BZPEERReading, trust and collaboration for research
Menu

Discover

GraphFollow connections around a paper, topic or saved view.

Workspaces

HomePick up where your research flow left off.InboxHandle requests, replies and notifications from one place.CollectionsCurate reading lists, evidence sets and shareable dossiers.ResearchSee your private provenance graph, trail and imports.CollaborationMove from discovery into focused discussion rooms.PublishDraft, preview and publish full-text research articles.

Network

ExpertsFind specialists worth following or asking for help.CommunitiesJoin research circles organized around shared work.PartnersSee external organizations active around the same topics.

Opportunities

ListingsBrowse roles, calls and collaborations with clearer fit signals.

Account

Log inReturn to your reading and collaboration workspace.Create accountStart saving work, following people and joining teams.
Log inCreate account

Researcher profile

Chengyue Gong

Chengyue Gong contributes to research discovery and scholarly infrastructure.

ResearcherAffiliation not importedOpen to collaborate
Machine LearningComputation and LanguageComputer VisionQuantitative MethodsArtificial IntelligenceCryptography and Security

Trust snapshot

Quick read

Trust 21 - EmergingVerification L1Unclaimed author
10works
0followers
6topics
4close collaborators

Actions

Decide how to stay connected

Follow researcher0

Identity and collaboration

How to connect with this researcher

Claiming links this public author record to a researcher profile and unlocks direct collaboration workflows.

Log in to claim

Direct collaboration

Open a focused conversation when the fit is right

Claim this author entity first to unlock direct invitations.

Research graph

See the researcher in context

Open full explorer

Inspect adjacent work, topics, institutions and collaborators without jumping out to a separate graph page.

Building this graph slice

BZPEER is loading the nearby papers, people, topics and institutions for this page.

Published work

10 published item(s)

preprint2026arXiv

A-CODE: Fully Atomic Protein Co-Design with Unified Multimodal Diffusion

We present A-CODE, a fully atomic unified one-stage protein co-design model that simultaneously refines discrete atom types and continuous atom coordinates. Unlike predominant two-stage methods that cascade structure design with amino acid-level sequence design, our approach is fully atomic within a unified multimodal diffusion framework, in which residue identities are inferred solely from atom-level predictions. Built upon the powerful all-atom architecture, A-CODE achieves superior designability for unconditional protein generation, outperforming all existing one-stage and two-stage design models. For binder design, A-CODE rivals and even outperforms existing state-of-the-art two-stage design models and, compared with the existing one-stage co-design model, achieves a drastic tenfold improvement in success rate on hard tasks. The inherent flexibility of our atomic formulation enables, for the first time, seamless adaptation to non-canonical amino acid (ncAA) modeling. Our fully atomic framework establishes a new, versatile foundation for all-atom generative modeling that can be naturally extended to complex biomolecular systems.

0 citations0 reviewsNo code linkedOpen access
preprint2026arXiv

ProtDBench: A Unified Benchmark of Protein Binder Design and Evaluation

Recent advances in de novo protein binder design have enabled increasing experimental validation, yet reported in silico metrics remain difficult to interpret or compare across studies due to non-standardized evaluation protocols. We introduce ProtDBench, a standardized and throughput-aware evaluation framework for protein binder design. ProtDBench defines unified benchmark tasks, evaluation protocols, and success criteria, enabling systematic analysis of how evaluation design influences observed performance. Using a large wet-lab annotated dataset, we analyze commonly used structure prediction models as evaluation verifiers, revealing substantial verifier-dependent bias and limited agreement under identical filtering protocols. We then benchmark representative open-source generative binder design methods across ten diverse protein targets under a fixed evaluation protocol. Beyond per-sequence success rates, ProtDBench incorporates throughput-aware metrics based on a fixed 24-hour budget, as well as cluster-level success criteria to account for structural diversity. Together, these results expose systematic differences induced by filtering rules, success definitions, and throughput-aware evaluation between computational efficiency, success rate, and structural diversity. Overall, ProtDBench provides a fair and reproducible evaluation pipeline that supports systematic and controlled comparison of protein binder design methods under realistic evaluation settings.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Diffusion-based Molecule Generation with Informative Prior Bridges

AI-based molecule generation provides a promising approach to a large area of biomedical sciences and engineering, such as antibody design, hydrolase engineering, or vaccine development. Because the molecules are governed by physical laws, a key challenge is to incorporate prior information into the training procedure to generate high-quality and realistic molecules. We propose a simple and novel approach to steer the training of diffusion-based generative models with physical and statistics prior information. This is achieved by constructing physically informed diffusion bridges, stochastic processes that guarantee to yield a given observation at the fixed terminal time. We develop a Lyapunov function based method to construct and determine bridges, and propose a number of proposals of informative prior bridges for both high-quality molecule generation and uniformity-promoted 3D point cloud generation. With comprehensive experiments, we show that our method provides a powerful approach to the 3D generation task, yielding molecule structures with better quality and stability scores and more uniformly distributed point clouds of high qualities.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Flow Straight and Fast: Learning to Generate and Transfer Data with Rectified Flow

We present rectified flow, a surprisingly simple approach to learning (neural) ordinary differential equation (ODE) models to transport between two empirically observed distributions π_0 and π_1, hence providing a unified solution to generative modeling and domain transfer, among various other tasks involving distribution transport. The idea of rectified flow is to learn the ODE to follow the straight paths connecting the points drawn from π_0 and π_1 as much as possible. This is achieved by solving a straightforward nonlinear least squares optimization problem, which can be easily scaled to large models without introducing extra parameters beyond standard supervised learning. The straight paths are special and preferred because they are the shortest paths between two points, and can be simulated exactly without time discretization and hence yield computationally efficient models. We show that the procedure of learning a rectified flow from data, called rectification, turns an arbitrary coupling of π_0 and π_1 to a new deterministic coupling with provably non-increasing convex transport costs. In addition, recursively applying rectification allows us to obtain a sequence of flows with increasingly straight paths, which can be simulated accurately with coarse time discretization in the inference phase. In empirical studies, we show that rectified flow performs superbly on image generation, image-to-image translation, and domain adaptation. In particular, on image generation and translation, our method yields nearly straight flows that give high quality results even with a single Euler discretization step.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

How to Fill the Optimum Set? Population Gradient Descent with Harmless Diversity

Although traditional optimization methods focus on finding a single optimal solution, most objective functions in modern machine learning problems, especially those in deep learning, often have multiple or infinite numbers of optima. Therefore, it is useful to consider the problem of finding a set of diverse points in the optimum set of an objective function. In this work, we frame this problem as a bi-level optimization problem of maximizing a diversity score inside the optimum set of the main loss function, and solve it with a simple population gradient descent framework that iteratively updates the points to maximize the diversity score in a fashion that does not hurt the optimization of the main loss. We demonstrate that our method can efficiently generate diverse solutions on a variety of applications, including text-to-image generation, text-to-mesh generation, molecular conformation generation and ensemble neural network training.

0 citations0 reviewsNo code linkedOpen access
preprint2021arXiv

Capturing Label Distribution: A Case Study in NLI

We study estimating inherent human disagreement (annotation label distribution) in natural language inference task. Post-hoc smoothing of the predicted label distribution to match the expected label entropy is very effective. Such simple manipulation can reduce KL divergence by almost half, yet will not improve majority label prediction accuracy or learn label distributions. To this end, we introduce a small amount of examples with multiple references into training. We depart from the standard practice of collecting a single reference per each training example, and find that collecting multiple references can achieve better accuracy under the fixed annotation budget. Lastly, we provide rich analyses comparing these two methods for improving label distribution estimation.

0 citations0 reviewsNo code linkedOpen access
preprint2021arXiv

FuseDream: Training-Free Text-to-Image Generation with Improved CLIP+GAN Space Optimization

Generating images from natural language instructions is an intriguing yet highly challenging task. We approach text-to-image generation by combining the power of the retrained CLIP representation with an off-the-shelf image generator (GANs), optimizing in the latent space of GAN to find images that achieve maximum CLIP score with the given input text. Compared to traditional methods that train generative models from text to image starting from scratch, the CLIP+GAN approach is training-free, zero shot and can be easily customized with different generators. However, optimizing CLIP score in the GAN space casts a highly challenging optimization problem and off-the-shelf optimizers such as Adam fail to yield satisfying results. In this work, we propose a FuseDream pipeline, which improves the CLIP+GAN approach with three key techniques: 1) an AugCLIP score which robustifies the CLIP objective by introducing random augmentation on image. 2) a novel initialization and over-parameterization strategy for optimization which allows us to efficiently navigate the non-convex landscape in GAN space. 3) a composed generation technique which, by leveraging a novel bi-level optimization formulation, can compose multiple images to extend the GAN space and overcome the data-bias. When promoted by different input text, FuseDream can generate high-quality images with varying objects, backgrounds, artistic styles, even novel counterfactual concepts that do not appear in the training data of the GAN we use. Quantitatively, the images generated by FuseDream yield top-level Inception score and FID score on MS COCO dataset, without additional architecture design or training. Our code is publicly available at \url{https://github.com/gnobitab/FuseDream}.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

FRAGE: Frequency-Agnostic Word Representation

Continuous word representation (aka word embedding) is a basic building block in many neural network-based models used in natural language processing tasks. Although it is widely accepted that words with similar semantics should be close to each other in the embedding space, we find that word embeddings learned in several tasks are biased towards word frequency: the embeddings of high-frequency and low-frequency words lie in different subregions of the embedding space, and the embedding of a rare word and a popular word can be far from each other even if they are semantically similar. This makes learned word embeddings ineffective, especially for rare words, and consequently limits the performance of these neural network models. In this paper, we develop a neat, simple yet effective way to learn \emph{FRequency-AGnostic word Embedding} (FRAGE) using adversarial training. We conducted comprehensive studies on ten datasets across four natural language processing tasks, including word similarity, language modeling, machine translation and text classification. Results show that with FRAGE, we achieve higher performance than the baselines in all tasks.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

MaxUp: A Simple Way to Improve Generalization of Neural Network Training

We propose \emph{MaxUp}, an embarrassingly simple, highly effective technique for improving the generalization performance of machine learning models, especially deep neural networks. The idea is to generate a set of augmented data with some random perturbations or transforms and minimize the maximum, or worst case loss over the augmented data. By doing so, we implicitly introduce a smoothness or robustness regularization against the random perturbations, and hence improve the generation performance. For example, in the case of Gaussian perturbation, \emph{MaxUp} is asymptotically equivalent to using the gradient norm of the loss as a penalty to encourage smoothness. We test \emph{MaxUp} on a range of tasks, including image classification, language modeling, and adversarial certification, on which \emph{MaxUp} consistently outperforms the existing best baseline methods, without introducing substantial computational overhead. In particular, we improve ImageNet classification from the state-of-the-art top-1 accuracy $85.5\%$ without extra data to $85.8\%$. Code will be released soon.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

SAFER: A Structure-free Approach for Certified Robustness to Adversarial Word Substitutions

State-of-the-art NLP models can often be fooled by human-unaware transformations such as synonymous word substitution. For security reasons, it is of critical importance to develop models with certified robustness that can provably guarantee that the prediction is can not be altered by any possible synonymous word substitution. In this work, we propose a certified robust method based on a new randomized smoothing technique, which constructs a stochastic ensemble by applying random word substitutions on the input sentences, and leverage the statistical properties of the ensemble to provably certify the robustness. Our method is simple and structure-free in that it only requires the black-box queries of the model outputs, and hence can be applied to any pre-trained models (such as BERT) and any types of models (world-level or subword-level). Our method significantly outperforms recent state-of-the-art methods for certified robustness on both IMDB and Amazon text classification tasks. To the best of our knowledge, we are the first work to achieve certified robustness on large systems such as BERT with practically meaningful certified accuracy.

0 citations0 reviewsNo code linkedOpen access