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Mar 12

Rethinking Symbolic Regression Datasets and Benchmarks for Scientific Discovery

This paper revisits datasets and evaluation criteria for Symbolic Regression, a task of expressing given data using mathematical equations, specifically focused on its potential for scientific discovery. Focused on a set of formulas used in the existing datasets based on Feynman Lectures on Physics, we recreate 120 datasets to discuss the performance of symbolic regression for scientific discovery (SRSD). For each of the 120 SRSD datasets, we carefully review the properties of the formula and its variables to design reasonably realistic sampling range of values so that our new SRSD datasets can be used for evaluating the potential of SRSD such as whether or not an SR method can (re)discover physical laws from such datasets. As an evaluation metric, we also propose to use normalized edit distances between a predicted equation and the ground-truth equation trees. While existing metrics are either binary or errors between the target values and an SR model's predicted values for a given input, normalized edit distances evaluate a sort of similarity between the ground-truth and predicted equation trees. We have conducted experiments on our new SRSD datasets using five state-of-the-art SR methods in SRBench and a simple baseline based on a recent Transformer architecture. The results show that we provide a more realistic performance evaluation and open up a new machine learning-based approach for scientific discovery. Our datasets and code repository are publicly available.

FRL: Federated Rank Learning

Federated learning (FL) allows mutually untrusted clients to collaboratively train a common machine learning model without sharing their private/proprietary training data among each other. FL is unfortunately susceptible to poisoning by malicious clients who aim to hamper the accuracy of the commonly trained model through sending malicious model updates during FL's training process. We argue that the key factor to the success of poisoning attacks against existing FL systems is the large space of model updates available to the clients, allowing malicious clients to search for the most poisonous model updates, e.g., by solving an optimization problem. To address this, we propose Federated Rank Learning (FRL). FRL reduces the space of client updates from model parameter updates (a continuous space of float numbers) in standard FL to the space of parameter rankings (a discrete space of integer values). To be able to train the global model using parameter ranks (instead of parameter weights), FRL leverage ideas from recent supermasks training mechanisms. Specifically, FRL clients rank the parameters of a randomly initialized neural network (provided by the server) based on their local training data. The FRL server uses a voting mechanism to aggregate the parameter rankings submitted by clients in each training epoch to generate the global ranking of the next training epoch. Intuitively, our voting-based aggregation mechanism prevents poisoning clients from making significant adversarial modifications to the global model, as each client will have a single vote! We demonstrate the robustness of FRL to poisoning through analytical proofs and experimentation. We also show FRL's high communication efficiency. Our experiments demonstrate the superiority of FRL in real-world FL settings.

Molecule3D: A Benchmark for Predicting 3D Geometries from Molecular Graphs

Graph neural networks are emerging as promising methods for modeling molecular graphs, in which nodes and edges correspond to atoms and chemical bonds, respectively. Recent studies show that when 3D molecular geometries, such as bond lengths and angles, are available, molecular property prediction tasks can be made more accurate. However, computing of 3D molecular geometries requires quantum calculations that are computationally prohibitive. For example, accurate calculation of 3D geometries of a small molecule requires hours of computing time using density functional theory (DFT). Here, we propose to predict the ground-state 3D geometries from molecular graphs using machine learning methods. To make this feasible, we develop a benchmark, known as Molecule3D, that includes a dataset with precise ground-state geometries of approximately 4 million molecules derived from DFT. We also provide a set of software tools for data processing, splitting, training, and evaluation, etc. Specifically, we propose to assess the error and validity of predicted geometries using four metrics. We implement two baseline methods that either predict the pairwise distance between atoms or atom coordinates in 3D space. Experimental results show that, compared with generating 3D geometries with RDKit, our method can achieve comparable prediction accuracy but with much smaller computational costs. Our Molecule3D is available as a module of the MoleculeX software library (https://github.com/divelab/MoleculeX).

Efficiently Computing Similarities to Private Datasets

Many methods in differentially private model training rely on computing the similarity between a query point (such as public or synthetic data) and private data. We abstract out this common subroutine and study the following fundamental algorithmic problem: Given a similarity function f and a large high-dimensional private dataset X subset R^d, output a differentially private (DP) data structure which approximates sum_{x in X} f(x,y) for any query y. We consider the cases where f is a kernel function, such as f(x,y) = e^{-|x-y|_2^2/sigma^2} (also known as DP kernel density estimation), or a distance function such as f(x,y) = |x-y|_2, among others. Our theoretical results improve upon prior work and give better privacy-utility trade-offs as well as faster query times for a wide range of kernels and distance functions. The unifying approach behind our results is leveraging `low-dimensional structures' present in the specific functions f that we study, using tools such as provable dimensionality reduction, approximation theory, and one-dimensional decomposition of the functions. Our algorithms empirically exhibit improved query times and accuracy over prior state of the art. We also present an application to DP classification. Our experiments demonstrate that the simple methodology of classifying based on average similarity is orders of magnitude faster than prior DP-SGD based approaches for comparable accuracy.

AutoKnots: Adaptive Knot Allocation for Spline Interpolation

In astrophysical and cosmological analyses, the increasing quality and volume of astronomical data demand efficient and precise computational tools. This work introduces a novel adaptive algorithm for automatic knots (AutoKnots) allocation in spline interpolation, designed to meet user-defined precision requirements. Unlike traditional methods that rely on manually configured knot distributions with numerous parameters, the proposed technique automatically determines the optimal number and placement of knots based on interpolation error criteria. This simplifies configuration, often requiring only a single parameter. The algorithm progressively improves the interpolation by adaptively sampling the function-to-be-approximated, f(x), in regions where the interpolation error exceeds the desired threshold. All function evaluations contribute directly to the final approximation, ensuring efficiency. While each resampling step involves recomputing the interpolation table, this process is highly optimized and usually computationally negligible compared to the cost of evaluating f(x). We show the algorithm's efficacy through a series of precision tests on different functions. However, the study underscores the necessity for caution when dealing with certain function types, notably those featuring plateaus. To address this challenge, a heuristic enhancement is incorporated, improving accuracy in flat regions. This algorithm has been extensively used and tested over the years. NumCosmo includes a comprehensive set of unit tests that rigorously evaluate the algorithm both directly and indirectly, underscoring its robustness and reliability. As a practical application, we compute the surface mass density Sigma(R) and the average surface mass density Sigma(<R) for Navarro-Frenk-White and Hernquist halo density profiles, which provide analytical benchmarks. (abridged)

SCott: Accelerating Diffusion Models with Stochastic Consistency Distillation

The iterative sampling procedure employed by diffusion models (DMs) often leads to significant inference latency. To address this, we propose Stochastic Consistency Distillation (SCott) to enable accelerated text-to-image generation, where high-quality generations can be achieved with just 1-2 sampling steps, and further improvements can be obtained by adding additional steps. In contrast to vanilla consistency distillation (CD) which distills the ordinary differential equation solvers-based sampling process of a pretrained teacher model into a student, SCott explores the possibility and validates the efficacy of integrating stochastic differential equation (SDE) solvers into CD to fully unleash the potential of the teacher. SCott is augmented with elaborate strategies to control the noise strength and sampling process of the SDE solver. An adversarial loss is further incorporated to strengthen the sample quality with rare sampling steps. Empirically, on the MSCOCO-2017 5K dataset with a Stable Diffusion-V1.5 teacher, SCott achieves an FID (Frechet Inceptio Distance) of 22.1, surpassing that (23.4) of the 1-step InstaFlow (Liu et al., 2023) and matching that of 4-step UFOGen (Xue et al., 2023b). Moreover, SCott can yield more diverse samples than other consistency models for high-resolution image generation (Luo et al., 2023a), with up to 16% improvement in a qualified metric. The code and checkpoints are coming soon.

Unified Functional Hashing in Automatic Machine Learning

The field of Automatic Machine Learning (AutoML) has recently attained impressive results, including the discovery of state-of-the-art machine learning solutions, such as neural image classifiers. This is often done by applying an evolutionary search method, which samples multiple candidate solutions from a large space and evaluates the quality of each candidate through a long training process. As a result, the search tends to be slow. In this paper, we show that large efficiency gains can be obtained by employing a fast unified functional hash, especially through the functional equivalence caching technique, which we also present. The central idea is to detect by hashing when the search method produces equivalent candidates, which occurs very frequently, and this way avoid their costly re-evaluation. Our hash is "functional" in that it identifies equivalent candidates even if they were represented or coded differently, and it is "unified" in that the same algorithm can hash arbitrary representations; e.g. compute graphs, imperative code, or lambda functions. As evidence, we show dramatic improvements on multiple AutoML domains, including neural architecture search and algorithm discovery. Finally, we consider the effect of hash collisions, evaluation noise, and search distribution through empirical analysis. Altogether, we hope this paper may serve as a guide to hashing techniques in AutoML.