HeMeNet: Heterogeneous Multichannel Equivariant Network for Protein Multitask Learning

Understanding and leveraging the 3D structures of proteins is central to a variety of biological and drug discovery tasks. While deep learning has been applied successfully for structure-based protein function prediction tasks, current methods usually employ distinct training for each task. However, each of the tasks is of small size, and such a single-task strategy hinders the models' performance and generalization ability. As some labeled 3D protein datasets are biologically related, combining multi-source datasets for larger-scale multi-task learning is one way to overcome this problem. In this paper, we propose a neural network model to address multiple tasks jointly upon the input of 3D protein structures. In particular, we first construct a standard structure-based multi-task benchmark called Protein-MT, consisting of 6 biologically relevant tasks, including affinity prediction and property prediction, integrated from 4 public datasets. Then, we develop a novel graph neural network for multi-task learning, dubbed Heterogeneous Multichannel Equivariant Network (HeMeNet), which is E(3) equivariant and able to capture heterogeneous relationships between different atoms. Besides, HeMeNet can achieve task-specific learning via the task-aware readout mechanism. Extensive evaluations on our benchmark verify the effectiveness of multi-task learning, and our model generally surpasses state-of-the-art models.

Pre-trained Universal Medical Image Transformer

Self-supervised learning has emerged as a viable method to leverage the abundance of unlabeled medical imaging data, addressing the challenge of labeled data scarcity in medical image analysis. In particular, masked image modeling (MIM) with visual token reconstruction has shown promising results in the general computer vision (CV) domain and serves as a candidate for medical image analysis. However, the presence of heterogeneous 2D and 3D medical images often limits the volume and diversity of training data that can be effectively used for a single model structure. In this work, we propose a spatially adaptive convolution (SAC) module, which adaptively adjusts convolution parameters based on the voxel spacing of the input images. Employing this SAC module, we build a universal visual tokenizer and a universal Vision Transformer (ViT) capable of effectively processing a wide range of medical images with various imaging modalities and spatial properties. Moreover, in order to enhance the robustness of the visual tokenizer's reconstruction objective for MIM, we suggest to generalize the discrete token output of the visual tokenizer to a probabilistic soft token. We show that the generalized soft token representation can be effectively integrated with the prior distribution regularization through a constructive interpretation. As a result, we pre-train a universal visual tokenizer followed by a universal ViT via visual token reconstruction on 55 public medical image datasets, comprising over 9 million 2D slices (including over 48,000 3D images). This represents the largest, most comprehensive, and diverse dataset for pre-training 3D medical image models to our knowledge. Experimental results on downstream medical image classification and segmentation tasks demonstrate the superior performance of our model and improved label efficiency.

Overview of the Ninth Dialog System Technology Challenge: DSTC9

This paper introduces the Ninth Dialog System Technology Challenge (DSTC-9). This edition of the DSTC focuses on applying end-to-end dialog technologies for four distinct tasks in dialog systems, namely, 1. Task-oriented dialog Modeling with unstructured knowledge access, 2. Multi-domain task-oriented dialog, 3. Interactive evaluation of dialog, and 4. Situated interactive multi-modal dialog. This paper describes the task definition, provided datasets, baselines and evaluation set-up for each track. We also summarize the results of the submitted systems to highlight the overall trends of the state-of-the-art technologies for the tasks.