arXiv subjects

Weichi Yao

Publications and source records attributed to Weichi Yao.

11 recordsLinked to original sources

arXiv2026

Fixed-Dimensional Latent Flow for Generating Variable-Size 3D Molecules

In molecular discovery, molecule size is coupled to composition, structure, and other target properties. Yet most 3D generators require molecule size to be specified before generation. Here, we introduce Equivariant-Free Transformer-Autoencoded Latent Flow Matching, a two-stage generative framework that relies entirely on a single fixed-dimensional molecule-level latent representation to generate variable-size molecules. The second-stage flow matching model samples this latent vector, and an autoregressive Transformer decoder then determines molecule size while generating atom types, coordinates, and chemically informative states. Canonical atom ordering and rigid-pose alignment enable standard Transformers without equivariant layers, while joint decoding of molecular geometry and an enriched chemical state enables reliable, deterministic, chemistry-guided graph recovery without requiring a learned dense pairwise bond decoder. The same fixed-dimensional latent supports unconditional and property-conditioned flow matching, while optional property supervision adds an internal ranking readout, with no separate predictor or reference calculations. On PCQM4Mv2, EF-TALFM achieves the highest fraction of molecules that are unique, training-set novel, pass sanitization and PoseBusters sanity checks, 89.4\%, compared with 75.6\% for UAE-3D and 69.8\% for FlowMol. EF-TALFM also achieves higher measured computational throughput for training and sampling. Across ten target HOMO--LUMO gaps, internal ranking doubles the density functional theory (DFT)-verified hit rate within $0.1\,\mathrm{eV}$, while preserving 97\% novelty among unique verified hits. These results demonstrate that fixed-dimensional molecule-level generation followed by symmetry-resolved autoregressive realization provides a practical architecture for open-ended and property-directed 3D molecular design.

physics.chem-ph↗

arXiv2026

Adapting Evidential Neural Networks to Test-Time Neighbor Fusion Improves Molecular Property Prediction

A trained molecular property model can be refined at test time by correcting each prediction with the measured labels of the most similar training molecules, a retraining-free procedure we call neighbor fusion; evidential neural networks make it principled by using their aleatoric and epistemic uncertainty to parameterize a Bayesian update. Our main contribution, PG-EVIKAL, learns a property-distance metric to re-rank structurally similar neighbors by their property relevance before fusion, building on EVIKAL (scalar Kalman filter) and GP-EVIKAL (Gaussian process variant handling correlated neighbors). Evaluated on 16 molecular datasets, PG-EVIKAL reduces RMSE relative to the evidential model baseline on 14 of them, with a median reduction of 19.4%, and improves calibration; in sequential-assay scenarios it further incorporates newly measured molecules, refining predictions as they arrive without retraining. This work demonstrates that evidential uncertainty decomposition is not merely a calibration objective but an actionable inference resource that enables test-time refinement of molecular property predictions.

cs.LG↗

arXiv2026

Goal-Oriented Influence-Maximizing Data Acquisition for Learning and Optimization

Active data acquisition is central to many learning and optimization tasks in deep neural networks, yet remains challenging because most approaches rely on predictive uncertainty estimates that are difficult to obtain reliably. To this end, we propose Goal-Oriented Influence- Maximizing Data Acquisition (GOIMDA), an active acquisition algorithm that avoids explicit posterior inference while remaining uncertainty-aware through inverse curvature. GOIMDA selects inputs by maximizing their expected influence on a user-specified goal functional, such as test loss, predictive entropy, or the value of an optimizer-recommended design. Leveraging first-order influence functions, we derive a tractable acquisition rule that combines the goal gradient, training-loss curvature, and candidate sensitivity to model parameters. We show theoretically that, for generalized linear models, GOIMDA approximates predictive-entropy minimization up to a correction term accounting for goal alignment and prediction bias, thereby, yielding uncertainty-aware behavior without maintaining a Bayesian posterior. Empirically, across learning tasks (including image and text classification) and optimization tasks (including noisy global optimization benchmarks and neural-network hyperparameter tuning), GOIMDA consistently reaches target performance with substantially fewer labeled samples or function evaluations than uncertainty-based active learning and Gaussian-process Bayesian optimization baselines.

stat.ML↗

arXiv2023

Towards fully covariant machine learning

Any representation of data involves arbitrary investigator choices. Because those choices are external to the data-generating process, each choice leads to an exact symmetry, corresponding to the group of transformations that takes one possible representation to another. These are the passive symmetries; they include coordinate freedom, gauge symmetry, and units covariance, all of which have led to important results in physics. In machine learning, the most visible passive symmetry is the relabeling or permutation symmetry of graphs. Our goal is to understand the implications for machine learning of the many passive symmetries in play. We discuss dos and don'ts for machine learning practice if passive symmetries are to be respected. We discuss links to causal modeling, and argue that the implementation of passive symmetries is particularly valuable when the goal of the learning problem is to generalize out of sample. This paper is conceptual: It translates among the languages of physics, mathematics, and machine-learning. We believe that consideration and implementation of passive symmetries might help machine learning in the same ways that it transformed physics in the twentieth century.

stat.ML↗

arXiv2023

Scalars are universal: Equivariant machine learning, structured like classical physics

There has been enormous progress in the last few years in designing neural networks that respect the fundamental symmetries and coordinate freedoms of physical law. Some of these frameworks make use of irreducible representations, some make use of high-order tensor objects, and some apply symmetry-enforcing constraints. Different physical laws obey different combinations of fundamental symmetries, but a large fraction (possibly all) of classical physics is equivariant to translation, rotation, reflection (parity), boost (relativity), and permutations. Here we show that it is simple to parameterize universally approximating polynomial functions that are equivariant under these symmetries, or under the Euclidean, Lorentz, and Poincaré groups, at any dimensionality $d$. The key observation is that nonlinear O($d$)-equivariant (and related-group-equivariant) functions can be universally expressed in terms of a lightweight collection of scalars -- scalar products and scalar contractions of the scalar, vector, and tensor inputs. We complement our theory with numerical examples that show that the scalar-based method is simple, efficient, and scalable.

cs.LG↗

arXiv2022

Dimensionless machine learning: Imposing exact units equivariance

Units equivariance (or units covariance) is the exact symmetry that follows from the requirement that relationships among measured quantities of physics relevance must obey self-consistent dimensional scalings. Here, we express this symmetry in terms of a (non-compact) group action, and we employ dimensional analysis and ideas from equivariant machine learning to provide a methodology for exactly units-equivariant machine learning: For any given learning task, we first construct a dimensionless version of its inputs using classic results from dimensional analysis, and then perform inference in the dimensionless space. Our approach can be used to impose units equivariance across a broad range of machine learning methods which are equivariant to rotations and other groups. We discuss the in-sample and out-of-sample prediction accuracy gains one can obtain in contexts like symbolic regression and emulation, where symmetry is important. We illustrate our approach with simple numerical examples involving dynamical systems in physics and ecology.

stat.ML↗

arXiv2022

Ensemble methods for survival function estimation with time-varying covariates

Survival data with time-varying covariates are common in practice. If relevant, they can improve on the estimation of survival function. However, the traditional survival forests - conditional inference forest, relative risk forest and random survival forest - have accommodated only time-invariant covariates. We generalize the conditional inference and relative risk forests to allow time-varying covariates. We also propose a general framework for estimation of a survival function in the presence of time-varying covariates. We compare their performance with that of the Cox model and transformation forest, adapted here to accommodate time-varying covariates, through a comprehensive simulation study in which the Kaplan-Meier estimate serves as a benchmark, and performance is compared using the integrated L2 difference between the true and estimated survival functions. In general, the performance of the two proposed forests substantially improves over the Kaplan-Meier estimate. Taking into account all other factors, under the proportional hazard (PH) setting, the best method is always one of the two proposed forests, while under the non-PH setting, it is the adapted transformation forest. K-fold cross-validation is used as an effective tool to choose between the methods in practice.

stat.AP↗

arXiv2021

A simple equivariant machine learning method for dynamics based on scalars

Physical systems obey strict symmetry principles. We expect that machine learning methods that intrinsically respect these symmetries should have higher prediction accuracy and better generalization in prediction of physical dynamics. In this work we implement a principled model based on invariant scalars, and release open-source code. We apply this Scalars method to a simple chaotic dynamical system, the springy double pendulum. We show that the Scalars method outperforms state-of-the-art approaches for learning the properties of physical systems with symmetries, both in terms of accuracy and speed. Because the method incorporates the fundamental symmetries, we expect it to generalize to different settings, such as changes in the force laws in the system.

cs.LG↗

arXiv2021

Dynamic estimation with random forests for discrete-time survival data

Time-varying covariates are often available in survival studies and estimation of the hazard function needs to be updated as new information becomes available. In this paper, we investigate several different easy-to-implement ways that random forests can be used for dynamic estimation of the survival or hazard function from discrete-time survival data. The results from a simulation study indicate that all methods can perform well, and that none dominates the others. In general, situations that are more difficult from an estimation point of view (such as weaker signals and less data) favour a global fit, pooling over all time points, while situations that are easier from an estimation point of view (such as stronger signals and more data) favor local fits.

stat.ME↗

arXiv2019

Experimental performance of graph neural networks on random instances of max-cut

This note explores the applicability of unsupervised machine learning techniques towards hard optimization problems on random inputs. In particular we consider Graph Neural Networks (GNNs) -- a class of neural networks designed to learn functions on graphs -- and we apply them to the max-cut problem on random regular graphs. We focus on the max-cut problem on random regular graphs because it is a fundamental problem that has been widely studied. In particular, even though there is no known explicit solution to compare the output of our algorithm to, we can leverage the known asymptotics of the optimal max-cut value in order to evaluate the performance of the GNNs. In order to put the performance of the GNNs in context, we compare it with the classical semidefinite relaxation approach by Goemans and Williamson~(SDP), and with extremal optimization, which is a local optimization heuristic from the statistical physics literature. The numerical results we obtain indicate that, surprisingly, Graph Neural Networks attain comparable performance to the Goemans and Williamson SDP. We also observe that extremal optimization consistently outperforms the other two methods. Furthermore, the performances of the three methods present similar patterns, that is, for sparser, and for larger graphs, the size of the found cuts are closer to the asymptotic optimal max-cut value.

math.OC↗

arXiv2019

An Ensemble Method for Interval-Censored Time-to-Event Data

Interval-censored data analysis is important in biomedical statistics for any type of time-to-event response where the time of response is not known exactly, but rather only known to occur between two assessment times. Many clinical trials and longitudinal studies generate interval-censored data; one common example occurs in medical studies that entail periodic follow-up. In this paper we propose a survival forest method for interval-censored data based on the conditional inference framework. We describe how this framework can be adapted to the situation of interval-censored data. We show that the tuning parameters have a non-negligible effect on the survival forest performance and guidance is provided on how to tune the parameters in a data-dependent way to improve the overall performance of the method. Using Monte Carlo simulations we find that the proposed survival forest is at least as effective as a survival tree method when the underlying model has a tree structure, performs similarly to an interval-censored Cox proportional hazards model fit when the true relationship is linear, and outperforms the survival tree method and Cox model when the true relationship is nonlinear. We illustrate the application of the method on a tooth emergence data set.

stat.ME↗