Harnessing Simulation for Molecular Embeddings

While deep learning has unlocked advances in computational biology once thought to be decades away, extending deep learning techniques to the molecular domain has proven challenging, as labeled data is scarce and the benefit from self-supervised learning can be negligible in many cases. In this work, we explore a different approach. Inspired by methods in deep reinforcement learning and robotics, we explore harnessing physics-based molecular simulation to develop molecular embeddings. By fitting a Graph Neural Network to simulation data, molecules that display similar interactions with biological targets under simulation develop similar representations in the embedding space. These embeddings can then be used to initialize the feature space of down-stream models trained on real-world data to encode information learned during simulation into a molecular prediction task. Our experimental findings indicate this approach improves the performance of existing deep learning models on real-world molecular prediction tasks by as much as 38% with minimal modification to the downstream model and no hyperparameter tuning.

Zero-shot causal learning

Predicting how different interventions will causally affect a specific individual is important in a variety of domains such as personalized medicine, public policy, and online marketing. However, most existing causal methods cannot generalize to predicting the effects of previously unseen interventions (e.g., a newly invented drug), because they require data for individuals who received the intervention. Here, we consider zero-shot causal learning: predicting the personalized effects of novel, previously unseen interventions. To tackle this problem, we propose CaML, a causal meta-learning framework which formulates the personalized prediction of each intervention's effect as a task. Rather than training a separate model for each intervention, CaML trains as a single meta-model across thousands of tasks, each constructed by sampling an intervention and individuals who either did or did not receive it. By leveraging both intervention information (e.g., a drug's attributes) and individual features (e.g., a patient's history), CaML is able to predict the personalized effects of unseen interventions. Experimental results on real world datasets in large-scale medical claims and cell-line perturbations demonstrate the effectiveness of our approach. Most strikingly, CaML zero-shot predictions outperform even strong baselines which have direct access to data of considered target interventions.

Learning Graph Search Heuristics

Searching for a path between two nodes in a graph is one of the most well-studied and fundamental problems in computer science. In numerous domains such as robotics, AI, or biology, practitioners develop search heuristics to accelerate their pathfinding algorithms. However, it is a laborious and complex process to hand-design heuristics based on the problem and the structure of a given use case. Here we present PHIL (Path Heuristic with Imitation Learning), a novel neural architecture and a training algorithm for discovering graph search and navigation heuristics from data by leveraging recent advances in imitation learning and graph representation learning. At training time, we aggregate datasets of search trajectories and ground-truth shortest path distances, which we use to train a specialized graph neural network-based heuristic function using backpropagation through steps of the pathfinding process. Our heuristic function learns graph embeddings useful for inferring node distances, runs in constant time independent of graph sizes, and can be easily incorporated in an algorithm such as A* at test time. Experiments show that PHIL reduces the number of explored nodes compared to state-of-the-art methods on benchmark datasets by 58.5\% on average, can be directly applied in diverse graphs ranging from biological networks to road networks, and allows for fast planning in time-critical robotics domains.

Retrieval-Augmented Multimodal Language Modeling

Recent multimodal models such as DALL-E and CM3 have achieved remarkable progress in text-to-image and image-to-text generation. However, these models store all learned knowledge (e.g., the appearance of the Eiffel Tower) in the model parameters, requiring increasingly larger models and training data to capture more knowledge. To integrate knowledge in a more scalable and modular way, we propose a retrieval-augmented multimodal model, which enables a base multimodal model (generator) to refer to relevant knowledge fetched by a retriever from external memory (e.g., multimodal documents on the web). Specifically, we implement a retriever using the pretrained CLIP model and a generator using the CM3 Transformer architecture, and train this model using the LAION dataset. Our resulting model, named Retrieval-Augmented CM3 (RA-CM3), is the first multimodal model that can retrieve and generate mixtures of text and images. We show that RA-CM3 significantly outperforms baseline multimodal models such as DALL-E and CM3 on both image and caption generation tasks (12 FID and 17 CIDEr improvements on MS-COCO), while requiring much less compute for training (<30% of DALL-E). Moreover, we show that RA-CM3 exhibits novel capabilities such as knowledge-intensive image generation and multimodal in-context learning.

CausalBench: A Large-scale Benchmark for Network Inference from Single-cell Perturbation Data

Mapping biological mechanisms in cellular systems is a fundamental step in early-stage drug discovery that serves to generate hypotheses on what disease-relevant molecular targets may effectively be modulated by pharmacological interventions. With the advent of high-throughput methods for measuring single-cell gene expression under genetic perturbations, we now have effective means for generating evidence for causal gene-gene interactions at scale. However, inferring graphical networks of the size typically encountered in real-world gene-gene interaction networks is difficult in terms of both achieving and evaluating faithfulness to the true underlying causal graph. Moreover, standardised benchmarks for comparing methods for causal discovery in perturbational single-cell data do not yet exist. Here, we introduce CausalBench - a comprehensive benchmark suite for evaluating network inference methods on large-scale perturbational single-cell gene expression data. CausalBench introduces several biologically meaningful performance metrics and operates on two large, curated and openly available benchmark data sets for evaluating methods on the inference of gene regulatory networks from single-cell data generated under perturbations. With real-world datasets consisting of over \numprint{200000} training samples under interventions, CausalBench could potentially help facilitate advances in causal network inference by providing what is - to the best of our knowledge - the largest openly available test bed for causal discovery from real-world perturbation data to date.

TuneUp: A Training Strategy for Improving Generalization of Graph Neural Networks

Despite many advances in Graph Neural Networks (GNNs), their training strategies simply focus on minimizing a loss over nodes in a graph. However, such simplistic training strategies may be sub-optimal as they neglect that certain nodes are much harder to make accurate predictions on than others. Here we present TuneUp, a curriculum learning strategy for better training GNNs. Crucially, TuneUp trains a GNN in two stages. The first stage aims to produce a strong base GNN. Such base GNNs tend to perform well on head nodes (nodes with large degrees) but less so on tail nodes (nodes with small degrees). So, the second stage of TuneUp specifically focuses on improving prediction on tail nodes. Concretely, TuneUp synthesizes many additional supervised tail node data by dropping edges from head nodes and reusing the supervision on the original head nodes. TuneUp then minimizes the loss over the synthetic tail nodes to finetune the base GNN. TuneUp is a general training strategy that can be used with any GNN architecture and any loss, making TuneUp applicable to a wide range of prediction tasks. Extensive evaluation of TuneUp on two GNN architectures, three types of prediction tasks, and both inductive and transductive settings shows that TuneUp significantly improves the performance of the base GNN on tail nodes, while often even improving the performance on head nodes, which together leads up to 58.5% relative improvement in GNN predictive performance. Moreover, TuneUp significantly outperforms its variants without the two-stage curriculum learning, existing graph data augmentation techniques, as well as other specialized methods for tail nodes.

Deep Bidirectional Language-Knowledge Graph Pretraining

Pretraining a language model (LM) on text has been shown to help various downstream NLP tasks. Recent works show that a knowledge graph (KG) can complement text data, offering structured background knowledge that provides a useful scaffold for reasoning. However, these works are not pretrained to learn a deep fusion of the two modalities at scale, limiting the potential to acquire fully joint representations of text and KG. Here we propose DRAGON (Deep Bidirectional Language-Knowledge Graph Pretraining), a self-supervised approach to pretraining a deeply joint language-knowledge foundation model from text and KG at scale. Specifically, our model takes pairs of text segments and relevant KG subgraphs as input and bidirectionally fuses information from both modalities. We pretrain this model by unifying two self-supervised reasoning tasks, masked language modeling and KG link prediction. DRAGON outperforms existing LM and LM+KG models on diverse downstream tasks including question answering across general and biomedical domains, with +5% absolute gain on average. In particular, DRAGON achieves notable performance on complex reasoning about language and knowledge (+10% on questions involving long contexts or multi-step reasoning) and low-resource QA (+8% on OBQA and RiddleSense), and new state-of-the-art results on various BioNLP tasks. Our code and trained models are available at https://github.com/michiyasunaga/dragon.

Few-shot Relational Reasoning via Connection Subgraph Pretraining

Few-shot knowledge graph (KG) completion task aims to perform inductive reasoning over the KG: given only a few support triplets of a new relation $\bowtie$ (e.g., (chop,$\bowtie$,kitchen), (read,$\bowtie$,library), the goal is to predict the query triplets of the same unseen relation $\bowtie$, e.g., (sleep,$\bowtie$,?). Current approaches cast the problem in a meta-learning framework, where the model needs to be first jointly trained over many training few-shot tasks, each being defined by its own relation, so that learning/prediction on the target few-shot task can be effective. However, in real-world KGs, curating many training tasks is a challenging ad hoc process. Here we propose Connection Subgraph Reasoner (CSR), which can make predictions for the target few-shot task directly without the need for pre-training on the human curated set of training tasks. The key to CSR is that we explicitly model a shared connection subgraph between support and query triplets, as inspired by the principle of eliminative induction. To adapt to specific KG, we design a corresponding self-supervised pretraining scheme with the objective of reconstructing automatically sampled connection subgraphs. Our pretrained model can then be directly applied to target few-shot tasks on without the need for training few-shot tasks. Extensive experiments on real KGs, including NELL, FB15K-237, and ConceptNet, demonstrate the effectiveness of our framework: we show that even a learning-free implementation of CSR can already perform competitively to existing methods on target few-shot tasks; with pretraining, CSR can achieve significant gains of up to 52% on the more challenging inductive few-shot tasks where the entities are also unseen during (pre)training.

ROLAND: Graph Learning Framework for Dynamic Graphs

Graph Neural Networks (GNNs) have been successfully applied to many real-world static graphs. However, the success of static graphs has not fully translated to dynamic graphs due to the limitations in model design, evaluation settings, and training strategies. Concretely, existing dynamic GNNs do not incorporate state-of-the-art designs from static GNNs, which limits their performance. Current evaluation settings for dynamic GNNs do not fully reflect the evolving nature of dynamic graphs. Finally, commonly used training methods for dynamic GNNs are not scalable. Here we propose ROLAND, an effective graph representation learning framework for real-world dynamic graphs. At its core, the ROLAND framework can help researchers easily repurpose any static GNN to dynamic graphs. Our insight is to view the node embeddings at different GNN layers as hierarchical node states and then recurrently update them over time. We then introduce a live-update evaluation setting for dynamic graphs that mimics real-world use cases, where GNNs are making predictions and being updated on a rolling basis. Finally, we propose a scalable and efficient training approach for dynamic GNNs via incremental training and meta-learning. We conduct experiments over eight different dynamic graph datasets on future link prediction tasks. Models built using the ROLAND framework achieve on average 62.7% relative mean reciprocal rank (MRR) improvement over state-of-the-art baselines under the standard evaluation settings on three datasets. We find state-of-the-art baselines experience out-of-memory errors for larger datasets, while ROLAND can easily scale to dynamic graphs with 56 million edges. After re-implementing these baselines using the ROLAND training strategy, ROLAND models still achieve on average 15.5% relative MRR improvement over the baselines.

ViRel: Unsupervised Visual Relations Discovery with Graph-level Analogy

Visual relations form the basis of understanding our compositional world, as relationships between visual objects capture key information in a scene. It is then advantageous to learn relations automatically from the data, as learning with predefined labels cannot capture all possible relations. However, current relation learning methods typically require supervision, and are not designed to generalize to scenes with more complicated relational structures than those seen during training. Here, we introduce ViRel, a method for unsupervised discovery and learning of Visual Relations with graph-level analogy. In a setting where scenes within a task share the same underlying relational subgraph structure, our learning method of contrasting isomorphic and non-isomorphic graphs discovers the relations across tasks in an unsupervised manner. Once the relations are learned, ViRel can then retrieve the shared relational graph structure for each task by parsing the predicted relational structure. Using a dataset based on grid-world and the Abstract Reasoning Corpus, we show that our method achieves above 95% accuracy in relation classification, discovers the relation graph structure for most tasks, and further generalizes to unseen tasks with more complicated relational structures.