Pushing the Limits of All-Atom Geometric Graph Neural Networks: Pre-Training, Scaling and Zero-Shot Transfer

Constructing transferable descriptors for conformation representation of molecular and biological systems finds numerous applications in drug discovery, learning-based molecular dynamics, and protein mechanism analysis. Geometric graph neural networks (Geom-GNNs) with all-atom information have transformed atomistic simulations by serving as a general learnable geometric descriptors for downstream tasks including prediction of interatomic potential and molecular properties. However, common practices involve supervising Geom-GNNs on specific downstream tasks, which suffer from the lack of high-quality data and inaccurate labels leading to poor generalization and performance degradation on out-of-distribution (OOD) scenarios. In this work, we explored the possibility of using pre-trained Geom-GNNs as transferable and highly effective geometric descriptors for improved generalization. To explore their representation power, we studied the scaling behaviors of Geom-GNNs under self-supervised pre-training, supervised and unsupervised learning setups. We find that the expressive power of different architectures can differ on the pre-training task. Interestingly, Geom-GNNs do not follow the power-law scaling on the pre-training task, and universally lack predictable scaling behavior on the supervised tasks with quantum chemical labels important for screening and design of novel molecules. More importantly, we demonstrate how all-atom graph embedding can be organically combined with other neural architectures to enhance the expressive power. Meanwhile, the low-dimensional projection of the latent space shows excellent agreement with conventional geometrical descriptors.

DeCaf: A Causal Decoupling Framework for OOD Generalization on Node Classification

Graph Neural Networks (GNNs) are susceptible to distribution shifts, creating vulnerability and security issues in critical domains. There is a pressing need to enhance the generalizability of GNNs on out-of-distribution (OOD) test data. Existing methods that target learning an invariant (feature, structure)-label mapping often depend on oversimplified assumptions about the data generation process, which do not adequately reflect the actual dynamics of distribution shifts in graphs. In this paper, we introduce a more realistic graph data generation model using Structural Causal Models (SCMs), allowing us to redefine distribution shifts by pinpointing their origins within the generation process. Building on this, we propose a casual decoupling framework, DeCaf, that independently learns unbiased feature-label and structure-label mappings. We provide a detailed theoretical framework that shows how our approach can effectively mitigate the impact of various distribution shifts. We evaluate DeCaf across both real-world and synthetic datasets that demonstrate different patterns of shifts, confirming its efficacy in enhancing the generalizability of GNNs.

Bridging the Training-Inference Gap in LLMs by Leveraging Self-Generated Tokens

Language models are often trained to maximize the likelihood of the next token given past tokens in the training dataset. However, during inference time, they are utilized differently, generating text sequentially and auto-regressively by using previously generated tokens as input to predict the next one. Marginal differences in predictions at each step can cascade over successive steps, resulting in different distributions from what the models were trained for and potentially leading to unpredictable behavior. This paper proposes two simple approaches based on model own generation to address this discrepancy between the training and inference time. Our first approach is Batch-Scheduled Sampling, where, during training, we stochastically choose between the ground-truth token from the dataset and the model's own generated token as input to predict the next token. This is done in an offline manner, modifying the context window by interleaving ground-truth tokens with those generated by the model. Our second approach is Reference-Answer-based Correction, where we explicitly incorporate a self-correction capability into the model during training. This enables the model to effectively self-correct the gaps between the generated sequences and the ground truth data without relying on an external oracle model. By incorporating our proposed strategies during training, we have observed an overall improvement in performance compared to baseline methods, as demonstrated by our extensive experiments using summarization, general question-answering, and math question-answering tasks.

AgentOccam: A Simple Yet Strong Baseline for LLM-Based Web Agents

Autonomy via agents using large language models (LLMs) for personalized, standardized tasks boosts human efficiency. Automating web tasks (like booking hotels within a budget) is increasingly sought after. Fulfilling practical needs, the web agent also serves as an important proof-of-concept example for various agent grounding scenarios, with its success promising advancements in many future applications. Prior research often handcrafts web agent strategies (e.g., prompting templates, multi-agent systems, search methods, etc.) and the corresponding in-context examples, which may not generalize well across all real-world scenarios. On the other hand, there has been limited study on the misalignment between a web agent's observation/action representation and the pre-training data of the LLM it's based on. This discrepancy is especially notable when LLMs are primarily trained for language completion rather than tasks involving embodied navigation actions and symbolic web elements. Our study enhances an LLM-based web agent by simply refining its observation and action space to better align with the LLM's capabilities. This approach enables our base agent to significantly outperform previous methods on a wide variety of web tasks. Specifically, on WebArena, a benchmark featuring general-purpose web interaction tasks, our agent AgentOccam surpasses the previous state-of-the-art and concurrent work by 9.8 (+29.4%) and 5.9 (+15.8%) absolute points respectively, and boosts the success rate by 26.6 points (+161%) over similar plain web agents with its observation and action space alignment. We achieve this without using in-context examples, new agent roles, online feedback or search strategies. AgentOccam's simple design highlights LLMs' impressive zero-shot performance on web tasks, and underlines the critical role of carefully tuning observation and action spaces for LLM-based agents.

FeatNavigator: Automatic Feature Augmentation on Tabular Data

Data-centric AI focuses on understanding and utilizing high-quality, relevant data in training machine learning (ML) models, thereby increasing the likelihood of producing accurate and useful results. Automatic feature augmentation, aiming to augment the initial base table with useful features from other tables, is critical in data preparation as it improves model performance, robustness, and generalizability. While recent works have investigated automatic feature augmentation, most of them have limited capabilities in utilizing all useful features as many of them are in candidate tables not directly joinable with the base table. Worse yet, with numerous join paths leading to these distant features, existing solutions fail to fully exploit them within a reasonable compute budget. We present FeatNavigator, an effective and efficient framework that explores and integrates high-quality features in relational tables for ML models. FeatNavigator evaluates a feature from two aspects: (1) the intrinsic value of a feature towards an ML task (i.e., feature importance) and (2) the efficacy of a join path connecting the feature to the base table (i.e., integration quality). FeatNavigator strategically selects a small set of available features and their corresponding join paths to train a feature importance estimation model and an integration quality prediction model. Furthermore, FeatNavigator's search algorithm exploits both estimated feature importance and integration quality to identify the optimized feature augmentation plan. Our experimental results show that FeatNavigator outperforms state-of-the-art solutions on five public datasets by up to 40.1% in ML model performance.

GraphStorm: all-in-one graph machine learning framework for industry applications

Graph machine learning (GML) is effective in many business applications. However, making GML easy to use and applicable to industry applications with massive datasets remain challenging. We developed GraphStorm, which provides an end-to-end solution for scalable graph construction, graph model training and inference. GraphStorm has the following desirable properties: (a) Easy to use: it can perform graph construction and model training and inference with just a single command; (b) Expert-friendly: GraphStorm contains many advanced GML modeling techniques to handle complex graph data and improve model performance; (c) Scalable: every component in GraphStorm can operate on graphs with billions of nodes and can scale model training and inference to different hardware without changing any code. GraphStorm has been used and deployed for over a dozen billion-scale industry applications after its release in May 2023. It is open-sourced in Github: https://github.com/awslabs/graphstorm.

DispaRisk: Assessing and Interpreting Disparity Risks in Datasets

Machine Learning algorithms (ML) impact virtually every aspect of human lives and have found use across diverse sectors, including healthcare, finance, and education. Often, ML algorithms have been found to exacerbate societal biases presented in datasets, leading to adversarial impacts on subsets/groups of individuals, in many cases minority groups. To effectively mitigate these untoward effects, it is crucial that disparities/biases are identified and assessed early in a ML pipeline. This proactive approach facilitates timely interventions to prevent bias amplification and reduce complexity at later stages of model development. In this paper, we introduce DispaRisk, a novel framework designed to proactively assess the potential risks of disparities in datasets during the initial stages of the ML pipeline. We evaluate DispaRisk's effectiveness by benchmarking it with commonly used datasets in fairness research. Our findings demonstrate the capabilities of DispaRisk to identify datasets with a high-risk of discrimination, model families prone to biases, and characteristics that heighten discrimination susceptibility in a ML pipeline. The code for our experiments is available in the following repository: https://github.com/jovasque156/disparisk

OpenTab: Advancing Large Language Models as Open-domain Table Reasoners

Large Language Models (LLMs) trained on large volumes of data excel at various natural language tasks, but they cannot handle tasks requiring knowledge that has not been trained on previously. One solution is to use a retriever that fetches relevant information to expand LLM's knowledge scope. However, existing textual-oriented retrieval-based LLMs are not ideal on structured table data due to diversified data modalities and large table sizes. In this work, we propose OpenTab, an open-domain table reasoning framework powered by LLMs. Overall, OpenTab leverages table retriever to fetch relevant tables and then generates SQL programs to parse the retrieved tables efficiently. Utilizing the intermediate data derived from the SQL executions, it conducts grounded inference to produce accurate response. Extensive experimental evaluation shows that OpenTab significantly outperforms baselines in both open- and closed-domain settings, achieving up to 21.5% higher accuracy. We further run ablation studies to validate the efficacy of our proposed designs of the system.

Which Examples to Annotate for In-Context Learning? Towards Effective and Efficient Selection

Large Language Models (LLMs) can adapt to new tasks via in-context learning (ICL). ICL is efficient as it does not require any parameter updates to the trained LLM, but only few annotated examples as input for the LLM. In this work, we investigate an active learning approach for ICL, where there is a limited budget for annotating examples. We propose a model-adaptive optimization-free algorithm, termed AdaICL, which identifies examples that the model is uncertain about, and performs semantic diversity-based example selection. Diversity-based sampling improves overall effectiveness, while uncertainty sampling improves budget efficiency and helps the LLM learn new information. Moreover, AdaICL poses its sampling strategy as a Maximum Coverage problem, that dynamically adapts based on the model's feedback and can be approximately solved via greedy algorithms. Extensive experiments on nine datasets and seven LLMs show that AdaICL improves performance by 4.4% accuracy points over SOTA (7.7% relative improvement), is up to 3x more budget-efficient than performing annotations uniformly at random, while it outperforms SOTA with 2x fewer ICL examples.

NameGuess: Column Name Expansion for Tabular Data

Recent advances in large language models have revolutionized many sectors, including the database industry. One common challenge when dealing with large volumes of tabular data is the pervasive use of abbreviated column names, which can negatively impact performance on various data search, access, and understanding tasks. To address this issue, we introduce a new task, called NameGuess, to expand column names (used in database schema) as a natural language generation problem. We create a training dataset of 384K abbreviated-expanded column pairs using a new data fabrication method and a human-annotated evaluation benchmark that includes 9.2K examples from real-world tables. To tackle the complexities associated with polysemy and ambiguity in NameGuess, we enhance auto-regressive language models by conditioning on table content and column header names -- yielding a fine-tuned model (with 2.7B parameters) that matches human performance. Furthermore, we conduct a comprehensive analysis (on multiple LLMs) to validate the effectiveness of table content in NameGuess and identify promising future opportunities. Code has been made available at https://github.com/amazon-science/nameguess.