Materials Discovery

Exploiting symmetry inherent in data can significantly improve the sample efficiency of a learning procedure and the generalization of learned models. When data clearly reveals underlying symmetry, leveraging this symmetry can naturally inform the design of model architectures or learning strategies. Yet, in numerous real-world scenarios, identifying the specific symmetry within a given data distribution often proves ambiguous. To tackle this, some existing works learn symmetry in a data-driven manner, parameterizing and learning expected symmetry through data. However, these methods often rely on explicit knowledge, such as pre-defined Lie groups, which are typically restricted to linear or affine transformations. In this paper, we propose a novel symmetry learning algorithm based on transformations defined with one-parameter groups, continuously parameterized transformations flowing along the directions of vector fields called infinitesimal generators. Our method is built upon minimal inductive biases, encompassing not only commonly utilized symmetries rooted in Lie groups but also extending to symmetries derived from nonlinear generators. To learn these symmetries, we introduce a notion of a validity score that examine whether the transformed data is still valid for the given task. The validity score is designed to be fully differentiable and easily computable, enabling effective searches for transformations that achieve symmetries innate to the data. We apply our method mainly in two domains: image data and partial differential equations, and demonstrate its advantages. Our codes are available at \url{https://github.com/kogyeonghoon/learning-symmetry-from-scratch.git}.

In this paper, we study a practical yet challenging task, On-the-fly Category Discovery (OCD), aiming to online discover the newly-coming stream data that belong to both known and unknown classes, by leveraging only known category knowledge contained in labeled data. Previous OCD methods employ the hash-based technique to represent old/new categories by hash codes for instance-wise inference. However, directly mapping features into low-dimensional hash space not only inevitably damages the ability to distinguish classes and but also causes ``high sensitivity'' issue, especially for fine-grained classes, leading to inferior performance. To address these drawbacks, we propose a novel Prototypical Hash Encoding (PHE) framework consisting of Category-aware Prototype Generation (CPG) and Discriminative Category Encoding (DCE) to mitigate the sensitivity of hash code while preserving rich discriminative information contained in high-dimension feature space, in a two-stage projection fashion. CPG enables the model to fully capture the intra-category diversity by representing each category with multiple prototypes. DCE boosts the discrimination ability of hash code with the guidance of the generated category prototypes and the constraint of minimum separation distance. By jointly optimizing CPG and DCE, we demonstrate that these two components are mutually beneficial towards an effective OCD. Extensive experiments show the significant superiority of our PHE over previous methods, e.g. obtaining an improvement of +5.3% in ALL ACC averaged on all datasets. Moreover, due to the nature of the interpretable prototypes, we visually analyze the underlying mechanism of how PHE helps group certain samples into either known or unknown categories. Code is available at https://github.com/HaiyangZheng/PHE.

Symmetry detection has been shown to improve various machine learning tasks. In the context of continuous symmetry detection, current state of the art experiments are limited to the detection of affine transformations. Under the manifold assumption, we outline a framework for discovering continuous symmetry in data beyond the affine transformation group. We also provide a similar framework for discovering discrete symmetry. We experimentally compare our method to an existing method known as LieGAN and show that our method is competitive at detecting affine symmetries for large sample sizes and superior than LieGAN for small sample sizes. We also show our method is able to detect continuous symmetries beyond the affine group and is generally more computationally efficient than LieGAN.

What data or environments to use for training to improve downstream performance is a longstanding and very topical question in reinforcement learning. In particular, Unsupervised Environment Design (UED) methods have gained recent attention as their adaptive curricula promise to enable agents to be robust to in- and out-of-distribution tasks. This work investigates how existing UED methods select training environments, focusing on task prioritisation metrics. Surprisingly, despite methods aiming to maximise regret in theory, the practical approximations do not correlate with regret but with success rate. As a result, a significant portion of an agent's experience comes from environments it has already mastered, offering little to no contribution toward enhancing its abilities. Put differently, current methods fail to predict intuitive measures of *learnability*. Specifically, they are unable to consistently identify those scenarios that the agent can sometimes solve, but not always. Based on our analysis, we develop a method that directly trains on scenarios with high learnability. This simple and intuitive approach outperforms existing UED methods in several binary-outcome environments, including the standard domain of Minigrid and a novel setting closely inspired by a real-world robotics problem. We further introduce a new adversarial evaluation procedure for directly measuring robustness, closely mirroring the conditional value at risk (CVaR). We open-source all our code and present visualisations of final policies here: https://github.com/amacrutherford/sampling-for-learnability.

Constantly discovering novel concepts is crucial in evolving environments. This paper explores the underexplored task of Continual Generalized Category Discovery (C-GCD), which aims to incrementally discover new classes from *unlabeled* data while maintaining the ability to recognize previously learned classes. Although several settings are proposed to study the C-GCD task, they have limitations that do not reflect real-world scenarios. We thus study a more practical C-GCD setting, which includes more new classes to be discovered over a longer period, without storing samples of past classes. In C-GCD, the model is initially trained on labeled data of known classes, followed by multiple incremental stages where the model is fed with unlabeled data containing both old and new classes. The core challenge involves two conflicting objectives: discover new classes and prevent forgetting old ones. We delve into the conflicts and identify that models are susceptible to *prediction bias* and *hardness bias*. To address these issues, we introduce a debiased learning framework, namely **Happy**, characterized by **H**ardness-**a**ware **p**rototype sampling and soft entro**py** regularization. For the *prediction bias*, we first introduce clustering-guided initialization to provide robust features. In addition, we propose soft entropy regularization to assign appropriate probabilities to new classes, which can significantly enhance the clustering performance of new classes. For the *harness bias*, we present the hardness-aware prototype sampling, which can effectively reduce the forgetting issue for previously seen classes, especially for difficult classes. Experimental results demonstrate our method proficiently manages the conflicts of C-GCD and achieves remarkable performance across various datasets, e.g., 7.5% overall gains on ImageNet-100. Our code is publicly available at https://github.com/mashijie1028/Happy-CGCD.

While deep learning has revolutionized computer-aided drug discovery, the AI community has predominantly focused on model innovation and placed less emphasis on establishing best benchmarking practices. We posit that without a sound model evaluation framework, the AI community's efforts cannot reach their full potential, thereby slowing the progress and transfer of innovation into real-world drug discovery. Thus, in this paper, we seek to establish a new gold standard for small molecule drug discovery benchmarking, *WelQrate*. Specifically, our contributions are threefold: ***WelQrate*** **dataset collection** - we introduce a meticulously curated collection of 9 datasets spanning 5 therapeutic target classes. Our hierarchical curation pipelines, designed by drug discovery experts, go beyond the primary high-throughput screen by leveraging additional confirmatory and counter screens along with rigorous domain-driven preprocessing, such as Pan-Assay Interference Compounds (PAINS) filtering, to ensure the high-quality data in the datasets; ***WelQrate*** **Evaluation Framework** - we propose a standardized model evaluation framework considering high-quality datasets, featurization, 3D conformation generation, evaluation metrics, and data splits, which provides a reliable benchmarking for drug discovery experts conducting real-world virtual screening; **Benchmarking** - we evaluate model performance through various research questions using the *WelQrate* dataset collection, exploring the effects of different models, dataset quality, featurization methods, and data splitting strategies on the results. In summary, we recommend adopting our proposed *WelQrate* as the gold standard in small molecule drug discovery benchmarking. The *WelQrate* dataset collection, along with the curation codes, and experimental scripts are all publicly available at www.WelQrate.org.

Generative models trained at scale can now produce novel text, video, and more recently, scientific data such as crystal structures. The ultimate goal for materials discovery, however, goes beyond generation: we desire a fully automated system that proposes, generates, and verifies crystal structures given a high-level user instruction. In this work, we formulate end-to-end language-to-structure generation as a multi-objective optimization problem, and propose Generative Hierarchical Materials Search (GenMS) for controllable generation of crystal structures. GenMS consists of (1) a language model that takes high-level natural language as input and generates intermediate textual information about a crystal (e.g., chemical formulae), and (2) a diffusion model that takes intermediate information as input and generates low-level continuous value crystal structures. GenMS additionally uses a graph neural network to predict properties (e.g., formation energy) from the generated crystal structures. During inference, GenMS leverages all three components to conduct a forward tree search over the space of possible structures. Experiments show that GenMS outperforms other alternatives both in satisfying user request and in generating low-energy structures. GenMS is able to generate complex structures such as double perovskites (or elpasolites), layered structures, and spinels, solely from natural language input.

Recent advancements have shown promise in applying traditional Semi-Supervised Learning strategies to the task of Generalized Category Discovery (GCD). Typically, this involves a teacher-student framework in which the teacher imparts knowledge to the student to classify categories, even in the absence of explicit labels. Nevertheless, GCD presents unique challenges, particularly the absence of priors for new classes, which can lead to the teacher's misguidance and unsynchronized learning with the student, culminating in suboptimal outcomes. In our work, we delve into why traditional teacher-student designs falter in generalized category discovery as compared to their success in closed-world semi-supervised learning. We identify inconsistent pattern learning as the crux of this issue and introduce FlipClass—a method that dynamically updates the teacher to align with the student's attention, instead of maintaining a static teacher reference. Our teacher-attention-update strategy refines the teacher's focus based on student feedback, promoting consistent pattern recognition and synchronized learning across old and new classes. Extensive experiments on a spectrum of benchmarks affirm that FlipClass significantly surpasses contemporary GCD methods, establishing new standards for the field.

Group equivariance has emerged as a valuable inductive bias in deep learning, enhancing generalization, data efficiency, and robustness. Classically, group equivariant methods require the groups of interest to be known beforehand, which may not be realistic for real-world data. Additionally, baking in fixed group equivariance may impose overly restrictive constraints on model architecture. This highlights the need for methods that can dynamically discover and apply symmetries as soft constraints. For neural network architectures, equivariance is commonly achieved through group transformations of a canonical weight tensor, resulting in weight sharing over a given group $G$. In this work, we propose to *learn* such a weight-sharing scheme by defining a collection of learnable doubly stochastic matrices that act as soft permutation matrices on canonical weight tensors, which can take regular group representations as a special case. This yields learnable kernel transformations that are jointly optimized with downstream tasks. We show that when the dataset exhibits strong symmetries, the permutation matrices will converge to regular group representations and our weight-sharing networks effectively become regular group convolutions. Additionally, the flexibility of the method enables it to effectively pick up on partial symmetries.

We consider the problem of crystal materials generation using language models (LMs). A key step is to convert 3D crystal structures into 1D sequences to be processed by LMs. Prior studies used the crystallographic information framework (CIF) file stream, which fails to ensure SE(3) and periodic invariance and may not lead to unique sequence representations for a given crystal structure. Here, we propose a novel method, known as Mat2Seq, to tackle this challenge. Mat2Seq converts 3D crystal structures into 1D sequences and ensures that different mathematical descriptions of the same crystal are represented in a single unique sequence, thereby provably achieving SE(3) and periodic invariance. Experimental results show that, with language models, Mat2Seq achieves promising performance in crystal structure generation as compared with prior methods.