Protein inverse folding has attracted increasing attention in recent years. However, we observe that current methods are usually limited to the CATH dataset and the recovery metric. The lack of a unified framework for ensembling and comparing different methods hinders the comprehensive investigation. In this paper, we propose ProteinInvBench, a new benchmark for protein design, which comprises extended protein design tasks, integrated models, and diverse evaluation metrics. We broaden the application of methods originally designed for single-chain protein design to new scenarios of multi-chain and de novo protein design. Recent impressive methods, including GraphTrans, StructGNN, GVP, GCA, AlphaDesign, ProteinMPNN, PiFold and KWDesign are integrated into our framework. In addition to the recovery, we also evaluate the confidence, diversity, sc-TM, efficiency, and robustness to thoroughly revisit current protein design approaches and inspire future work. As a result, we establish the first comprehensive benchmark for protein design, which is publicly available at https://github.com/A4Bio/OpenCPD.

We introduce general tools for designing efficient private estimation algorithms, in the high-dimensional settings, whose statistical guarantees almost match those of the best known non-private algorithms. To illustrate our techniques, we consider two problems: recovery of stochastic block models and learning mixtures of spherical Gaussians. For the former, we present the first efficient (ε,δ)-differentially private algorithms for both weak recovery and exact recovery. Previously known algorithms achieving comparable guarantees required quasi-polynomial time. We complement these results with an information-theoretic lower bound that highlights how the guarantees of our algorithms are almost tight. For the latter, we design an (ε,δ)-differentially private algorithm that recovers the centers of the k-mixture when the minimum separation is at least O(k1/t t). For all choices of t, this algorithm requires sample complexity n kO(1)dO(t) and time complexity (nd)O(t). Prior work required either an additional additive Ω( logn) term in the minimum separation or an explicit upper bound on the Euclidean norm of the centers.

Dataset condensation (DC) distills a large real-world dataset into a small synthetic dataset, with the goal of training a network from scratch on the latter that performs similarly to the former. State-of-the-art (SOTA) DC methods have achieved satisfactory results through techniques such as accuracy, gradient, training trajectory, or distribution matching. However, these works all perform matching in the high-dimension pixel space, ignoring that natural images are usually locally connected and have lower intrinsic dimensions, resulting in low condensation efficiency. In this work, we propose a simple-yet-efficient dataset condensation plugin that matches the raw and synthetic datasets in a low-dimensional manifold.

Equivariant deep learning architectures exploit symmetries in learning problems to improve the sample efficiency of neural-network-based models and their ability to generalise. However, when modelling real-world data, learning problems are often not equivariant, but only approximately. For example, when estimating the global temperature field from weather station observations, local topographical features like mountains break translation equivariance. In these scenarios, it is desirable to construct architectures that can flexibly depart from exact equivariance in a data-driven way. Current approaches to achieving this cannot usually be applied out-of-the-box to any architecture and symmetry group. In this paper, we develop a general approach to achieving this using existing equivariant architectures. Our approach is agnostic to both the choice of symmetry group and model architecture, making it widely applicable. We consider the use of approximately equivariant architectures in neural processes (NPs), a popular family of meta-learning models. We demonstrate the effectiveness of our approach on a number of synthetic and real-world regression experiments, showing that approximately equivariant NP models can outperform both their non-equivariant and strictly equivariant counterparts.

This paper introduces the novel concept of few-shot weakly supervised learning for pathology Whole Slide Image (WSI) classification, denoted as FSWC. A solution is proposed based on prompt learning and the utilization of a large language model, GPT-4. Since a WSI is too large and needs to be divided into patches for processing, WSI classification is commonly approached as a Multiple Instance Learning (MIL) problem. In this context, each WSI is considered a bag, and the obtained patches are treated as instances. The objective of FSWC is to classify both bags and instances with only a limited number of labeled bags. Unlike conventional few-shot learning problems, FSWC poses additional challenges due to its weak bag labels within the MIL framework.

Knowledge distillation with unlabeled examples is a powerful training paradigm for generating compact and lightweight student models in applications where the amount of labeled data is limited but one has access to a large pool of unlabeled data. In this setting, a large teacher model generates "soft" pseudo-labels for the unlabeled dataset which are then used for training the student model. Despite its success in a wide variety of applications, a shortcoming of this approach is that the teacher's pseudo-labels are often noisy, leading to impaired student performance. In this paper, we present a principled method for knowledge distillation with unlabeled examples that we call Student-Label Mixing (SLaM) and we show that it consistently improves over prior approaches by evaluating it on several standard benchmarks. Finally, we show that SLaM comes with theoretical guarantees; along the way we give an algorithm improving the best-known sample complexity for learning halfspaces with margin under random classification noise, and provide the first convergence analysis for so-called "forward loss-adjustment" methods.

Recently, commonsense reasoning in text generation has attracted much attention. Generative commonsense reasoning is the task that requires machines, given a group of keywords, to compose a single coherent sentence with commonsense plausibility. While existing datasets targeting generative commonsense reasoning focus on everyday scenarios, it is unclear how well machines reason under specific geographical and temporal contexts. We formalize this challenging task as SITUATEDGEN, where machines with commonsense should generate a pair of contrastive sentences given a group of keywords including geographical or temporal entities. We introduce a corresponding English dataset consisting of 8,268 contrastive sentence pairs, which are built upon several existing commonsense reasoning benchmarks with minimal manual labor. Experiments show that state-of-the-art generative language models struggle to generate sentences with commonsense plausibility and still lag far behind human performance.