ChefFusion: Multimodal Foundation Model Integrating Recipe and Food Image Generation

Significant work has been conducted in the domain of food computing, yet these studies typically focus on single tasks such as t2t (instruction generation from food titles and ingredients), i2t (recipe generation from food images), or t2i (food image generation from recipes). None of these approaches integrate all modalities simultaneously. To address this gap, we introduce a novel food computing foundation model that achieves true multimodality, encompassing tasks such as t2t, t2i, i2t, it2t, and t2ti. By leveraging large language models (LLMs) and pre-trained image encoder and decoder models, our model can perform a diverse array of food computing-related tasks, including food understanding, food recognition, recipe generation, and food image generation. Compared to previous models, our foundation model demonstrates a significantly broader range of capabilities and exhibits superior performance, particularly in food image generation and recipe generation tasks. We open-sourced ChefFusion at GitHub.

Machine Unlearning in Generative AI: A Survey

Generative AI technologies have been deployed in many places, such as (multimodal) large language models and vision generative models. Their remarkable performance should be attributed to massive training data and emergent reasoning abilities. However, the models would memorize and generate sensitive, biased, or dangerous information originated from the training data especially those from web crawl. New machine unlearning (MU) techniques are being developed to reduce or eliminate undesirable knowledge and its effects from the models, because those that were designed for traditional classification tasks could not be applied for Generative AI. We offer a comprehensive survey on many things about MU in Generative AI, such as a new problem formulation, evaluation methods, and a structured discussion on the advantages and limitations of different kinds of MU techniques. It also presents several critical challenges and promising directions in MU research. A curated list of readings can be found: https://github.com/franciscoliu/GenAI-MU-Reading.

Deconstructing The Ethics of Large Language Models from Long-standing Issues to New-emerging Dilemmas

Large Language Models (LLMs) have achieved unparalleled success across diverse language modeling tasks in recent years. However, this progress has also intensified ethical concerns, impacting the deployment of LLMs in everyday contexts. This paper provides a comprehensive survey of ethical challenges associated with LLMs, from longstanding issues such as copyright infringement, systematic bias, and data privacy, to emerging problems like truthfulness and social norms. We critically analyze existing research aimed at understanding, examining, and mitigating these ethical risks. Our survey underscores integrating ethical standards and societal values into the development of LLMs, thereby guiding the development of responsible and ethically aligned language models.

Post-Fair Federated Learning: Achieving Group and Community Fairness in Federated Learning via Post-processing

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

Protein-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

Protein-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

The 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?

Graph 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.

G-Retriever: Retrieval-Augmented Generation for Textual Graph Understanding and Question Answering

Given 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.)

UGMAE: A Unified Framework for Graph Masked Autoencoders

Generative 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.