Adaptive Catalyst Discovery Using Multicriteria Bayesian Optimization with Representation Learning

High-performance catalysts are crucial for sustainable energy conversion and human health. However, the discovery of catalysts faces challenges due to the absence of efficient approaches to navigating vast and high-dimensional structure and composition spaces. In this study, we propose a high-throughput computational catalyst screening approach integrating density functional theory (DFT) and Bayesian Optimization (BO). Within the BO framework, we propose an uncertainty-aware atomistic machine learning model, UPNet, which enables automated representation learning directly from high-dimensional catalyst structures and achieves principled uncertainty quantification. Utilizing a constrained expected improvement acquisition function, our BO framework simultaneously considers multiple evaluation criteria. Using the proposed methods, we explore catalyst discovery for the CO2 reduction reaction. The results demonstrate that our approach achieves high prediction accuracy, facilitates interpretable feature extraction, and enables multicriteria design optimization, leading to significant reduction of computing power and time (10x reduction of required DFT calculations) in high-performance catalyst discovery.

Overcoming Pitfalls in Graph Contrastive Learning Evaluation: Toward Comprehensive Benchmarks

The rise of self-supervised learning, which operates without the need for labeled data, has garnered significant interest within the graph learning community. This enthusiasm has led to the development of numerous Graph Contrastive Learning (GCL) techniques, all aiming to create a versatile graph encoder that leverages the wealth of unlabeled data for various downstream tasks. However, the current evaluation standards for GCL approaches are flawed due to the need for extensive hyper-parameter tuning during pre-training and the reliance on a single downstream task for assessment. These flaws can skew the evaluation away from the intended goals, potentially leading to misleading conclusions. In our paper, we thoroughly examine these shortcomings and offer fresh perspectives on how GCL methods are affected by hyper-parameter choices and the choice of downstream tasks for their evaluation. Additionally, we introduce an enhanced evaluation framework designed to more accurately gauge the effectiveness, consistency, and overall capability of GCL methods.

Data Augmentation for Supervised Graph Outlier Detection with Latent Diffusion Models

Graph outlier detection is a prominent task of research and application in the realm of graph neural networks. It identifies the outlier nodes that exhibit deviation from the majority in the graph. One of the fundamental challenges confronting supervised graph outlier detection algorithms is the prevalent issue of class imbalance, where the scarcity of outlier instances compared to normal instances often results in suboptimal performance. Conventional methods mitigate the imbalance by reweighting instances in the estimation of the loss function, assigning higher weights to outliers and lower weights to inliers. Nonetheless, these strategies are prone to overfitting and underfitting, respectively. Recently, generative models, especially diffusion models, have demonstrated their efficacy in synthesizing high-fidelity images. Despite their extraordinary generation quality, their potential in data augmentation for supervised graph outlier detection remains largely underexplored. To bridge this gap, we introduce GODM, a novel data augmentation for mitigating class imbalance in supervised Graph Outlier detection with latent Diffusion Models. Specifically, our proposed method consists of three key components: (1) Variantioanl Encoder maps the heterogeneous information inherent within the graph data into a unified latent space. (2) Graph Generator synthesizes graph data that are statistically similar to real outliers from latent space, and (3) Latent Diffusion Model learns the latent space distribution of real organic data by iterative denoising. Extensive experiments conducted on multiple datasets substantiate the effectiveness and efficiency of GODM. The case study further demonstrated the generation quality of our synthetic data. To foster accessibility and reproducibility, we encapsulate GODM into a plug-and-play package and release it at the Python Package Index (PyPI).

MolSets: Molecular Graph Deep Sets Learning for Mixture Property Modeling

Recent advances in machine learning (ML) have expedited materials discovery and design. One significant challenge faced in ML for materials is the expansive combinatorial space of potential materials formed by diverse constituents and their flexible configurations. This complexity is particularly evident in molecular mixtures, a frequently explored space for materials such as battery electrolytes. Owing to the complex structures of molecules and the sequence-independent nature of mixtures, conventional ML methods have difficulties in modeling such systems. Here we present MolSets, a specialized ML model for molecular mixtures. Representing individual molecules as graphs and their mixture as a set, MolSets leverages a graph neural network and the deep sets architecture to extract information at the molecule level and aggregate it at the mixture level, thus addressing local complexity while retaining global flexibility. We demonstrate the efficacy of MolSets in predicting the conductivity of lithium battery electrolytes and highlight its benefits in virtual screening of the combinatorial chemical space.

A Hardware Evaluation Framework for Large Language Model Inference

The past year has witnessed the increasing popularity of Large Language Models (LLMs). Their unprecedented scale and associated high hardware cost have impeded their broader adoption, calling for efficient hardware designs. With the large hardware needed to simply run LLM inference, evaluating different hardware designs becomes a new bottleneck. This work introduces LLMCompass, a hardware evaluation framework for LLM inference workloads. LLMCompass is fast, accurate, versatile, and able to describe and evaluate different hardware designs. LLMCompass includes a mapper to automatically find performance-optimal mapping and scheduling. It also incorporates an area-based cost model to help architects reason about their design choices. Compared to real-world hardware, LLMCompass' estimated latency achieves an average 10.4% error rate across various operators with various input sizes and an average 4.1% error rate for LLM inference. With LLMCompass, simulating a 4-NVIDIA A100 GPU node running GPT-3 175B inference can be done within 16 minutes on commodity hardware, including 26,400 rounds of the mapper's parameter search. With the aid of LLMCompass, this work draws architectural implications and explores new cost-effective hardware designs. By reducing the compute capability or replacing High Bandwidth Memory (HBM) with traditional DRAM, these new designs can achieve as much as 3.41x improvement in performance/cost compared to an NVIDIA A100, making them promising choices for democratizing LLMs. LLMCompass is planned to be fully open-source.

Mixed-Type Tabular Data Synthesis with Score-based Diffusion in Latent Space

Recent advances in tabular data generation have greatly enhanced synthetic data quality. However, extending diffusion models to tabular data is challenging due to the intricately varied distributions and a blend of data types of tabular data. This paper introduces TABSYN, a methodology that synthesizes tabular data by leveraging a diffusion model within a variational autoencoder (VAE) crafted latent space. The key advantages of the proposed TABSYN include (1) Generality: the ability to handle a broad spectrum of data types by converting them into a single unified space and explicitly capture inter-column relations; (2) Quality: optimizing the distribution of latent embeddings to enhance the subsequent training of diffusion models, which helps generate high-quality synthetic data, (3) Speed: much fewer number of reverse steps and faster synthesis speed than existing diffusion-based methods. Extensive experiments on six datasets with five metrics demonstrate that TABSYN outperforms existing methods. Specifically, it reduces the error rates by 86% and 67% for column-wise distribution and pair-wise column correlation estimations compared with the most competitive baselines.

DRL4Route: A Deep Reinforcement Learning Framework for Pick-up and Delivery Route Prediction

Pick-up and Delivery Route Prediction (PDRP), which aims to estimate the future service route of a worker given his current task pool, has received rising attention in recent years. Deep neural networks based on supervised learning have emerged as the dominant model for the task because of their powerful ability to capture workers' behavior patterns from massive historical data. Though promising, they fail to introduce the non-differentiable test criteria into the training process, leading to a mismatch in training and test criteria. Which considerably trims down their performance when applied in practical systems. To tackle the above issue, we present the first attempt to generalize Reinforcement Learning (RL) to the route prediction task, leading to a novel RL-based framework called DRL4Route. It combines the behavior-learning abilities of previous deep learning models with the non-differentiable objective optimization ability of reinforcement learning. DRL4Route can serve as a plug-and-play component to boost the existing deep learning models. Based on the framework, we further implement a model named DRL4Route-GAE for PDRP in logistic service. It follows the actor-critic architecture which is equipped with a Generalized Advantage Estimator that can balance the bias and variance of the policy gradient estimates, thus achieving a more optimal policy. Extensive offline experiments and the online deployment show that DRL4Route-GAE improves Location Square Deviation (LSD) by 0.9%-2.7%, and Accuracy@3 (ACC@3) by 2.4%-3.2% over existing methods on the real-world dataset.

Simplifying and Empowering Transformers for Large-Graph Representations

Learning representations on large-sized graphs is a long-standing challenge due to the inter-dependence nature involved in massive data points. Transformers, as an emerging class of foundation encoders for graph-structured data, have shown promising performance on small graphs due to its global attention capable of capturing all-pair influence beyond neighboring nodes. Even so, existing approaches tend to inherit the spirit of Transformers in language and vision tasks, and embrace complicated models by stacking deep multi-head attentions. In this paper, we critically demonstrate that even using a one-layer attention can bring up surprisingly competitive performance across node property prediction benchmarks where node numbers range from thousand-level to billion-level. This encourages us to rethink the design philosophy for Transformers on large graphs, where the global attention is a computation overhead hindering the scalability. We frame the proposed scheme as Simplified Graph Transformers (SGFormer), which is empowered by a simple attention model that can efficiently propagate information among arbitrary nodes in one layer. SGFormer requires none of positional encodings, feature/graph pre-processing or augmented loss. Empirically, SGFormer successfully scales to the web-scale graph ogbn-papers100M and yields up to 141x inference acceleration over SOTA Transformers on medium-sized graphs. Beyond current results, we believe the proposed methodology alone enlightens a new technical path of independent interest for building Transformers on large graphs.

OrthoReg: Improving Graph-regularized MLPs via Orthogonality Regularization

Graph Neural Networks (GNNs) are currently dominating in modeling graph-structure data, while their high reliance on graph structure for inference significantly impedes them from widespread applications. By contrast, Graph-regularized MLPs (GR-MLPs) implicitly inject the graph structure information into model weights, while their performance can hardly match that of GNNs in most tasks. This motivates us to study the causes of the limited performance of GR-MLPs. In this paper, we first demonstrate that node embeddings learned from conventional GR-MLPs suffer from dimensional collapse, a phenomenon in which the largest a few eigenvalues dominate the embedding space, through empirical observations and theoretical analysis. As a result, the expressive power of the learned node representations is constrained. We further propose OrthoReg, a novel GR-MLP model to mitigate the dimensional collapse issue. Through a soft regularization loss on the correlation matrix of node embeddings, OrthoReg explicitly encourages orthogonal node representations and thus can naturally avoid dimensionally collapsed representations. Experiments on traditional transductive semi-supervised classification tasks and inductive node classification for cold-start scenarios demonstrate its effectiveness and superiority.

Localized Contrastive Learning on Graphs

Contrastive learning methods based on InfoNCE loss are popular in node representation learning tasks on graph-structured data. However, its reliance on data augmentation and its quadratic computational complexity might lead to inconsistency and inefficiency problems. To mitigate these limitations, in this paper, we introduce a simple yet effective contrastive model named Localized Graph Contrastive Learning (Local-GCL in short). Local-GCL consists of two key designs: 1) We fabricate the positive examples for each node directly using its first-order neighbors, which frees our method from the reliance on carefully-designed graph augmentations; 2) To improve the efficiency of contrastive learning on graphs, we devise a kernelized contrastive loss, which could be approximately computed in linear time and space complexity with respect to the graph size. We provide theoretical analysis to justify the effectiveness and rationality of the proposed methods. Experiments on various datasets with different scales and properties demonstrate that in spite of its simplicity, Local-GCL achieves quite competitive performance in self-supervised node representation learning tasks on graphs with various scales and properties.