Utilizing Large Language Models in An Iterative Paradigm with Domain Feedback for Molecule Optimization

Molecule optimization is a critical task in drug discovery to optimize desired properties of a given molecule through chemical modification. Despite Large Language Models (LLMs) holding the potential to efficiently simulate this task by using natural language to direct the optimization, straightforwardly utilizing shows limited performance. In this work, we facilitate utilizing LLMs in an iterative paradigm by proposing a simple yet highly effective domain feedback provider, namely $\text{Re}^2$DF. In detail, $\text{Re}^2$DF harnesses an external toolkit, RDKit, to handle the molecule hallucination, if the modified molecule is chemically invalid. Otherwise, its desired properties are computed and compared to the original one, establishing reliable domain feedback with correct direction and distance towards the objective, followed by a retrieved example, to explicitly guide the LLM to refine the modified molecule. We conduct experiments across both single- and multi-property objectives with 2 thresholds, where $\text{Re}^2$DF shows significant improvements. Particularly, for 20 single-property objectives, $\text{Re}^2$DF enhances the Hit ratio by 16.95\% and 20.76\% under loose and strict thresholds, respectively. For 32 multi-property objectives, $\text{Re}^2$DF enhances the Hit ratio by 6.04\% and 5.25\%.

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.

MetaLLM: A High-performant and Cost-efficient Dynamic Framework for Wrapping LLMs

The rapid progress in machine learning (ML) has brought forth many large language models (LLMs) that excel in various tasks and areas. These LLMs come with different abilities and costs in terms of computation or pricing. Since the demand for each query can vary, e.g., because of the queried domain or its complexity, defaulting to one LLM in an application is not usually the best choice, whether it is the biggest, priciest, or even the one with the best average test performance. Consequently, picking the right LLM that is both accurate and cost-effective for an application remains a challenge. In this paper, we introduce MetaLLM, a framework that dynamically and intelligently routes each query to the optimal LLM (among several available LLMs) for classification tasks, achieving significantly improved accuracy and cost-effectiveness. By framing the selection problem as a multi-armed bandit, MetaLLM balances prediction accuracy and cost efficiency under uncertainty. Our experiments, conducted on popular LLM platforms such as OpenAI's GPT models, Amazon's Titan, Anthropic's Claude, and Meta's LLaMa, showcase MetaLLM's efficacy in real-world scenarios, laying the groundwork for future extensions beyond classification tasks.

The Hidden Influence of Latent Feature Magnitude When Learning with Imbalanced Data

Machine learning (ML) models have difficulty generalizing when the number of training class instances are numerically imbalanced. The problem of generalization in the face of data imbalance has largely been attributed to the lack of training data for under-represented classes and to feature overlap. The typical remedy is to implement data augmentation for classes with fewer instances or to assign a higher cost to minority class prediction errors or to undersample the prevalent class. However, we show that one of the central causes of impaired generalization when learning with imbalanced data is the inherent manner in which ML models perform inference. These models have difficulty generalizing due to their heavy reliance on the magnitude of encoded signals. During inference, the models predict classes based on a combination of encoded signal magnitudes that linearly sum to the largest scalar. We demonstrate that even with aggressive data augmentation, which generally improves minority class prediction accuracy, parametric ML models still associate a class label with a limited number of feature combinations that sum to a prediction, which can affect generalization.

MolX: Enhancing Large Language Models for Molecular Learning with A Multi-Modal Extension

Recently, Large Language Models (LLMs) with their strong task-handling capabilities have shown remarkable advancements across a spectrum of fields, moving beyond natural language understanding. However, their proficiency within the chemistry domain remains restricted, especially in solving professional molecule-related tasks. This challenge is attributed to their inherent limitations in comprehending molecules using only common textual representations, i.e., SMILES strings. In this study, we seek to enhance the ability of LLMs to comprehend molecules by designing and equipping them with a multi-modal external module, namely MolX. In particular, instead of directly using a SMILES string to represent a molecule, we utilize specific encoders to extract fine-grained features from both SMILES string and 2D molecular graph representations for feeding into an LLM. Moreover, a human-defined molecular fingerprint is incorporated to leverage its embedded domain knowledge. Then, to establish an alignment between MolX and the LLM's textual input space, the whole model in which the LLM is frozen, is pre-trained with a versatile strategy including a diverse set of tasks. Extensive experimental evaluations demonstrate that our proposed method only introduces a small number of trainable parameters while outperforming baselines on various downstream molecule-related tasks ranging from molecule-to-text translation to retrosynthesis, with and without fine-tuning the LLM.

Safety in Graph Machine Learning: Threats and Safeguards

Graph Machine Learning (Graph ML) has witnessed substantial advancements in recent years. With their remarkable ability to process graph-structured data, Graph ML techniques have been extensively utilized across diverse applications, including critical domains like finance, healthcare, and transportation. Despite their societal benefits, recent research highlights significant safety concerns associated with the widespread use of Graph ML models. Lacking safety-focused designs, these models can produce unreliable predictions, demonstrate poor generalizability, and compromise data confidentiality. In high-stakes scenarios such as financial fraud detection, these vulnerabilities could jeopardize both individuals and society at large. Therefore, it is imperative to prioritize the development of safety-oriented Graph ML models to mitigate these risks and enhance public confidence in their applications. In this survey paper, we explore three critical aspects vital for enhancing safety in Graph ML: reliability, generalizability, and confidentiality. We categorize and analyze threats to each aspect under three headings: model threats, data threats, and attack threats. This novel taxonomy guides our review of effective strategies to protect against these threats. Our systematic review lays a groundwork for future research aimed at developing practical, safety-centered Graph ML models. Furthermore, we highlight the significance of safe Graph ML practices and suggest promising avenues for further investigation in this crucial area.

You do not have to train Graph Neural Networks at all on text-attributed graphs

Graph structured data, specifically text-attributed graphs (TAG), effectively represent relationships among varied entities. Such graphs are essential for semi-supervised node classification tasks. Graph Neural Networks (GNNs) have emerged as a powerful tool for handling this graph-structured data. Although gradient descent is commonly utilized for training GNNs for node classification, this study ventures into alternative methods, eliminating the iterative optimization processes. We introduce TrainlessGNN, a linear GNN model capitalizing on the observation that text encodings from the same class often cluster together in a linear subspace. This model constructs a weight matrix to represent each class's node attribute subspace, offering an efficient approach to semi-supervised node classification on TAG. Extensive experiments reveal that our trainless models can either match or even surpass their conventionally trained counterparts, demonstrating the possibility of refraining from gradient descent in certain configurations.

CORE: Data Augmentation for Link Prediction via Information Bottleneck

Link prediction (LP) is a fundamental task in graph representation learning, with numerous applications in diverse domains. However, the generalizability of LP models is often compromised due to the presence of noisy or spurious information in graphs and the inherent incompleteness of graph data. To address these challenges, we draw inspiration from the Information Bottleneck principle and propose a novel data augmentation method, COmplete and REduce (CORE) to learn compact and predictive augmentations for LP models. In particular, CORE aims to recover missing edges in graphs while simultaneously removing noise from the graph structures, thereby enhancing the model's robustness and performance. Extensive experiments on multiple benchmark datasets demonstrate the applicability and superiority of CORE over state-of-the-art methods, showcasing its potential as a leading approach for robust LP in graph representation learning.

Universal Link Predictor By In-Context Learning on Graphs

Link prediction is a crucial task in graph machine learning, where the goal is to infer missing or future links within a graph. Traditional approaches leverage heuristic methods based on widely observed connectivity patterns, offering broad applicability and generalizability without the need for model training. Despite their utility, these methods are limited by their reliance on human-derived heuristics and lack the adaptability of data-driven approaches. Conversely, parametric link predictors excel in automatically learning the connectivity patterns from data and achieving state-of-the-art but fail short to directly transfer across different graphs. Instead, it requires the cost of extensive training and hyperparameter optimization to adapt to the target graph. In this work, we introduce the Universal Link Predictor (UniLP), a novel model that combines the generalizability of heuristic approaches with the pattern learning capabilities of parametric models. UniLP is designed to autonomously identify connectivity patterns across diverse graphs, ready for immediate application to any unseen graph dataset without targeted training. We address the challenge of conflicting connectivity patterns-arising from the unique distributions of different graphs-through the implementation of In-context Learning (ICL). This approach allows UniLP to dynamically adjust to various target graphs based on contextual demonstrations, thereby avoiding negative transfer. Through rigorous experimentation, we demonstrate UniLP's effectiveness in adapting to new, unseen graphs at test time, showcasing its ability to perform comparably or even outperform parametric models that have been finetuned for specific datasets. Our findings highlight UniLP's potential to set a new standard in link prediction, combining the strengths of heuristic and parametric methods in a single, versatile framework.

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.