arXiv subjects

Ruoxue Wu

Publications and source records attributed to Ruoxue Wu.

3 recordsLinked to original sources

arXiv2023

Diffusion-Driven Generative Framework for Molecular Conformation Prediction

The task of deducing three-dimensional molecular configurations from their two-dimensional graph representations holds paramount importance in the fields of computational chemistry and pharmaceutical development. The rapid advancement of machine learning, particularly within the domain of deep generative networks, has revolutionized the precision of predictive modeling in this context. Traditional approaches often adopt a two-step strategy: initially estimating interatomic distances and subsequently refining the spatial molecular structure by solving a distance geometry problem. However, this sequential approach occasionally falls short in accurately capturing the intricacies of local atomic arrangements, thereby compromising the fidelity of the resulting structural models. Addressing these limitations, this research introduces a cutting-edge generative framework named DDGF. This framework is grounded in the principles of diffusion observed in classical non-equilibrium thermodynamics. DDGF views atoms as discrete entities and excels in guiding the reversal of diffusion, transforming a distribution of stochastic noise back into coherent molecular structures through a process akin to a Markov chain. This transformation commences with the initial representation of a molecular graph in an abstract latent space, culminating in the realization of three-dimensional structures via a sophisticated bilevel optimization scheme meticulously tailored to meet the specific requirements of the task. One of the formidable challenges in this modeling endeavor involves preserving roto-translational invariance to ensure that the generated molecular conformations adhere to the laws of physics. Extensive experimental evaluations confirm the efficacy of the proposed DDGF in comparison to state-of-the-art methods.

q-bio.BM↗

arXiv2023

Music Generation based on Generative Adversarial Networks with Transformer

Autoregressive models based on Transformers have become the prevailing approach for generating music compositions that exhibit comprehensive musical structure. These models are typically trained by minimizing the negative log-likelihood (NLL) of the observed sequence in an autoregressive manner. However, when generating long sequences, the quality of samples from these models tends to significantly deteriorate due to exposure bias. To address this issue, we leverage classifiers trained to differentiate between real and sampled sequences to identify these failures. This observation motivates our exploration of adversarial losses as a complement to the NLL objective. We employ a pre-trained Span-BERT model as the discriminator in the Generative Adversarial Network (GAN) framework, which enhances training stability in our experiments. To optimize discrete sequences within the GAN framework, we utilize the Gumbel-Softmax trick to obtain a differentiable approximation of the sampling process. Additionally, we partition the sequences into smaller chunks to ensure that memory constraints are met. Through human evaluations and the introduction of a novel discriminative metric, we demonstrate that our approach outperforms a baseline model trained solely on likelihood maximization.

cs.SD↗

arXiv2023

A Milstein-type method for highly non-linear non-autonomous time-changed stochastic differential equations

A Milstein-type method is proposed for some highly non-linear non-autonomous time-changed stochastic differential equations (SDEs). The spatial variables in the coefficients of the time-changed SDEs satisfy the super-linear growth condition and the temporal variables obey some Hölder's continuity condition. The strong convergence in the finite time is studied and the convergence order is obtained.

math.NA↗