arXiv subjects

Wentao Guo

Publications and source records attributed to Wentao Guo.

31 records · Page 2Linked to original sources

arXiv2024

Towards a Unified Benchmark and Framework for Deep Learning-Based Prediction of Nuclear Magnetic Resonance Chemical Shifts

The study of structure-spectrum relationships is essential for spectral interpretation, impacting structural elucidation and material design. Predicting spectra from molecular structures is challenging due to their complex relationships. Herein, we introduce NMRNet, a deep learning framework using the SE(3) Transformer for atomic environment modeling, following a pre-training and fine-tuning paradigm. To support the evaluation of NMR chemical shift prediction models, we have established a comprehensive benchmark based on previous research and databases, covering diverse chemical systems. Applying NMRNet to these benchmark datasets, we achieve state-of-the-art performance in both liquid-state and solid-state NMR datasets, demonstrating its robustness and practical utility in real-world scenarios. This marks the first integration of solid and liquid state NMR within a unified model architecture, highlighting the need for domainspecific handling of different atomic environments. Our work sets a new standard for NMR prediction, advancing deep learning applications in analytical and structural chemistry.

physics.comp-ph↗

arXiv2024

MMPolymer: A Multimodal Multitask Pretraining Framework for Polymer Property Prediction

Polymers are high-molecular-weight compounds constructed by the covalent bonding of numerous identical or similar monomers so that their 3D structures are complex yet exhibit unignorable regularity. Typically, the properties of a polymer, such as plasticity, conductivity, bio-compatibility, and so on, are highly correlated with its 3D structure. However, existing polymer property prediction methods heavily rely on the information learned from polymer SMILES sequences (P-SMILES strings) while ignoring crucial 3D structural information, resulting in sub-optimal performance. In this work, we propose MMPolymer, a novel multimodal multitask pretraining framework incorporating polymer 1D sequential and 3D structural information to encourage downstream polymer property prediction tasks. Besides, considering the scarcity of polymer 3D data, we further introduce the "Star Substitution" strategy to extract 3D structural information effectively. During pretraining, in addition to predicting masked tokens and recovering clear 3D coordinates, MMPolymer achieves the cross-modal alignment of latent representations. Then we further fine-tune the pretrained MMPolymer for downstream polymer property prediction tasks in the supervised learning paradigm. Experiments show that MMPolymer achieves state-of-the-art performance in downstream property prediction tasks. Moreover, given the pretrained MMPolymer, utilizing merely a single modality in the fine-tuning phase can also outperform existing methods, showcasing the exceptional capability of MMPolymer in polymer feature extraction and utilization.

cs.LG↗

arXiv2024

A WT-ResNet based fault diagnosis model for the urban rail train transmission system

This study presents a novel fault diagnosis model for urban rail transit systems based on Wavelet Transform Residual Neural Network (WT-ResNet). The model integrates the advantages of wavelet transform for feature extraction and ResNet for pattern recognition, offering enhanced diagnostic accuracy and robustness. Experimental results demonstrate the effectiveness of the proposed model in identifying faults in urban rail trains, paving the way for improved maintenance strategies and reduced downtime.

cs.IR↗

arXiv2024

Zeroth-Order Fine-Tuning of LLMs with Extreme Sparsity

Zeroth-order optimization (ZO) is a memory-efficient strategy for fine-tuning Large Language Models using only forward passes. However, the application of ZO fine-tuning in memory-constrained settings such as mobile phones and laptops is still challenging since full precision forward passes are infeasible. In this study, we address this limitation by integrating sparsity and quantization into ZO fine-tuning of LLMs. Specifically, we investigate the feasibility of fine-tuning an extremely small subset of LLM parameters using ZO. This approach allows the majority of un-tuned parameters to be quantized to accommodate the constraint of limited device memory. Our findings reveal that the pre-training process can identify a set of "sensitive parameters" that can guide the ZO fine-tuning of LLMs on downstream tasks. Our results demonstrate that fine-tuning 0.1% sensitive parameters in the LLM with ZO can outperform the full ZO fine-tuning performance, while offering wall-clock time speedup. Additionally, we show that ZO fine-tuning targeting these 0.1% sensitive parameters, combined with 4 bit quantization, enables efficient ZO fine-tuning of an Llama2-7B model on a GPU device with less than 8 GiB of memory and notably reduced latency.

cs.LG↗

arXiv2024

Node-Aligned Graph-to-Graph (NAG2G): Elevating Template-Free Deep Learning Approaches in Single-Step Retrosynthesis

Single-step retrosynthesis (SSR) in organic chemistry is increasingly benefiting from deep learning (DL) techniques in computer-aided synthesis design. While template-free DL models are flexible and promising for retrosynthesis prediction, they often ignore vital 2D molecular information and struggle with atom alignment for node generation, resulting in lower performance compared to the template-based and semi-template-based methods. To address these issues, we introduce Node-Aligned Graph-to-Graph (NAG2G), a transformer-based template-free DL model. NAG2G combines 2D molecular graphs and 3D conformations to retain comprehensive molecular details and incorporates product-reactant atom mapping through node alignment which determines the order of the node-by-node graph outputs process in an auto-regressive manner. Through rigorous benchmarking and detailed case studies, we have demonstrated that NAG2G stands out with its remarkable predictive accuracy on the expansive datasets of USPTO-50k and USPTO-FULL. Moreover, the model's practical utility is underscored by its successful prediction of synthesis pathways for multiple drug candidate molecules. This not only proves NAG2G's robustness but also its potential to revolutionize the prediction of complex chemical synthesis processes for future synthetic route design tasks.

cs.LG↗

arXiv2023

Coordinating Distributed Example Orders for Provably Accelerated Training

Recent research on online Gradient Balancing (GraB) has revealed that there exist permutation-based example orderings for SGD that are guaranteed to outperform random reshuffling (RR). Whereas RR arbitrarily permutes training examples, GraB leverages stale gradients from prior epochs to order examples -- achieving a provably faster convergence rate than RR. However, GraB is limited by design: while it demonstrates an impressive ability to scale-up training on centralized data, it does not naturally extend to modern distributed ML workloads. We therefore propose Coordinated Distributed GraB (CD-GraB), which uses insights from prior work on kernel thinning to translate the benefits of provably faster permutation-based example ordering to distributed settings. With negligible overhead, CD-GraB exhibits a linear speedup in convergence rate over centralized GraB and outperforms distributed RR on a variety of benchmark tasks.

cs.LG↗

arXiv2023

Ranking with Slot Constraints

We introduce the problem of ranking with slot constraints, which can be used to model a wide range of application problems -- from college admission with limited slots for different majors, to composing a stratified cohort of eligible participants in a medical trial. We show that the conventional Probability Ranking Principle (PRP) can be highly sub-optimal for slot-constrained ranking problems, and we devise a new ranking algorithm, called MatchRank. The goal of MatchRank is to produce rankings that maximize the number of filled slots if candidates are evaluated by a human decision maker in the order of the ranking. In this way, MatchRank generalizes the PRP, and it subsumes the PRP as a special case when there are no slot constraints. Our theoretical analysis shows that MatchRank has a strong approximation guarantee without any independence assumptions between slots or candidates. Furthermore, we show how MatchRank can be implemented efficiently. Beyond the theoretical guarantees, empirical evaluations show that MatchRank can provide substantial improvements over a range of synthetic and real-world tasks.

cs.IR↗

arXiv2023

Photo Rater: Photographs Auto-Selector with Deep Learning

Photo Rater is a computer vision project that uses neural networks to help photographers select the best photo among those that are taken based on the same scene. This process is usually referred to as "culling" in photography, and it can be tedious and time-consuming if done manually. Photo Rater utilizes three separate neural networks to complete such a task: one for general image quality assessment, one for classifying whether the photo is blurry (either due to unsteady hands or out-of-focusness), and one for assessing general aesthetics (including the composition of the photo, among others). After feeding the image through each neural network, Photo Rater outputs a final score for each image, ranking them based on this score and presenting it to the user.

cs.CV↗

arXiv2023

Assessing the efficacy of large language models in generating accurate teacher responses

(Tack et al., 2023) organized the shared task hosted by the 18th Workshop on Innovative Use of NLP for Building Educational Applications on generation of teacher language in educational dialogues. Following the structure of the shared task, in this study, we attempt to assess the generative abilities of large language models in providing informative and helpful insights to students, thereby simulating the role of a knowledgeable teacher. To this end, we present an extensive evaluation of several benchmarking generative models, including GPT-4 (few-shot, in-context learning), fine-tuned GPT-2, and fine-tuned DialoGPT. Additionally, to optimize for pedagogical quality, we fine-tuned the Flan-T5 model using reinforcement learning. Our experimental findings on the Teacher-Student Chatroom Corpus subset indicate the efficacy of GPT-4 over other fine-tuned models, measured using BERTScore and DialogRPT. We hypothesize that several dataset characteristics, including sampling, representativeness, and dialog completeness, pose significant challenges to fine-tuning, thus contributing to the poor generalizability of the fine-tuned models. Finally, we note the need for these generative models to be evaluated with a metric that relies not only on dialog coherence and matched language modeling distribution but also on the model's ability to showcase pedagogical skills.

cs.CL↗

arXiv2023

GraB: Finding Provably Better Data Permutations than Random Reshuffling

Random reshuffling, which randomly permutes the dataset each epoch, is widely adopted in model training because it yields faster convergence than with-replacement sampling. Recent studies indicate greedily chosen data orderings can further speed up convergence empirically, at the cost of using more computation and memory. However, greedy ordering lacks theoretical justification and has limited utility due to its non-trivial memory and computation overhead. In this paper, we first formulate an example-ordering framework named herding and answer affirmatively that SGD with herding converges at the rate $O(T^{-2/3})$ on smooth, non-convex objectives, faster than the $O(n^{1/3}T^{-2/3})$ obtained by random reshuffling, where $n$ denotes the number of data points and $T$ denotes the total number of iterations. To reduce the memory overhead, we leverage discrepancy minimization theory to propose an online Gradient Balancing algorithm (GraB) that enjoys the same rate as herding, while reducing the memory usage from $O(nd)$ to just $O(d)$ and computation from $O(n^2)$ to $O(n)$, where $d$ denotes the model dimension. We show empirically on applications including MNIST, CIFAR10, WikiText and GLUE that GraB can outperform random reshuffling in terms of both training and validation performance, and even outperform state-of-the-art greedy ordering while reducing memory usage over $100\times$.

cs.LG↗

arXiv2022

MCTensor: A High-Precision Deep Learning Library with Multi-Component Floating-Point

In this paper, we introduce MCTensor, a library based on PyTorch for providing general-purpose and high-precision arithmetic for DL training. MCTensor is used in the same way as PyTorch Tensor: we implement multiple basic, matrix-level computation operators and NN modules for MCTensor with identical PyTorch interface. Our algorithms achieve high precision computation and also benefits from heavily-optimized PyTorch floating-point arithmetic. We evaluate MCTensor arithmetic against PyTorch native arithmetic for a series of tasks, where models using MCTensor in float16 would match or outperform the PyTorch model with float32 or float64 precision.

cs.LG↗

arXiv2022

Cyclical Kernel Adaptive Metropolis

We propose cKAM, cyclical Kernel Adaptive Metropolis, which incorporates a cyclical stepsize scheme to allow control for exploration and sampling. We show that on a crafted bimodal distribution, existing Adaptive Metropolis type algorithms would fail to converge to the true posterior distribution. We point out that this is because adaptive samplers estimates the local/global covariance structure using past history of the chain, which will lead to adaptive algorithms be trapped in a local mode. We demonstrate that cKAM encourages exploration of the posterior distribution and allows the sampler to escape from a local mode, while maintaining the high performance of adaptive methods.

cs.LG↗

arXiv2017

Optimizing Gross Merchandise Volume via DNN-MAB Dynamic Ranking Paradigm

With the transition from people's traditional `brick-and-mortar' shopping to online mobile shopping patterns in web 2.0 $\mathit{era}$, the recommender system plays a critical role in E-Commerce and E-Retails. This is especially true when designing this system for more than $\mathbf{236~million}$ daily active users. Ranking strategy, the key module of the recommender system, needs to be precise, accurate, and responsive for estimating customers' intents. We propose a dynamic ranking paradigm, named as DNN-MAB, that is composed of a pairwise deep neural network (DNN) $\mathit{pre}$-ranker connecting a revised multi-armed bandit (MAB) dynamic $\mathit{post}$-ranker. By taking into account of explicit and implicit user feedbacks such as impressions, clicks, conversions, etc. DNN-MAB is able to adjust DNN $\mathit{pre}$-ranking scores to assist customers locating items they are interested in most so that they can converge quickly and frequently. To the best of our knowledge, frameworks like DNN-MAB have not been discussed in the previous literature to either E-Commerce or machine learning audiences. In practice, DNN-MAB has been deployed to production and it easily outperforms against other state-of-the-art models by significantly lifting the gross merchandise volume (GMV) which is the objective metrics at JD.

cs.AI↗