Molecule property prediction has gained significant attention in recent years. The main bottleneck is the label insufficiency caused by expensive lab experiments. In order to alleviate this issue and to better leverage textual knowledge for tasks, this study investigates the feasibility of employing natural language instructions to accomplish molecule-related tasks in a zero-shot setting. We discover that existing molecule-text models perform poorly in this setting due to inadequate treatment of instructions and limited capacity for graphs. To overcome these issues, we propose GIMLET, which unifies language models for both graph and text data. By adopting generalized position embedding, our model is extended to encode both graph structures and instruction text without additional graph encoding modules.

More precisely, we use batches of size 2. Each batch contains one patch with the foreground oversampled. Furthermore, we split each silo's data into training and validation data with 80% and 20% split, respectively. All this pre-processing and patching is done using the nnU-Net library [IJK+21]. Loss function We use the same loss function as proposed by nnU-Net [IJK+21] for the KiTS19 dataset which is based on DICE [Dic45] and on the Cross Entropy loss.

Federated Learning (FL) is a novel approach enabling several clients holding sensitive data to collaboratively train machine learning models, without centralizing data. The cross-silo FL setting corresponds to the case of few (2-50) reliable clients, each holding medium to large datasets, and is typically found in applications such as healthcare, finance, or industry. While previous works have proposed representative datasets for cross-device FL, few realistic healthcare cross-silo FL datasets exist, thereby slowing algorithmic research in this critical application. In this work, we propose a novel cross-silo dataset suite focused on healthcare, FLamby (Federated Learning AMple Benchmark of Your cross-silo strategies), to bridge the gap between theory and practice of cross-silo FL. FLamby encompasses 7 healthcare datasets with natural splits, covering multiple tasks, modalities, and data volumes, each accompanied with baseline training code.

Language models (LMs) trained on vast quantities of unlabelled data have greatly advanced the field of natural language processing (NLP). In this study, we re-visit the widely accepted notion in NLP that continued pre-training LMs on task-related texts improves the performance of fine-tuning (FT) in downstream tasks. Through experiments on eight single-sentence tasks and eight sentence-pair tasks in both semi-supervised and fully-supervised settings, we find that conventional continued pre-training does not consistently provide benefits and can even be detrimental for sentence-pair tasks or when prompt-based FT is used. To tackle these issues, we propose Prompt-based Continued Pre-training (PCP), which combines the idea of instruction tuning with conventional continued pre-training. Our approach aims to improve the performance of prompt-based FT by presenting both taskrelated texts and prompt templates to LMs through unsupervised pre-training objectives before fine-tuning for the target task. Our empirical evaluations on 21 benchmarks demonstrate that the PCP consistently improves the performance of state-of-the-art prompt-based FT approaches (up to 20.1% absolute) in both semisupervised and fully-supervised settings, even with only hundreds of unlabelled examples. Additionally, prompt-based FT with the PCP outperforms state-of-theart semi-supervised approaches with greater simplicity, eliminating the need for an iterative process and extra data augmentation. Our further analysis explores the performance lower bound of the PCP and reveals that the advantages of PCP persist across different sizes of models and datasets.

In this paper, we investigate the question: Given a small number of datapoints, for example N = 30, how tight can PAC-Bayes and test set bounds be made? For such small datasets, test set bounds adversely affect generalisation performance by withholding data from the training procedure. In this setting, PAC-Bayes bounds are especially attractive, due to their ability to use all the data to simultaneouslylearn a posterior and bound its generalisation risk. We focus on the case of i.i.d.