Yiheng Zhu

Yiheng Zhu, Jialu Wu, Chaowen Hu et al.

Many crucial scientific problems involve designing novel molecules with desired properties, which can be formulated as a black-box optimization problem over the discrete chemical space. In practice, multiple conflicting objectives and costly evaluations (e.g., wet-lab experiments) make the diversity of candidates paramount. Computational methods have achieved initial success but still struggle with considering diversity in both objective and search space. To fill this gap, we propose a multi-objective Bayesian optimization (MOBO) algorithm leveraging the hypernetwork-based GFlowNets (HN-GFN) as an acquisition function optimizer, with the purpose of sampling a diverse batch of candidate molecular graphs from an approximate Pareto front. Using a single preference-conditioned hypernetwork, HN-GFN learns to explore various trade-offs between objectives. We further propose a hindsight-like off-policy strategy to share high-performing molecules among different preferences in order to speed up learning for HN-GFN. We empirically illustrate that HN-GFN has adequate capacity to generalize over preferences. Moreover, experiments in various real-world MOBO settings demonstrate that our framework predominantly outperforms existing methods in terms of candidate quality and sample efficiency. The code is available at https://github.com/violet-sto/HN-GFN.

Shuhong Chen, Kevin Zhang, Yichun Shi et al.

We propose PAniC-3D, a system to reconstruct stylized 3D character heads directly from illustrated (p)ortraits of (ani)me (c)haracters. Our anime-style domain poses unique challenges to single-view reconstruction; compared to natural images of human heads, character portrait illustrations have hair and accessories with more complex and diverse geometry, and are shaded with non-photorealistic contour lines. In addition, there is a lack of both 3D model and portrait illustration data suitable to train and evaluate this ambiguous stylized reconstruction task. Facing these challenges, our proposed PAniC-3D architecture crosses the illustration-to-3D domain gap with a line-filling model, and represents sophisticated geometries with a volumetric radiance field. We train our system with two large new datasets (11.2k Vroid 3D models, 1k Vtuber portrait illustrations), and evaluate on a novel AnimeRecon benchmark of illustration-to-3D pairs. PAniC-3D significantly outperforms baseline methods, and provides data to establish the task of stylized reconstruction from portrait illustrations.

Yixuan Wu, Jintai Chen, Jiahuan Yan et al.

Since annotating medical images for segmentation tasks commonly incurs expensive costs, it is highly desirable to design an annotation-efficient method to alleviate the annotation burden. Recently, contrastive learning has exhibited a great potential in learning robust representations to boost downstream tasks with limited labels. In medical imaging scenarios, ready-made meta labels (i.e., specific attribute information of medical images) inherently reveal semantic relationships among images, which have been used to define positive pairs in previous work. However, the multi-perspective semantics revealed by various meta labels are usually incompatible and can incur intractable "semantic contradiction" when combining different meta labels. In this paper, we tackle the issue of "semantic contradiction" in a gradient-guided manner using our proposed Gradient Mitigator method, which systematically unifies multi-perspective meta labels to enable a pre-trained model to attain a better high-level semantic recognition ability. Moreover, we emphasize that the fine-grained discrimination ability is vital for segmentation-oriented pre-training, and develop a novel method called Gradient Filter to dynamically screen pixel pairs with the most discriminating power based on the magnitude of gradients. Comprehensive experiments on four medical image segmentation datasets verify that our new method GCL: (1) learns informative image representations and considerably boosts segmentation performance with limited labels, and (2) shows promising generalizability on out-of-distribution datasets.

Mingze Yin, Hanjing Zhou, Yiheng Zhu et al.

Proteins govern most biological functions essential for life, but achieving controllable protein discovery and optimization remains challenging. Recently, machine learning-assisted protein editing (MLPE) has shown promise in accelerating optimization cycles and reducing experimental workloads. However, current methods struggle with the vast combinatorial space of potential protein edits and cannot explicitly conduct protein editing using biotext instructions, limiting their interactivity with human feedback. To fill these gaps, we propose a novel method called ProtET for efficient CLIP-informed protein editing through multi-modality learning. Our approach comprises two stages: in the pretraining stage, contrastive learning aligns protein-biotext representations encoded by two large language models (LLMs), respectively. Subsequently, during the protein editing stage, the fused features from editing instruction texts and original protein sequences serve as the final editing condition for generating target protein sequences. Comprehensive experiments demonstrated the superiority of ProtET in editing proteins to enhance human-expected functionality across multiple attribute domains, including enzyme catalytic activity, protein stability and antibody specific binding ability. And ProtET improves the state-of-the-art results by a large margin, leading to significant stability improvements of 16.67% and 16.90%. This capability positions ProtET to advance real-world artificial protein editing, potentially addressing unmet academic, industrial, and clinical needs.

Yiheng Zhu, Zhenqiu Ouyang, Ben Liao et al.

Molecular de novo design is a critical yet challenging task in scientific fields, aiming to design novel molecular structures with desired property profiles. Significant progress has been made by resorting to generative models for graphs. However, limited attention is paid to hierarchical generative models, which can exploit the inherent hierarchical structure (with rich semantic information) of the molecular graphs and generate complex molecules of larger size that we shall demonstrate to be difficult for most existing models. The primary challenge to hierarchical generation is the non-differentiable issue caused by the generation of intermediate discrete coarsened graph structures. To sidestep this issue, we cast the tricky hierarchical generation problem over discrete spaces as the reverse process of hierarchical representation learning and propose MolHF, a new hierarchical flow-based model that generates molecular graphs in a coarse-to-fine manner. Specifically, MolHF first generates bonds through a multi-scale architecture, then generates atoms based on the coarsened graph structure at each scale. We demonstrate that MolHF achieves state-of-the-art performance in random generation and property optimization, implying its high capacity to model data distribution. Furthermore, MolHF is the first flow-based model that can be applied to model larger molecules (polymer) with more than 100 heavy atoms. The code and models are available at https://github.com/violet-sto/MolHF.

Xiaoyu Xiang, Ding Liu, Xiao Yang et al.

In this paper, we explore open-domain sketch-to-photo translation, which aims to synthesize a realistic photo from a freehand sketch with its class label, even if the sketches of that class are missing in the training data. It is challenging due to the lack of training supervision and the large geometric distortion between the freehand sketch and photo domains. To synthesize the absent freehand sketches from photos, we propose a framework that jointly learns sketch-to-photo and photo-to-sketch generation. However, the generator trained from fake sketches might lead to unsatisfying results when dealing with sketches of missing classes, due to the domain gap between synthesized sketches and real ones. To alleviate this issue, we further propose a simple yet effective open-domain sampling and optimization strategy to "fool" the generator into treating fake sketches as real ones. Our method takes advantage of the learned sketch-to-photo and photo-to-sketch mapping of in-domain data and generalizes it to the open-domain classes. We validate our method on the Scribble and SketchyCOCO datasets. Compared with the recent competing methods, our approach shows impressive results in synthesizing realistic color, texture, and maintaining the geometric composition for various categories of open-domain sketches. Our code is available at https://github.com/Mukosame/AODA

Jiahuan Yan, Bo Zheng, Hongxia Xu et al.

The transferability of deep neural networks (DNNs) has made significant progress in image and language processing. However, due to the heterogeneity among tables, such DNN bonus is still far from being well exploited on tabular data prediction (e.g., regression or classification tasks). Condensing knowledge from diverse domains, language models (LMs) possess the capability to comprehend feature names from various tables, potentially serving as versatile learners in transferring knowledge across distinct tables and diverse prediction tasks, but their discrete text representation space is inherently incompatible with numerical feature values in tables. In this paper, we present TP-BERTa, a specifically pre-trained LM for tabular data prediction. Concretely, a novel relative magnitude tokenization converts scalar numerical feature values to finely discrete, high-dimensional tokens, and an intra-feature attention approach integrates feature values with the corresponding feature names. Comprehensive experiments demonstrate that our pre-trained TP-BERTa leads the performance among tabular DNNs and is competitive with Gradient Boosted Decision Tree models in typical tabular data regime.

Yiheng Zhu, Zitai Kong, Jialu Wu et al.

The design of novel protein sequences with targeted functionalities underpins a central theme in protein engineering, impacting diverse fields such as drug discovery and enzymatic engineering. However, navigating this vast combinatorial search space remains a severe challenge due to time and financial constraints. This scenario is rapidly evolving as the transformative advancements in AI, particularly in the realm of generative models and optimization algorithms, have been propelling the protein design field towards an unprecedented revolution. In this survey, we systematically review recent advances in generative AI for controllable protein sequence design. To set the stage, we first outline the foundational tasks in protein sequence design in terms of the constraints involved and present key generative models and optimization algorithms. We then offer in-depth reviews of each design task and discuss the pertinent applications. Finally, we identify the unresolved challenges and highlight research opportunities that merit deeper exploration.

Zitai Kong, Yiheng Zhu, Yinlong Xu et al.

The design of protein sequences with desired functionalities is a fundamental task in protein engineering. Deep generative methods, such as autoregressive models and diffusion models, have greatly accelerated the discovery of novel protein sequences. However, these methods mainly focus on local or shallow residual semantics and suffer from low inference efficiency, large modeling space and high training cost. To address these challenges, we introduce ProtFlow, a fast flow matching-based protein sequence design framework that operates on embeddings derived from semantically meaningful latent space of protein language models. By compressing and smoothing the latent space, ProtFlow enhances performance while training on limited computational resources. Leveraging reflow techniques, ProtFlow enables high-quality single-step sequence generation. Additionally, we develop a joint design pipeline for the design scene of multichain proteins. We evaluate ProtFlow across diverse protein design tasks, including general peptides and long-chain proteins, antimicrobial peptides, and antibodies. Experimental results demonstrate that ProtFlow outperforms task-specific methods in these applications, underscoring its potential and broad applicability in computational protein sequence design and analysis.

Mingze Yin, Hanjing Zhou, Jialu Wu et al.

Antibodies safeguard our health through their precise and potent binding to specific antigens, demonstrating promising therapeutic efficacy in the treatment of numerous diseases, including COVID-19. Recent advancements in biomedical language models have shown the great potential to interpret complex biological structures and functions. However, existing antibody specific models have a notable limitation that they lack explicit consideration for antibody structural information, despite the fact that both 1D sequence and 3D structure carry unique and complementary insights into antibody behavior and functionality. This paper proposes Sequence-Structure multi-level pre-trained Antibody Language Model (S$^2$ALM), combining holistic sequential and structural information in one unified, generic antibody foundation model. We construct a hierarchical pre-training paradigm incorporated with two customized multi-level training objectives to facilitate the modeling of comprehensive antibody representations. S$^2$ALM's representation space uncovers inherent functional binding mechanisms, biological evolution properties and structural interaction patterns. Pre-trained over 75 million sequences and 11.7 million structures, S$^2$ALM can be adopted for diverse downstream tasks: accurately predicting antigen-antibody binding affinities, precisely distinguishing B cell maturation stages, identifying antibody crucial binding positions, and specifically designing novel coronavirus-binding antibodies. Remarkably, S$^2$ALM outperforms well-established and renowned baselines and sets new state-of-the-art performance across extensive antibody specific understanding and generation tasks. S$^2$ALM's ability to model comprehensive and generalized representations further positions its potential to advance real-world therapeutic antibody development, potentially addressing unmet academic, industrial, and clinical needs.

Yuan Gao, Yiheng Zhu, Yuanbin Cao et al.

Open Domain Multi-Hop Question Answering (ODMHQA) plays a crucial role in Natural Language Processing (NLP) by aiming to answer complex questions through multi-step reasoning over retrieved information from external knowledge sources. Recently, Large Language Models (LLMs) have demonstrated remarkable performance in solving ODMHQA owing to their capabilities including planning, reasoning, and utilizing tools. However, LLMs may generate off-topic answers when attempting to solve ODMHQA, namely the generated answers are irrelevant to the original questions. This issue of off-topic answers accounts for approximately one-third of incorrect answers, yet remains underexplored despite its significance. To alleviate this issue, we propose the Discriminate->Re-Compose->Re- Solve->Re-Decompose (Dr3) mechanism. Specifically, the Discriminator leverages the intrinsic capabilities of LLMs to judge whether the generated answers are off-topic. In cases where an off-topic answer is detected, the Corrector performs step-wise revisions along the reversed reasoning chain (Re-Compose->Re-Solve->Re-Decompose) until the final answer becomes on-topic. Experimental results on the HotpotQA and 2WikiMultiHopQA datasets demonstrate that our Dr3 mechanism considerably reduces the occurrence of off-topic answers in ODMHQA by nearly 13%, improving the performance in Exact Match (EM) by nearly 3% compared to the baseline method without the Dr3 mechanism.

Tianlang Chen, Chen Fang, Xiaohui Shen et al.

In this work, we propose a new solution to 3D human pose estimation in videos. Instead of directly regressing the 3D joint locations, we draw inspiration from the human skeleton anatomy and decompose the task into bone direction prediction and bone length prediction, from which the 3D joint locations can be completely derived. Our motivation is the fact that the bone lengths of a human skeleton remain consistent across time. This promotes us to develop effective techniques to utilize global information across all the frames in a video for high-accuracy bone length prediction. Moreover, for the bone direction prediction network, we propose a fully-convolutional propagating architecture with long skip connections. Essentially, it predicts the directions of different bones hierarchically without using any time-consuming memory units e.g. LSTM). A novel joint shift loss is further introduced to bridge the training of the bone length and bone direction prediction networks. Finally, we employ an implicit attention mechanism to feed the 2D keypoint visibility scores into the model as extra guidance, which significantly mitigates the depth ambiguity in many challenging poses. Our full model outperforms the previous best results on Human3.6M and MPI-INF-3DHP datasets, where comprehensive evaluation validates the effectiveness of our model.

Yiheng Zhu, Yichen Yao, Zili Wu et al.

Convolutional neural networks (CNNs) are effective at solving difficult problems like visual recognition, speech recognition and natural language processing. However, performance gain comes at the cost of laborious trial-and-error in designing deeper CNN architectures. In this paper, a genetic programming (GP) framework for convolutional neural network architecture search, abbreviated as GP-CNAS, is proposed to automatically search for optimal CNN architectures. GP-CNAS encodes CNNs as trees where leaf nodes (GP terminals) are selected residual blocks and non-leaf nodes (GP functions) specify the block assembling procedure. Our tree-based representation enables easy design and flexible implementation of genetic operators. Specifically, we design a dynamic crossover operator that strikes a balance between exploration and exploitation, which emphasizes CNN complexity at early stage and CNN diversity at later stage. Therefore, the desired CNN architecture with balanced depth and width can be found within limited trials. Moreover, our GP-CNAS framework is highly compatible with other manually-designed and NAS-generated block types as well. Experimental results on the CIFAR-10 dataset show that GP-CNAS is competitive among the state-of-the-art automatic and semi-automatic NAS algorithms.