Veronika Thost

Minghao Guo, Veronika Thost, Beichen Li et al.

The problem of molecular generation has received significant attention recently. Existing methods are typically based on deep neural networks and require training on large datasets with tens of thousands of samples. In practice, however, the size of class-specific chemical datasets is usually limited (e.g., dozens of samples) due to labor-intensive experimentation and data collection. This presents a considerable challenge for the deep learning generative models to comprehensively describe the molecular design space. Another major challenge is to generate only physically synthesizable molecules. This is a non-trivial task for neural network-based generative models since the relevant chemical knowledge can only be extracted and generalized from the limited training data. In this work, we propose a data-efficient generative model that can be learned from datasets with orders of magnitude smaller sizes than common benchmarks. At the heart of this method is a learnable graph grammar that generates molecules from a sequence of production rules. Without any human assistance, these production rules are automatically constructed from training data. Furthermore, additional chemical knowledge can be incorporated in the model by further grammar optimization. Our learned graph grammar yields state-of-the-art results on generating high-quality molecules for three monomer datasets that contain only ${\sim}20$ samples each. Our approach also achieves remarkable performance in a challenging polymer generation task with only $117$ training samples and is competitive against existing methods using $81$k data points. Code is available at https://github.com/gmh14/data_efficient_grammar.

Minghao Guo, Veronika Thost, Samuel W Song et al.

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.

Yuankai Luo, Veronika Thost, Lei Shi

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.

Kimia Hamidieh, Veronika Thost, Walter Gerych et al.

Large language models (LLMs) often produce confident yet incorrect responses, and uncertainty quantification is one potential solution to more robust usage. Recent works routinely rely on self-consistency to estimate aleatoric uncertainty (AU), yet this proxy collapses when models are overconfident and produce the same incorrect answer across samples. We analyze this regime and show that cross-model semantic disagreement is higher on incorrect answers precisely when AU is low. Motivated by this, we introduce an epistemic uncertainty (EU) term that operates in the black-box access setting: EU uses only generated text from a small, scale-matched ensemble and is computed as the gap between inter-model and intra-model sequence-semantic similarity. We then define total uncertainty (TU) as the sum of AU and EU. In a comprehensive study across five 7-9B instruction-tuned models and ten long-form tasks, TU improves ranking calibration and selective abstention relative to AU, and EU reliably flags confident failures where AU is low. We further characterize when EU is most useful via agreement and complementarity diagnostics.

Yuankai Luo, Lei Shi, Veronika Thost

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.

Junhyun Lee, Veronika Thost, Bumsoo Kim et al.

Message Passing Neural Networks (MPNNs) hold a key position in machine learning on graphs, but they struggle with unintended behaviors, such as over-smoothing and over-squashing, due to irregular data structures. The observation and formulation of these limitations have become foundational in constructing more informative graph representations. In this paper, we delve into the limitations of MPNNs, focusing on aspects that have previously been overlooked. Our observations reveal that even within a single layer, the information specific to an individual node can become significantly diluted. To delve into this phenomenon in depth, we present the concept of Over-dilution and formulate it with two dilution factors: intra-node dilution for attribute-level and inter-node dilution for node-level representations. We also introduce a transformer-based solution that alleviates over-dilution and complements existing node embedding methods like MPNNs. Our findings provide new insights and contribute to the development of informative representations. The implementation and supplementary materials are publicly available at https://github.com/LeeJunHyun/NATR.

Jamison Meindl, Yunsheng Tian, Tony Cui et al.

Global optimization of expensive, derivative-free black-box functions requires extreme sample efficiency. While Bayesian optimization (BO) is the current state-of-the-art, its performance hinges on surrogate and acquisition function hyper-parameters that are often hand-tuned and fail to generalize across problem landscapes. We present ZeroShotOpt, a general-purpose, pretrained model for continuous black-box optimization tasks ranging from 2D to 20D. Our approach leverages offline reinforcement learning on large-scale optimization trajectories collected from 12 BO variants. To scale pretraining, we generate millions of synthetic Gaussian process-based functions with diverse landscapes, enabling the model to learn transferable optimization policies. As a result, ZeroShotOpt achieves robust zero-shot generalization on a wide array of unseen benchmarks, matching or surpassing the sample efficiency of leading global optimizers, including BO, while also offering a reusable foundation for future extensions and improvements. Our open-source code, dataset, and model are available at: https://github.com/jamisonmeindl/zeroshotopt

Mehdi Ali, Max Berrendorf, Mikhail Galkin et al.

For many years, link prediction on knowledge graphs (KGs) has been a purely transductive task, not allowing for reasoning on unseen entities. Recently, increasing efforts are put into exploring semi- and fully inductive scenarios, enabling inference over unseen and emerging entities. Still, all these approaches only consider triple-based \glspl{kg}, whereas their richer counterparts, hyper-relational KGs (e.g., Wikidata), have not yet been properly studied. In this work, we classify different inductive settings and study the benefits of employing hyper-relational KGs on a wide range of semi- and fully inductive link prediction tasks powered by recent advancements in graph neural networks. Our experiments on a novel set of benchmarks show that qualifiers over typed edges can lead to performance improvements of 6% of absolute gains (for the Hits@10 metric) compared to triple-only baselines. Our code is available at \url{https://github.com/mali-git/hyper_relational_ilp}.

Jiannan Yang, Veronika Thost, Tengfei Ma

Self-supervised learning (SSL) plays a central role in molecular representation learning. Yet, many recent innovations in masking-based pretraining are introduced as heuristics and lack principled evaluation, obscuring which design choices are genuinely effective. This work cast the entire pretrain-finetune workflow into a unified probabilistic framework, enabling a transparent comparison and deeper understanding of masking strategies. Building on this formalism, we conduct a controlled study of three core design dimensions: masking distribution, prediction target, and encoder architecture, under rigorously controlled settings. We further employ information-theoretic measures to assess the informativeness of pretraining signals and connect them to empirically benchmarked downstream performance. Our findings reveal a surprising insight: sophisticated masking distributions offer no consistent benefit over uniform sampling for common node-level prediction tasks. Instead, the choice of prediction target and its synergy with the encoder architecture are far more critical. Specifically, shifting to semantically richer targets yields substantial downstream improvements, particularly when paired with expressive Graph Transformer encoders. These insights offer practical guidance for developing more effective SSL methods for molecular graphs.

Michael Sun, Minghao Guo, Weize Yuan et al.

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.

Lovis Heindrich, Philip Torr, Fazl Barez et al.

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, partly self-constructed 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 show inconsistent out-of-domain transfer, with performance varying from almost random to outperforming residual stream probes. Overall, this demonstrates the need for robust evaluation methods and quantitative approaches to predict feature generalization in SAE-based interpretability.

Jamison Meindl, Yunsheng Tian, Tony Cui et al.

Global optimization of expensive, derivative-free black-box functions demands extreme sample efficiency. Classical methods such as Bayesian Optimization (BO) can be effective, but they often require careful parameter tuning to each application domain. At the same time, Large Language Models (LLMs) have shown broad capabilities, yet state-of-the-art models remain limited in solving continuous black-box optimization tasks. We introduce GPTOpt, an LLM-based optimization method that equips LLMs with continuous black-box optimization capabilities. By fine-tuning large language models on extensive synthetic datasets derived from diverse BO parameterizations, GPTOpt leverages LLM pre-training to generalize across optimization tasks. On a variety of black-box optimization benchmarks, GPTOpt surpasses traditional optimizers, highlighting the capacity of LLMs for advanced numerical reasoning and introducing a flexible framework for global optimization without parameter tuning.

Yufan Zhuang, Sahil Suneja, Veronika Thost et al.

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.

Arthur Feeney, Rishabh Gupta, Veronika Thost et al.

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.

Ruchir Puri, David S. Kung, Geert Janssen et al.

Over the last several decades, software has been woven into the fabric of every aspect of our society. As software development surges and code infrastructure of enterprise applications ages, it is now more critical than ever to increase software development productivity and modernize legacy applications. Advances in deep learning and machine learning algorithms have enabled numerous breakthroughs, motivating researchers to leverage AI techniques to improve software development efficiency. Thus, the fast-emerging research area of AI for Code has garnered new interest and gathered momentum. In this paper, we present a large-scale dataset CodeNet, consisting of over 14 million code samples and about 500 million lines of code in 55 different programming languages, which is aimed at teaching AI to code. In addition to its large scale, CodeNet has a rich set of high-quality annotations to benchmark and help accelerate research in AI techniques for a variety of critical coding tasks, including code similarity and classification, code translation between a large variety of programming languages, and code performance (runtime and memory) improvement techniques. Additionally, CodeNet provides sample input and output test sets for 98.5% of the code samples, which can be used as an oracle for determining code correctness and potentially guide reinforcement learning for code quality improvements. As a usability feature, we provide several pre-processing tools in CodeNet to transform source code into representations that can be readily used as inputs into machine learning models. Results of code classification and code similarity experiments using the CodeNet dataset are provided as a reference. We hope that the scale, diversity and rich, high-quality annotations of CodeNet will offer unprecedented research opportunities at the intersection of AI and Software Engineering.

Veronika Thost, Jie Chen

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 \emph{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.

Luca Buratti, Saurabh Pujar, Mihaela Bornea et al.

The Software Naturalness hypothesis argues that programming languages can be understood through the same techniques used in natural language processing. We explore this hypothesis through the use of a pre-trained transformer-based language model to perform code analysis tasks. Present approaches to code analysis depend heavily on features derived from the Abstract Syntax Tree (AST) while our transformer-based language models work on raw source code. This work is the first to investigate whether such language models can discover AST features automatically. To achieve this, we introduce a sequence labeling task that directly probes the language models understanding of AST. Our results show that transformer based language models achieve high accuracy in the AST tagging task. Furthermore, we evaluate our model on a software vulnerability identification task. Importantly, we show that our approach obtains vulnerability identification results comparable to graph based approaches that rely heavily on compilers for feature extraction.

Ibrahim Abdelaziz, Veronika Thost, Maxwell Crouse et al.

Automated theorem proving in first-order logic is an active research area which is successfully supported by machine learning. While there have been various proposals for encoding logical formulas into numerical vectors -- from simple strings to more involved graph-based embeddings -- little is known about how these different encodings compare. In this paper, we study and experimentally compare pattern-based embeddings that are applied in current systems with popular graph-based encodings, most of which have not been considered in the theorem proving context before. Our experiments show that the advantages of simpler encoding schemes in terms of runtime are outdone by more complex graph-based embeddings, which yield more efficient search strategies and simpler proofs. To support this, we present a detailed analysis across several dimensions of theorem prover performance beyond just proof completion rate, thus providing empirical evidence to help guide future research on neural-guided theorem proving towards the most promising directions.

Maxwell Crouse, Ibrahim Abdelaziz, Cristina Cornelio et al.

Recent advances in the integration of deep learning with automated theorem proving have centered around the representation of logical formulae as inputs to deep learning systems. In particular, there has been a growing interest in adapting structure-aware neural methods to work with the underlying graph representations of logical expressions. While more effective than character and token-level approaches, graph-based methods have often made representational trade-offs that limited their ability to capture key structural properties of their inputs. In this work we propose a novel approach for embedding logical formulae that is designed to overcome the representational limitations of prior approaches. Our architecture works for logics of different expressivity; e.g., first-order and higher-order logic. We evaluate our approach on two standard datasets and show that the proposed architecture achieves state-of-the-art performance on both premise selection and proof step classification.

Maxwell Crouse, Ibrahim Abdelaziz, Bassem Makni et al.

Automated theorem provers have traditionally relied on manually tuned heuristics to guide how they perform proof search. Deep reinforcement learning has been proposed as a way to obviate the need for such heuristics, however, its deployment in automated theorem proving remains a challenge. In this paper we introduce TRAIL, a system that applies deep reinforcement learning to saturation-based theorem proving. TRAIL leverages (a) a novel neural representation of the state of a theorem prover and (b) a novel characterization of the inference selection process in terms of an attention-based action policy. We show through systematic analysis that these mechanisms allow TRAIL to significantly outperform previous reinforcement-learning-based theorem provers on two benchmark datasets for first-order logic automated theorem proving (proving around 15% more theorems).

Pavan Kapanipathi, Veronika Thost, Siva Sankalp Patel et al.

Textual entailment is a fundamental task in natural language processing. Most approaches for solving the problem use only the textual content present in training data. A few approaches have shown that information from external knowledge sources like knowledge graphs (KGs) can add value, in addition to the textual content, by providing background knowledge that may be critical for a task. However, the proposed models do not fully exploit the information in the usually large and noisy KGs, and it is not clear how it can be effectively encoded to be useful for entailment. We present an approach that complements text-based entailment models with information from KGs by (1) using Personalized PageR- ank to generate contextual subgraphs with reduced noise and (2) encoding these subgraphs using graph convolutional networks to capture KG structure. Our technique extends the capability of text models exploiting structural and semantic information found in KGs. We evaluate our approach on multiple textual entailment datasets and show that the use of external knowledge helps improve prediction accuracy. This is particularly evident in the challenging BreakingNLI dataset, where we see an absolute improvement of 5-20% over multiple text-based entailment models.

Cristina Cornelio, Veronika Thost

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, including new performance measures.