchical prompt learning framework has demonstrated superior performance and training efficiency over state-of-the-art pre-training-based methods in mutation effect prediction and a case study of optimizing human antibodies against SARS-CoV-2.
MAPE-PPI: Towards Effective and Efficient Protein-Protein Interaction Prediction via Microenvironment-Aware Protein Embedding
Feb 22, 2024Protein-Protein Interactions (PPIs) are fundamental in various biological processes and play a key role in life activities. The growing demand and cost of experimental PPI assays require computational methods for efficient PPI prediction. While existing methods rely heavily on protein sequence for PPI prediction, it is the protein structure that is the key to determine the interactions. To take both protein modalities into account, we define the microenvironment of an amino acid residue by its sequence and structural contexts, which describe the surrounding chemical properties and geometric features. In addition, microenvironments defined in previous work are largely based on experimentally assayed physicochemical properties, for which the "vocabulary" is usually extremely small. This makes it difficult to cover the diversity and complexity of microenvironments. In this paper, we propose Microenvironment-Aware Protein Embedding for PPI prediction (MPAE-PPI), which encodes microenvironments into chemically meaningful discrete codes via a sufficiently large microenvironment "vocabulary" (i.e., codebook). Moreover, we propose a novel pre-training strategy, namely Masked Codebook Modeling (MCM), to capture the dependencies between different microenvironments by randomly masking the codebook and reconstructing the input. With the learned microenvironment codebook, we can reuse it as an off-the-shelf tool to efficiently and effectively encode proteins of different sizes and functions for large-scale PPI prediction. Extensive experiments show that MAPE-PPI can scale to PPI prediction with millions of PPIs with superior trade-offs between effectiveness and computational efficiency than the state-of-the-art competitors.
Towards Safer Large Language Models through Machine Unlearning
Feb 15, 2024The rapid advancement of Large Language Models (LLMs) has demonstrated their vast potential across various domains, attributed to their extensive pretraining knowledge and exceptional generalizability. However, LLMs often encounter challenges in generating harmful content when faced with problematic prompts. To address this problem, existing work attempted to implement a gradient ascent based approach to prevent LLMs from producing harmful output. While these methods can be effective, they frequently impact the model utility in responding to normal prompts. To address this gap, we introduce Selective Knowledge negation Unlearning (SKU), a novel unlearning framework for LLMs, designed to eliminate harmful knowledge while preserving utility on normal prompts. Specifically, SKU is consisted of two stages: harmful knowledge acquisition stage and knowledge negation stage. The first stage aims to identify and acquire harmful knowledge within the model, whereas the second is dedicated to remove this knowledge. SKU selectively isolates and removes harmful knowledge in model parameters, ensuring the model's performance remains robust on normal prompts. Our experiments conducted across various LLM architectures demonstrate that SKU identifies a good balance point between removing harmful information and preserving utility.
Can we soft prompt LLMs for graph learning tasks?
Feb 15, 2024Graph plays an important role in representing complex relationships in real-world applications such as social networks, biological data and citation networks. In recent years, Large Language Models (LLMs) have achieved tremendous success in various domains, which makes applying LLMs to graphs particularly appealing. However, directly applying LLMs to graph modalities presents unique challenges due to the discrepancy and mismatch between the graph and text modalities. Hence, to further investigate LLMs' potential for comprehending graph information, we introduce GraphPrompter, a novel framework designed to align graph information with LLMs via soft prompts. Specifically, GraphPrompter consists of two main components: a graph neural network to encode complex graph information and an LLM that effectively processes textual information. Comprehensive experiments on various benchmark datasets under node classification and link prediction tasks demonstrate the effectiveness of our proposed method. The GraphPrompter framework unveils the substantial capabilities of LLMs as predictors in graph-related tasks, enabling researchers to utilize LLMs across a spectrum of real-world graph scenarios more effectively.
UGMAE: A Unified Framework for Graph Masked Autoencoders
Feb 12, 2024Generative self-supervised learning on graphs, particularly graph masked autoencoders, has emerged as a popular learning paradigm and demonstrated its efficacy in handling non-Euclidean data. However, several remaining issues limit the capability of existing methods: 1) the disregard of uneven node significance in masking, 2) the underutilization of holistic graph information, 3) the ignorance of semantic knowledge in the representation space due to the exclusive use of reconstruction loss in the output space, and 4) the unstable reconstructions caused by the large volume of masked contents. In light of this, we propose UGMAE, a unified framework for graph masked autoencoders to address these issues from the perspectives of adaptivity, integrity, complementarity, and consistency. Specifically, we first develop an adaptive feature mask generator to account for the unique significance of nodes and sample informative masks (adaptivity). We then design a ranking-based structure reconstruction objective joint with feature reconstruction to capture holistic graph information and emphasize the topological proximity between neighbors (integrity). After that, we present a bootstrapping-based similarity module to encode the high-level semantic knowledge in the representation space, complementary to the low-level reconstruction in the output space (complementarity). Finally, we build a consistency assurance module to provide reconstruction objectives with extra stabilized consistency targets (consistency). Extensive experiments demonstrate that UGMAE outperforms both contrastive and generative state-of-the-art baselines on several tasks across multiple datasets.
G-Retriever: Retrieval-Augmented Generation for Textual Graph Understanding and Question Answering
Feb 12, 2024Given a graph with textual attributes, we enable users to `chat with their graph': that is, to ask questions about the graph using a conversational interface. In response to a user's questions, our method provides textual replies and highlights the relevant parts of the graph. While existing works integrate large language models (LLMs) and graph neural networks (GNNs) in various ways, they mostly focus on either conventional graph tasks (such as node, edge, and graph classification), or on answering simple graph queries on small or synthetic graphs. In contrast, we develop a flexible question-answering framework targeting real-world textual graphs, applicable to multiple applications including scene graph understanding, common sense reasoning, and knowledge graph reasoning. Toward this goal, we first develop our Graph Question Answering (GraphQA) benchmark with data collected from different tasks. Then, we propose our G-Retriever approach, which integrates the strengths of GNNs, LLMs, and Retrieval-Augmented Generation (RAG), and can be fine-tuned to enhance graph understanding via soft prompting. To resist hallucination and to allow for textual graphs that greatly exceed the LLM's context window size, G-Retriever performs RAG over a graph by formulating this task as a Prize-Collecting Steiner Tree optimization problem. Empirical evaluations show that our method outperforms baselines on textual graph tasks from multiple domains, scales well with larger graph sizes, and resists hallucination. (Our codes and datasets are available at: https://github.com/XiaoxinHe/G-Retriever.)
TinyLLM: Learning a Small Student from Multiple Large Language Models
Feb 07, 2024Transferring the reasoning capability from stronger large language models (LLMs) to smaller ones has been quite appealing, as smaller LLMs are more flexible to deploy with less expense. Among the existing solutions, knowledge distillation stands out due to its outstanding efficiency and generalization. However, existing methods suffer from several drawbacks, including limited knowledge diversity and the lack of rich contextual information. To solve the problems and facilitate the learning of compact language models, we propose TinyLLM, a novel knowledge distillation paradigm to learn a small student LLM from multiple large teacher LLMs. In particular, we encourage the student LLM to not only generate the correct answers but also understand the rationales behind these answers. Given that different LLMs possess diverse reasoning skills, we guide the student model to assimilate knowledge from various teacher LLMs. We further introduce an in-context example generator and a teacher-forcing Chain-of-Thought strategy to ensure that the rationales are accurate and grounded in contextually appropriate scenarios. Extensive experiments on six datasets across two reasoning tasks demonstrate the superiority of our method. Results show that TinyLLM can outperform large teacher LLMs significantly, despite having a considerably smaller model size.
Democratizing Large Language Models via Personalized Parameter-Efficient Fine-tuning
Feb 06, 2024Personalization in large language models (LLMs) is increasingly important, aiming to align LLM's interactions, content, and recommendations with individual user preferences. Recent advances in LLM personalization have spotlighted effective prompt design, by enriching user queries with non-parametric knowledge through behavior history retrieval and textual profiles. However, these approaches were limited due to a lack of model ownership, resulting in constrained customization and privacy issues. Moreover, they often failed to accurately capture user behavior patterns, especially in cases where user data were complex and dynamic. To address these shortcomings, we introduce One PEFT Per User (OPPU), which employs personalized parameter-efficient fine-tuning (PEFT) modules, to store user-specific behavior patterns and preferences. By plugging in users' personal PEFT parameters, they can own and use their LLMs personally. OPPU integrates parametric user knowledge in the personal PEFT parameters with the non-parametric knowledge acquired through retrieval and profile. This integration adapts individual LLMs to user behavior shifts. Experimental results demonstrate that OPPU significantly outperforms existing prompt-based methods across seven diverse tasks in the LaMP benchmark. Further in-depth studies reveal OPPU's enhanced capabilities in handling user behavior shifts, modeling users at different active levels, maintaining robustness across various user history formats, and displaying versatility with different PEFT methods.
Data-Centric Evolution in Autonomous Driving: A Comprehensive Survey of Big Data System, Data Mining, and Closed-Loop Technologies
Jan 26, 2024The aspiration of the next generation's autonomous driving (AD) technology relies on the dedicated integration and interaction among intelligent perception, prediction, planning, and low-level control. There has been a huge bottleneck regarding the upper bound of autonomous driving algorithm performance, a consensus from academia and industry believes that the key to surmount the bottleneck lies in data-centric autonomous driving technology. Recent advancement in AD simulation, closed-loop model training, and AD big data engine have gained some valuable experience. However, there is a lack of systematic knowledge and deep understanding regarding how to build efficient data-centric AD technology for AD algorithm self-evolution and better AD big data accumulation. To fill in the identified research gaps, this article will closely focus on reviewing the state-of-the-art data-driven autonomous driving technologies, with an emphasis on the comprehensive taxonomy of autonomous driving datasets characterized by milestone generations, key features, data acquisition settings, etc. Furthermore, we provide a systematic review of the existing benchmark closed-loop AD big data pipelines from the industrial frontier, including the procedure of closed-loop frameworks, key technologies, and empirical studies. Finally, the future directions, potential applications, limitations and concerns are discussed to arouse efforts from both academia and industry for promoting the further development of autonomous driving. The project repository is available at: https://github.com/LincanLi98/Awesome-Data-Centric-Autonomous-Driving.