Sparse autoencoders (SAEs) have emerged as a promising approach in language model interpretability, offering unsupervised extraction of sparse features. For interpretability methods to succeed, they must identify abstract features across domains, and these features can often manifest differently in each context. We examine this through "answerability"-a model's ability to recognize answerable questions. We extensively evaluate SAE feature generalization across diverse answerability datasets for Gemma 2 SAEs. Our analysis reveals that residual stream probes outperform SAE features within domains, but generalization performance differs sharply. SAE features demonstrate inconsistent transfer ability, and residual stream probes similarly show high variance out of distribution. Overall, this demonstrates the need for quantitative methods to predict feature generalization in SAE-based interpretability.

Recent research in molecular discovery has primarily been devoted to small, drug-like molecules, leaving many similarly important applications in material design without adequate technology. These applications often rely on more complex molecular structures with fewer examples that are carefully designed using known substructures. We propose a data-efficient and interpretable model for representing and reasoning over such molecules in terms of graph grammars that explicitly describe the hierarchical design space featuring motifs to be the design basis. We present a novel representation in the form of random walks over the design space, which facilitates both molecule generation and property prediction. We demonstrate clear advantages over existing methods in terms of performance, efficiency, and synthesizability of predicted molecules, and we provide detailed insights into the method's chemical interpretability.

Self-supervised learning (SSL) has great potential for molecular representation learning given the complexity of molecular graphs, the large amounts of unlabelled data available, the considerable cost of obtaining labels experimentally, and the hence often only small training datasets. The importance of the topic is reflected in the variety of paradigms and architectures that have been investigated recently. Yet the differences in performance seem often minor and are barely understood to date. In this paper, we study SSL based on persistent homology (PH), a mathematical tool for modeling topological features of data that persist across multiple scales. It has several unique features which particularly suit SSL, naturally offering: different views of the data, stability in terms of distance preservation, and the opportunity to flexibly incorporate domain knowledge. We (1) investigate an autoencoder, which shows the general representational power of PH, and (2) propose a contrastive loss that complements existing approaches. We rigorously evaluate our approach for molecular property prediction and demonstrate its particular features in improving the embedding space: after SSL, the representations are better and offer considerably more predictive power than the baselines over different probing tasks; our loss increases baseline performance, sometimes largely; and we often obtain substantial improvements over very small datasets, a common scenario in practice.

Transformer models have recently gained popularity in graph representation learning as they have the potential to learn complex relationships beyond the ones captured by regular graph neural networks. The main research question is how to inject the structural bias of graphs into the transformer architecture, and several proposals have been made for undirected molecular graphs and, recently, also for larger network graphs. In this paper, we study transformers over directed acyclic graphs (DAGs) and propose architecture adaptations tailored to DAGs: (1) An attention mechanism that is considerably more efficient than the regular quadratic complexity of transformers and at the same time faithfully captures the DAG structure, and (2) a positional encoding of the DAG's partial order, complementing the former. We rigorously evaluate our approach over various types of tasks, ranging from classifying source code graphs to nodes in citation networks, and show that it is effective in two important aspects: in making graph transformers generally outperform graph neural networks tailored to DAGs and in improving SOTA graph transformer performance in terms of both quality and efficiency.

The prediction of molecular properties is a crucial task in the field of material and drug discovery. The potential benefits of using deep learning techniques are reflected in the wealth of recent literature. Still, these techniques are faced with a common challenge in practice: Labeled data are limited by the cost of manual extraction from literature and laborious experimentation. In this work, we propose a data-efficient property predictor by utilizing a learnable hierarchical molecular grammar that can generate molecules from grammar production rules. Such a grammar induces an explicit geometry of the space of molecular graphs, which provides an informative prior on molecular structural similarity. The property prediction is performed using graph neural diffusion over the grammar-induced geometry. On both small and large datasets, our evaluation shows that this approach outperforms a wide spectrum of baselines, including supervised and pre-trained graph neural networks. We include a detailed ablation study and further analysis of our solution, showing its effectiveness in cases with extremely limited data. Code is available at https://github.com/gmh14/Geo-DEG.

Identifying vulnerable code is a precautionary measure to counter software security breaches. Tedious expert effort has been spent to build static analyzers, yet insecure patterns are barely fully enumerated. This work explores a deep learning approach to automatically learn the insecure patterns from code corpora. Because code naturally admits graph structures with parsing, we develop a novel graph neural network (GNN) to exploit both the semantic context and structural regularity of a program, in order to improve prediction performance. Compared with a generic GNN, our enhancements include a synthesis of multiple representations learned from the several parsed graphs of a program, and a new training loss metric that leverages the fine granularity of labeling. Our model outperforms multiple text, image and graph-based approaches, across two real-world datasets.

Sampling is an established technique to scale graph neural networks to large graphs. Current approaches however assume the graphs to be homogeneous in terms of relations and ignore relation types, critically important in biomedical graphs. Multi-relational graphs contain various types of relations that usually come with variable frequency and have different importance for the problem at hand. We propose an approach to modeling the importance of relation types for neighborhood sampling in graph neural networks and show that we can learn the right balance: relation-type probabilities that reflect both frequency and importance. Our experiments on drug-drug interaction prediction show that state-of-the-art graph neural networks profit from relation-dependent sampling in terms of both accuracy and efficiency.

Advancements in deep learning and machine learning algorithms have enabled breakthrough progress in computer vision, speech recognition, natural language processing and beyond. In addition, over the last several decades, software has been built into the fabric of every aspect of our society. Together, these two trends have generated new interest in the fast-emerging research area of AI for Code. As software development becomes ubiquitous across all industries and code infrastructure of enterprise legacy applications ages, it is more critical than ever to increase software development productivity and modernize legacy applications. Over the last decade, datasets like ImageNet, with its large scale and diversity, have played a pivotal role in algorithmic advancements from computer vision to language and speech understanding. In this paper, we present Project CodeNet, a first-of-its-kind, very large scale, diverse, and high-quality dataset to accelerate the algorithmic advancements in AI for Code. It consists of 14M code samples and about 500M lines of code in 55 different programming languages. Project CodeNet is not only unique in its scale, but also in the diversity of coding tasks it can help benchmark: from code similarity and classification for advances in code recommendation algorithms, and code translation between a large variety programming languages, to advances in code performance (both runtime, and memory) improvement techniques. CodeNet also provides sample input and output test sets for over 7M code samples, which can be critical for determining code equivalence in different languages. As a usability feature, we provide several preprocessing tools in Project CodeNet to transform source codes into representations that can be readily used as inputs into machine learning models.

Graph-structured data ubiquitously appears in science and engineering. Graph neural networks (GNNs) are designed to exploit the relational inductive bias exhibited in graphs; they have been shown to outperform other forms of neural networks in scenarios where structure information supplements node features. The most common GNN architecture aggregates information from neighborhoods based on message passing. Its generality has made it broadly applicable. In this paper, we focus on a special, yet widely used, type of graphs--DAGs--and inject a stronger inductive bias--partial ordering--into the neural network design. We propose the directed acyclic graph neural network, DAGNN, an architecture that processes information according to the flow defined by the partial order. DAGNN can be considered a framework that entails earlier works as special cases (e.g., models for trees and models updating node representations recurrently), but we identify several crucial components that prior architectures lack. We perform comprehensive experiments, including ablation studies, on representative DAG datasets (i.e., source code, neural architectures, and probabilistic graphical models) and demonstrate the superiority of DAGNN over simpler DAG architectures as well as general graph architectures. Graph-structured data is ubiquitous across various disciplines (Gilmer et al., 2017; Zitnik et al., 2018; Sanchez-Gonzalez et al., 2020). Graph neural networks (GNNs) use both the graph structure and node features to produce a vectorial representation, which can be used for classification, regression (Hu et al., 2020), and graph decoding (Li et al., 2018; Zhang et al., 2019). Most popular GNNs update node representations through iterative message passing between neighboring nodes, followed by pooling (either flat or hierarchical (Lee et al., 2019; Ranjan et al., 2020)), to produce a graph representation (Li et al., 2016; Kipf & Welling, 2017; Gilmer et al., 2017; Veličković et al., 2018; Xu et al., 2019). The relational inductive bias (Santoro et al., 2017; Battaglia et al., 2018; Xu et al., 2020)--neighborhood aggregation--empowers GNNs to outperform graph-agnostic neural networks. For notational simplicity, we omit edge attributes; but they can be straightforwardly incorporated into the framework (1)-(2).

Logical rules are a popular knowledge representation language in many domains, representing background knowledge and encoding information that can be derived from given facts in a compact form. However, rule formulation is a complex process that requires deep domain expertise, and is further challenged by today's often large, heterogeneous, and incomplete knowledge graphs. Several approaches for learning rules automatically, given a set of input example facts, have been proposed over time, including, more recently, neural systems. Yet, the area is missing adequate datasets and evaluation approaches: existing datasets often resemble toy examples that neither cover the various kinds of dependencies between rules nor allow for testing scalability. We present a tool for generating different kinds of datasets and for evaluating rule learning systems.