Learn how to leverage generative AI to support and improve your productivity at work. The next cohort will take place online on April 28 and 30, 2026, in French.
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Understanding complex interactions in biomedical networks is crucial for advancements in biomedicine, but traditional link prediction (LP) m… (see more)ethods are limited in capturing this complexity. Representation-based learning techniques improve prediction accuracy by mapping nodes to low-dimensional embeddings, yet they often struggle with interpretability and scalability. We present BioPathNet, a novel graph neural network framework based on the Neural Bellman-Ford Network (NBFNet), addressing these limitations through path-based reasoning for LP in biomedical knowledge graphs. Unlike node-embedding frameworks, BioPathNet learns representations between node pairs by considering all relations along paths, enhancing prediction accuracy and interpretability. This allows visualization of influential paths and facilitates biological validation. BioPathNet leverages a background regulatory graph (BRG) for enhanced message passing and uses stringent negative sampling to improve precision. In evaluations across various LP tasks, such as gene function annotation, drug-disease indication, synthetic lethality, and lncRNA-mRNA interaction prediction, BioPathNet consistently outperformed shallow node embedding methods, relational graph neural networks and task-specific state-of-the-art methods, demonstrating robust performance and versatility. Our study predicts novel drug indications for diseases like acute lymphoblastic leukemia (ALL) and Alzheimer’s, validated by medical experts and clinical trials. We also identified new synthetic lethality gene pairs and regulatory interactions involving lncRNAs and target genes, confirmed through literature reviews. BioPathNet’s interpretability will enable researchers to trace prediction paths and gain molecular insights, making it a valuable tool for drug discovery, personalized medicine and biology in general.
In this blogpost we discuss the idea of teaching neural networks to reach fixed points when reasoning. Specifically, on the algorithmic reas… (see more)oning benchmark CLRS the current neural networks are told the number of reasoning steps they need. While a quick fix is to add a termination network that predicts when to stop, a much more salient inductive bias is that the neural network shouldn't change it's answer any further once the answer is correct, i.e. it should reach a fixed point. This is supported by denotational semantics, which tells us that while loops that terminate are the minimum fixed points of a function. We implement this idea with the help of deep equilibrium models and discuss several hurdles one encounters along the way. We show on several algorithms from the CLRS benchmark the partial success of this approach and the difficulty in making it work robustly across all algorithms.
Despite significant investment into safety training, large language models (LLMs) deployed in the real world still suffer from numerous vuln… (see more)erabilities. One perspective on LLM safety training is that it algorithmically forbids the model from answering toxic or harmful queries. To assess the effectiveness of safety training, in this work, we study forbidden tasks, i.e., tasks the model is designed to refuse to answer. Specifically, we investigate whether in-context learning (ICL) can be used to re-learn forbidden tasks despite the explicit fine-tuning of the model to refuse them. We first examine a toy example of refusing sentiment classification to demonstrate the problem. Then, we use ICL on a model fine-tuned to refuse to summarise made-up news articles. Finally, we investigate whether ICL can undo safety training, which could represent a major security risk. For the safety task, we look at Vicuna-7B, Starling-7B, and Llama2-7B. We show that the attack works out-of-the-box on Starling-7B and Vicuna-7B but fails on Llama2-7B. Finally, we propose an ICL attack that uses the chat template tokens like a prompt injection attack to achieve a better attack success rate on Vicuna-7B and Starling-7B.
Trigger Warning: the appendix contains LLM-generated text with violence, suicide, and misinformation.
Reasoning on large-scale knowledge graphs has been long dominated by embedding methods. While path-based methods possess the inductive capac… (see more)ity that embeddings lack, their scalability is limited by the exponential number of paths. Here we present A*Net, a scalable path-based method for knowledge graph reasoning. Inspired by the A* algorithm for shortest path problems, our A*Net learns a priority function to select important nodes and edges at each iteration, to reduce time and memory footprint for both training and inference. The ratio of selected nodes and edges can be specified to trade off between performance and efficiency. Experiments on both transductive and inductive knowledge graph reasoning benchmarks show that A*Net achieves competitive performance with existing state-of-the-art path-based methods, while merely visiting 10% nodes and 10% edges at each iteration. On a million-scale dataset ogbl-wikikg2, A*Net not only achieves a new state-of-the-art result, but also converges faster than embedding methods. A*Net is the first path-based method for knowledge graph reasoning at such scale.
