Towards Foundational Models for Molecular Learning on Large-Scale Multi-Task Datasets

Recently, pre-trained foundation models have enabled significant advancements in multiple fields. In molecular machine learning, however, where datasets are often hand-curated, and hence typically small, the lack of datasets with labeled features, and codebases to manage those datasets, has hindered the development of foundation models. In this work, we present seven novel datasets categorized by size into three distinct categories: ToyMix, LargeMix and UltraLarge. These datasets push the boundaries in both the scale and the diversity of supervised labels for molecular learning. They cover nearly 100 million molecules and over 3000 sparsely defined tasks, totaling more than 13 billion individual labels of both quantum and biological nature. In comparison, our datasets contain 300 times more data points than the widely used OGB-LSC PCQM4Mv2 dataset, and 13 times more than the quantum-only QM1B dataset. In addition, to support the development of foundational models based on our proposed datasets, we present the Graphium graph machine learning library which simplifies the process of building and training molecular machine learning models for multi-task and multi-level molecular datasets. Finally, we present a range of baseline results as a starting point of multi-task and multi-level training on these datasets. Empirically, we observe that performance on low-resource biological datasets show improvement by also training on large amounts of quantum data. This indicates that there may be potential in multi-task and multi-level training of a foundation model and fine-tuning it to resource-constrained downstream tasks.

Large Language Models can Learn Rules

When prompted with a few examples and intermediate steps, large language models (LLMs) have demonstrated impressive performance in various reasoning tasks. However, prompting methods that rely on implicit knowledge in an LLM often hallucinate incorrect answers when the implicit knowledge is wrong or inconsistent with the task. To tackle this problem, we present Hypotheses-to-Theories (HtT), a framework that learns a rule library for reasoning with LLMs. HtT contains two stages, an induction stage and a deduction stage. In the induction stage, an LLM is first asked to generate and verify rules over a set of training examples. Rules that appear and lead to correct answers sufficiently often are collected to form a rule library. In the deduction stage, the LLM is then prompted to employ the learned rule library to perform reasoning to answer test questions. Experiments on both numerical reasoning and relational reasoning problems show that HtT improves existing prompting methods, with an absolute gain of 11-27% in accuracy. The learned rules are also transferable to different models and to different forms of the same problem.

Towards Foundation Models for Knowledge Graph Reasoning

Foundation models in language and vision have the ability to run inference on any textual and visual inputs thanks to the transferable representations such as a vocabulary of tokens in language. Knowledge graphs (KGs) have different entity and relation vocabularies that generally do not overlap. The key challenge of designing foundation models on KGs is to learn such transferable representations that enable inference on any graph with arbitrary entity and relation vocabularies. In this work, we make a step towards such foundation models and present ULTRA, an approach for learning universal and transferable graph representations. ULTRA builds relational representations as a function conditioned on their interactions. Such a conditioning strategy allows a pre-trained ULTRA model to inductively generalize to any unseen KG with any relation vocabulary and to be fine-tuned on any graph. Conducting link prediction experiments on 57 different KGs, we find that the zero-shot inductive inference performance of a single pre-trained ULTRA model on unseen graphs of various sizes is often on par or better than strong baselines trained on specific graphs. Fine-tuning further boosts the performance.

GraphText: Graph Reasoning in Text Space

Large Language Models (LLMs) have gained the ability to assimilate human knowledge and facilitate natural language interactions with both humans and other LLMs. However, despite their impressive achievements, LLMs have not made significant advancements in the realm of graph machine learning. This limitation arises because graphs encapsulate distinct relational data, making it challenging to transform them into natural language that LLMs understand. In this paper, we bridge this gap with a novel framework, GraphText, that translates graphs into natural language. GraphText derives a graph-syntax tree for each graph that encapsulates both the node attributes and inter-node relationships. Traversal of the tree yields a graph text sequence, which is then processed by an LLM to treat graph tasks as text generation tasks. Notably, GraphText offers multiple advantages. It introduces training-free graph reasoning: even without training on graph data, GraphText with ChatGPT can achieve on par with, or even surpassing, the performance of supervised-trained graph neural networks through in-context learning (ICL). Furthermore, GraphText paves the way for interactive graph reasoning, allowing both humans and LLMs to communicate with the model seamlessly using natural language. These capabilities underscore the vast, yet-to-be-explored potential of LLMs in the domain of graph machine learning.

DTF-Net: Category-Level Pose Estimation and Shape Reconstruction via Deformable Template Field

Estimating 6D poses and reconstructing 3D shapes of objects in open-world scenes from RGB-depth image pairs is challenging. Many existing methods rely on learning geometric features that correspond to specific templates while disregarding shape variations and pose differences among objects in the same category. As a result, these methods underperform when handling unseen object instances in complex environments. In contrast, other approaches aim to achieve category-level estimation and reconstruction by leveraging normalized geometric structure priors, but the static prior-based reconstruction struggles with substantial intra-class variations. To solve these problems, we propose the DTF-Net, a novel framework for pose estimation and shape reconstruction based on implicit neural fields of object categories. In DTF-Net, we design a deformable template field to represent the general category-wise shape latent features and intra-category geometric deformation features. The field establishes continuous shape correspondences, deforming the category template into arbitrary observed instances to accomplish shape reconstruction. We introduce a pose regression module that shares the deformation features and template codes from the fields to estimate the accurate 6D pose of each object in the scene. We integrate a multi-modal representation extraction module to extract object features and semantic masks, enabling end-to-end inference. Moreover, during training, we implement a shape-invariant training strategy and a viewpoint sampling method to further enhance the model's capability to extract object pose features. Extensive experiments on the REAL275 and CAMERA25 datasets demonstrate the superiority of DTF-Net in both synthetic and real scenes. Furthermore, we show that DTF-Net effectively supports grasping tasks with a real robot arm.

Machine-Learning-Assisted and Real-Time-Feedback-Controlled Growth of InAs/GaAs Quantum Dots

Self-assembled InAs/GaAs quantum dots (QDs) have properties highly valuable for developing various optoelectronic devices such as QD lasers and single photon sources. The applications strongly rely on the density and quality of these dots, which has motivated studies of the growth process control to realize high-quality epi-wafers and devices. Establishing the process parameters in molecular beam epitaxy (MBE) for a specific density of QDs is a multidimensional optimization challenge, usually addressed through time-consuming and iterative trial-and-error. Here, we report a real-time feedback control method to realize the growth of QDs with arbitrary and precise density, which is fully automated and intelligent. We developed a machine learning (ML) model named 3D ResNet, specially designed for training RHEED videos instead of static images and providing real-time feedback on surface morphologies for process control. As a result, we demonstrated that ML from previous growth could predict the post-growth density of QDs, by successfully tuning the QD densities in near-real time from 1.5E10 cm-2 down to 3.8E8 cm-2 or up to 1.4E11 cm-2. Compared to traditional methods, our approach, with in-situ tuning capabilities and excellent reliability, can dramatically expedite the material optimization process and improve the reproducibility of MBE growth, constituting significant progress for thin film growth techniques. The concepts and methodologies proved feasible in this work are promising to be applied to a variety of material growth processes, which will revolutionize semiconductor manufacturing for microelectronic and optoelectronic industries.

Evolving Computation Graphs

Graph neural networks (GNNs) have demonstrated success in modeling relational data, especially for data that exhibits homophily: when a connection between nodes tends to imply that they belong to the same class. However, while this assumption is true in many relevant situations, there are important real-world scenarios that violate this assumption, and this has spurred research into improving GNNs for these cases. In this work, we propose Evolving Computation Graphs (ECGs), a novel method for enhancing GNNs on heterophilic datasets. Our approach builds on prior theoretical insights linking node degree, high homophily, and inter vs intra-class embedding similarity by rewiring the GNNs' computation graph towards adding edges that connect nodes that are likely to be in the same class. We utilise weaker classifiers to identify these edges, ultimately improving GNN performance on non-homophilic data as a result. We evaluate ECGs on a diverse set of recently-proposed heterophilous datasets and demonstrate improvements over the relevant baselines. ECG presents a simple, intuitive and elegant approach for improving GNN performance on heterophilic datasets without requiring prior domain knowledge.