Jiahuan Yan

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.

Jintai Chen, Jiahuan Yan, Qiyuan Chen et al.

Data organized in tabular format is ubiquitous in real-world applications, and users often craft tables with biased feature definitions and flexibly set prediction targets of their interests. Thus, a rapid development of a robust, effective, dataset-versatile, user-friendly tabular prediction approach is highly desired. While Gradient Boosting Decision Trees (GBDTs) and existing deep neural networks (DNNs) have been extensively utilized by professional users, they present several challenges for casual users, particularly: (i) the dilemma of model selection due to their different dataset preferences, and (ii) the need for heavy hyperparameter searching, failing which their performances are deemed inadequate. In this paper, we delve into this question: Can we develop a deep learning model that serves as a "sure bet" solution for a wide range of tabular prediction tasks, while also being user-friendly for casual users? We delve into three key drawbacks of deep tabular models, encompassing: (P1) lack of rotational variance property, (P2) large data demand, and (P3) over-smooth solution. We propose ExcelFormer, addressing these challenges through a semi-permeable attention module that effectively constrains the influence of less informative features to break the DNNs' rotational invariance property (for P1), data augmentation approaches tailored for tabular data (for P2), and attentive feedforward network to boost the model fitting capability (for P3). These designs collectively make ExcelFormer a "sure bet" solution for diverse tabular datasets. Extensive and stratified experiments conducted on real-world datasets demonstrate that our model outperforms previous approaches across diverse tabular data prediction tasks, and this framework can be friendly to casual users, offering ease of use without the heavy hyperparameter tuning.

Shuo Sun, Yuchen Zhang, Jiahuan Yan et al.

The success of ChatGPT has ignited an AI race, with researchers striving to develop new large language models (LLMs) that can match or surpass the language understanding and generation abilities of commercial ones. In recent times, a number of models have emerged, claiming performance near that of GPT-3.5 or GPT-4 through various instruction-tuning methods. As practitioners of Text-to-SQL parsing, we are grateful for their valuable contributions to open-source research. However, it is important to approach these claims with a sense of scrutiny and ascertain the actual effectiveness of these models. Therefore, we pit six popular large language models against each other, systematically evaluating their Text-to-SQL parsing capability on nine benchmark datasets with five different prompting strategies, covering both zero-shot and few-shot scenarios. Regrettably, the open-sourced models fell significantly short of the performance achieved by closed-source models like GPT-3.5, highlighting the need for further work to bridge the performance gap between these models.

Jiahuan Yan, Jintai Chen, Yixuan Wu et al.

Recent development of deep neural networks (DNNs) for tabular learning has largely benefited from the capability of DNNs for automatic feature interaction. However, the heterogeneity nature of tabular features makes such features relatively independent, and developing effective methods to promote tabular feature interaction still remains an open problem. In this paper, we propose a novel Graph Estimator, which automatically estimates the relations among tabular features and builds graphs by assigning edges between related features. Such relation graphs organize independent tabular features into a kind of graph data such that interaction of nodes (tabular features) can be conducted in an orderly fashion. Based on our proposed Graph Estimator, we present a bespoke Transformer network tailored for tabular learning, called T2G-Former, which processes tabular data by performing tabular feature interaction guided by the relation graphs. A specific Cross-level Readout collects salient features predicted by the layers in T2G-Former across different levels, and attains global semantics for final prediction. Comprehensive experiments show that our T2G-Former achieves superior performance among DNNs and is competitive with non-deep Gradient Boosted Decision Tree models.

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.

Jiahuan Yan, Jintai Chen, Qianxing Wang et al.

Tabular datasets play a crucial role in various applications. Thus, developing efficient, effective, and widely compatible prediction algorithms for tabular data is important. Currently, two prominent model types, Gradient Boosted Decision Trees (GBDTs) and Deep Neural Networks (DNNs), have demonstrated performance advantages on distinct tabular prediction tasks. However, selecting an effective model for a specific tabular dataset is challenging, often demanding time-consuming hyperparameter tuning. To address this model selection dilemma, this paper proposes a new framework that amalgamates the advantages of both GBDTs and DNNs, resulting in a DNN algorithm that is as efficient as GBDTs and is competitively effective regardless of dataset preferences for GBDTs or DNNs. Our idea is rooted in an observation that deep learning (DL) offers a larger parameter space that can represent a well-performing GBDT model, yet the current back-propagation optimizer struggles to efficiently discover such optimal functionality. On the other hand, during GBDT development, hard tree pruning, entropy-driven feature gate, and model ensemble have proved to be more adaptable to tabular data. By combining these key components, we present a Tree-hybrid simple MLP (T-MLP). In our framework, a tensorized, rapidly trained GBDT feature gate, a DNN architecture pruning approach, as well as a vanilla back-propagation optimizer collaboratively train a randomly initialized MLP model. Comprehensive experiments show that T-MLP is competitive with extensively tuned DNNs and GBDTs in their dominating tabular benchmarks (88 datasets) respectively, all achieved with compact model storage and significantly reduced training duration.

Jiahuan Yan, Haojun Gao, Zhang Kai et al.

Deep learning approaches exhibit promising performances on various text tasks. However, they are still struggling on medical text classification since samples are often extremely imbalanced and scarce. Different from existing mainstream approaches that focus on supplementary semantics with external medical information, this paper aims to rethink the data challenges in medical texts and present a novel framework-agnostic algorithm called Text2Tree that only utilizes internal label hierarchy in training deep learning models. We embed the ICD code tree structure of labels into cascade attention modules for learning hierarchy-aware label representations. Two new learning schemes, Similarity Surrogate Learning (SSL) and Dissimilarity Mixup Learning (DML), are devised to boost text classification by reusing and distinguishing samples of other labels following the label representation hierarchy, respectively. Experiments on authoritative public datasets and real-world medical records show that our approach stably achieves superior performances over classical and advanced imbalanced classification methods.

Jiahuan Yan, Zhouyang Hong, Yu Zhao et al.

Imitation based robot learning has recently gained significant attention in the robotics field due to its theoretical potential for transferability and generalizability. However, it remains notoriously costly, both in terms of hardware and data collection, and deploying it in real-world environments demands meticulous setup of robots and precise experimental conditions. In this paper, we present a low-cost robot learning framework that is both easily reproducible and transferable to various robots and environments. We demonstrate that deployable imitation learning can be successfully applied even to industrial-grade robots, not just expensive collaborative robotic arms. Furthermore, our results show that multi-task robot learning is achievable with simple network architectures and fewer demonstrations than previously thought necessary. As the current evaluating method is almost subjective when it comes to real-world manipulation tasks, we propose Voting Positive Rate (VPR) - a novel evaluation strategy that provides a more objective assessment of performance. We conduct an extensive comparison of success rates across various self-designed tasks to validate our approach. To foster collaboration and support the robot learning community, we have open-sourced all relevant datasets and model checkpoints, available at huggingface.co/ZhiChengAI.

Yiheng Zhu, Jialu Wu, Qiuyi Li et al.

Inverse protein folding is a fundamental task in computational protein design, which aims to design protein sequences that fold into the desired backbone structures. While the development of machine learning algorithms for this task has seen significant success, the prevailing approaches, which predominantly employ a discriminative formulation, frequently encounter the error accumulation issue and often fail to capture the extensive variety of plausible sequences. To fill these gaps, we propose Bridge-IF, a generative diffusion bridge model for inverse folding, which is designed to learn the probabilistic dependency between the distributions of backbone structures and protein sequences. Specifically, we harness an expressive structure encoder to propose a discrete, informative prior derived from structures, and establish a Markov bridge to connect this prior with native sequences. During the inference stage, Bridge-IF progressively refines the prior sequence, culminating in a more plausible design. Moreover, we introduce a reparameterization perspective on Markov bridge models, from which we derive a simplified loss function that facilitates more effective training. We also modulate protein language models (PLMs) with structural conditions to precisely approximate the Markov bridge process, thereby significantly enhancing generation performance while maintaining parameter-efficient training. Extensive experiments on well-established benchmarks demonstrate that Bridge-IF predominantly surpasses existing baselines in sequence recovery and excels in the design of plausible proteins with high foldability. The code is available at https://github.com/violet-sto/Bridge-IF.

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.

Yaojun Hu, Jintai Chen, Lianting Hu et al.

Heart diseases rank among the leading causes of global mortality, demonstrating a crucial need for early diagnosis and intervention. Most traditional electrocardiogram (ECG) based automated diagnosis methods are trained at population level, neglecting the customization of personalized ECGs to enhance individual healthcare management. A potential solution to address this limitation is to employ digital twins to simulate symptoms of diseases in real patients. In this paper, we present an innovative prospective learning approach for personalized heart disease detection, which generates digital twins of healthy individuals' anomalous ECGs and enhances the model sensitivity to the personalized symptoms. In our approach, a vector quantized feature separator is proposed to locate and isolate the disease symptom and normal segments in ECG signals with ECG report guidance. Thus, the ECG digital twins can simulate specific heart diseases used to train a personalized heart disease detection model. Experiments demonstrate that our approach not only excels in generating high-fidelity ECG signals but also improves personalized heart disease detection. Moreover, our approach ensures robust privacy protection, safeguarding patient data in model development.

Yiqi Huang, Travis Davies, Jiahuan Yan et al.

Imitation learning and world models have shown significant promise in advancing generalizable robotic learning, with robotic grasping remaining a critical challenge for achieving precise manipulation. Existing methods often rely heavily on robot arm state data and RGB images, leading to overfitting to specific object shapes or positions. To address these limitations, we propose RoboGrasp, a universal grasping policy framework that integrates pretrained grasp detection models with robotic learning. By leveraging robust visual guidance from object detection and segmentation tasks, RoboGrasp significantly enhances grasp precision, stability, and generalizability, achieving up to 34% higher success rates in few-shot learning and grasping box prompt tasks. Built on diffusion-based methods, RoboGrasp is adaptable to various robotic learning paradigms, enabling precise and reliable manipulation across diverse and complex scenarios. This framework represents a scalable and versatile solution for tackling real-world challenges in robotic grasping.

Travis Davies, Jiahuan Yan, Xiang Chen et al.

Recent advances in imitation learning have shown significant promise for robotic control and embodied intelligence. However, achieving robust generalization across diverse mounted camera observations remains a critical challenge. In this paper, we introduce a video-based spatial perception framework that leverages 3D spatial representations to address environmental variability, with a focus on handling lighting changes. Our approach integrates a novel image augmentation technique, AugBlender, with a state-of-the-art monocular depth estimation model trained on internet-scale data. Together, these components form a cohesive system designed to enhance robustness and adaptability in dynamic scenarios. Our results demonstrate that our approach significantly boosts the success rate across diverse camera exposures, where previous models experience performance collapse. Our findings highlight the potential of video-based spatial perception models in advancing robustness for end-to-end robotic learning, paving the way for scalable, low-cost solutions in embodied intelligence.

Jiahuan Yan, Jintai Chen, Chaowen Hu et al.

Recent development in large language models (LLMs) has demonstrated impressive domain proficiency on unstructured textual or multi-modal tasks. However, despite with intrinsic world knowledge, their application on structured tabular data prediction still lags behind, primarily due to the numerical insensitivity and modality discrepancy that brings a gap between LLM reasoning and statistical tabular learning. Unlike textual or vision data (e.g., electronic clinical notes or medical imaging data), tabular data is often presented in heterogeneous numerical values (e.g., CBC reports). This ubiquitous data format requires intensive expert annotation, and its numerical nature limits LLMs' capability to effectively transfer untapped domain expertise. In this paper, we propose SERSAL, a general self-prompting method by synergy learning with small models to enhance LLM tabular prediction in an unsupervised manner. Specifically, SERSAL utilizes the LLM's prior outcomes as original soft noisy annotations, which are dynamically leveraged to teach a better small student model. Reversely, the outcomes from the trained small model are used to teach the LLM to further refine its real capability. This process can be repeatedly applied to gradually distill refined knowledge for continuous progress. Comprehensive experiments on widely used medical domain tabular datasets show that, without access to gold labels, applying SERSAL to OpenAI GPT reasoning process attains substantial improvement compared to linguistic prompting methods, which serves as an orthogonal direction for tabular LLM, and increasing prompting bonus is observed as more powerful LLMs appear.

Yiqi Huang, Travis Davies, Jiahuan Yan et al.

Achieving generalizable and precise robotic manipulation across diverse environments remains a critical challenge, largely due to limitations in spatial perception. While prior imitation-learning approaches have made progress, their reliance on raw RGB inputs and handcrafted features often leads to overfitting and poor 3D reasoning under varied lighting, occlusion, and object conditions. In this paper, we propose a unified framework that couples robust multimodal perception with reliable grasp prediction. Our architecture fuses domain-randomized augmentation, monocular depth estimation, and a depth-aware 6-DoF Grasp Prompt into a single spatial representation for downstream action planning. Conditioned on this encoding and a high-level task prompt, our diffusion-based policy yields precise action sequences, achieving up to 40% improvement in grasp success and 45% higher task success rates under environmental variation. These results demonstrate that spatially grounded perception, paired with diffusion-based imitation learning, offers a scalable and robust solution for general-purpose robotic grasping.

Yu Zhao, Huxian Liu, Xiang Chen et al.

Physical intelligence holds immense promise for advancing embodied intelligence, enabling robots to acquire complex behaviors from demonstrations. However, achieving generalization and transfer across diverse robotic platforms and environments requires careful design of model architectures, training strategies, and data diversity. Meanwhile existing systems often struggle with scalability, adaptability to heterogeneous hardware, and objective evaluation in real-world settings. We present a generalized end-to-end robotic learning framework designed to bridge this gap. Our framework introduces a unified architecture that supports cross-platform adaptability, enabling seamless deployment across industrial-grade robots, collaborative arms, and novel embodiments without task-specific modifications. By integrating multi-task learning with streamlined network designs, it achieves more robust performance than conventional approaches, while maintaining compatibility with varying sensor configurations and action spaces. We validate our framework through extensive experiments on seven manipulation tasks. Notably, Diffusion-based models trained in our framework demonstrated superior performance and generalizability compared to the LeRobot framework, achieving performance improvements across diverse robotic platforms and environmental conditions.