Binghong Chen

Rui Feng, Qi Zhu, Huan Tran et al.

Recent works have shown the promise of learning pre-trained models for 3D molecular representation. However, existing pre-training models focus predominantly on equilibrium data and largely overlook off-equilibrium conformations. It is challenging to extend these methods to off-equilibrium data because their training objective relies on assumptions of conformations being the local energy minima. We address this gap by proposing a force-centric pretraining model for 3D molecular conformations covering both equilibrium and off-equilibrium data. For off-equilibrium data, our model learns directly from their atomic forces. For equilibrium data, we introduce zero-force regularization and forced-based denoising techniques to approximate near-equilibrium forces. We obtain a unified pre-trained model for 3D molecular representation with over 15 million diverse conformations. Experiments show that, with our pre-training objective, we increase forces accuracy by around 3 times compared to the un-pre-trained Equivariant Transformer model. By incorporating regularizations on equilibrium data, we solved the problem of unstable MD simulations in vanilla Equivariant Transformers, achieving state-of-the-art simulation performance with 2.45 times faster inference time than NequIP. As a powerful molecular encoder, our pre-trained model achieves on-par performance with state-of-the-art property prediction tasks.

Binghong Chen, Daniel Tarlow, Kevin Swersky et al.

Improvements in the performance of computing systems, driven by Moore's Law, have transformed society. As such hardware-driven gains slow down, it becomes even more important for software developers to focus on performance and efficiency during development. While several studies have demonstrated the potential from such improved code efficiency (e.g., 2x better generational improvements compared to hardware), unlocking these gains in practice has been challenging. Reasoning about algorithmic complexity and the interaction of coding patterns on hardware can be challenging for the average programmer, especially when combined with pragmatic constraints around development velocity and multi-person development. This paper seeks to address this problem. We analyze a large competitive programming dataset from the Google Code Jam competition and find that efficient code is indeed rare, with a 2x runtime difference between the median and the 90th percentile of solutions. We propose using machine learning to automatically provide prescriptive feedback in the form of hints, to guide programmers towards writing high-performance code. To automatically learn these hints from the dataset, we propose a novel discrete variational auto-encoder, where each discrete latent variable represents a different learned category of code-edit that increases performance. We show that this method represents the multi-modal space of code efficiency edits better than a sequence-to-sequence baseline and generates a distribution of more efficient solutions.

Yaru Niu, Zhenlong Fang, Binghong Chen et al.

Humanoid robots promise general-purpose assistance, yet real-world humanoid loco-manipulation remains challenging because it requires whole-body stability, dexterous hands, and contact-aware perception under frequent contact changes. In this work, we study dexterous, contact-rich humanoid loco-manipulation. We first develop an RL-based whole-body controller that provides stable lower-body and torso execution during complex manipulation. Built on this controller, we develop a whole-body humanoid data collection system that combines VR-based teleoperation with human-to-humanoid motion mapping, enabling efficient collection of real-world demonstrations. We then propose Humanoid Transformer with Touch Dreaming (HTD), a multimodal encoder--decoder Transformer that models touch as a core modality alongside multi-view vision and proprioception. HTD is trained in a single stage with behavioral cloning augmented by touch dreaming: in addition to predicting action chunks, the policy predicts future hand-joint forces and future tactile latents, encouraging the shared Transformer trunk to learn contact-aware representations for dexterous interaction. Across five contact-rich tasks, Insert-T, Book Organization, Towel Folding, Cat Litter Scooping, and Tea Serving, HTD achieves a 90.9% relative improvement in average success rate over the stronger baseline. Ablation results further show that latent-space tactile prediction is more effective than raw tactile prediction, yielding a 30% relative gain in success rate. These results demonstrate that combining robust whole-body execution, scalable humanoid data collection, and predictive touch-centered learning enables versatile, high-dexterity humanoid manipulation in the real world. Project webpage: humanoid-touch-dream.github.io.

Binghong Chen, Tingting Chai, Wei Jiang et al.

Image denoising is essential in low-level vision applications such as photography and automated driving. Existing methods struggle with distinguishing complex noise patterns in real-world scenes and consume significant computational resources due to reliance on Transformer-based models. In this work, the Context-guided Receptance Weighted Key-Value (\M) model is proposed, combining enhanced multi-view feature integration with efficient sequence modeling. Our approach introduces the Context-guided Token Shift (CTS) paradigm, which effectively captures local spatial dependencies and enhance the model's ability to model real-world noise distributions. Additionally, the Frequency Mix (FMix) module extracting frequency-domain features is designed to isolate noise in high-frequency spectra, and is integrated with spatial representations through a multi-view learning process. To improve computational efficiency, the Bidirectional WKV (BiWKV) mechanism is adopted, enabling full pixel-sequence interaction with linear complexity while overcoming the causal selection constraints. The model is validated on multiple real-world image denoising datasets, outperforming the existing state-of-the-art methods quantitatively and reducing inference time up to 40\%. Qualitative results further demonstrate the ability of our model to restore fine details in various scenes.

Lin Chen, Jun Chen, Minghui Qiu et al.

Reconstructing high-resolution rainfall fields is essential for flood forecasting, hydrological modeling, and climate analysis. However, existing spatial interpolation methods-whether based on automatic weather station (AWS) measurements or enhanced with satellite/radar observations often over-smooth critical structures, failing to capture sharp transitions and localized extremes. We introduce RainSeer, a structure-aware reconstruction framework that reinterprets radar reflectivity as a physically grounded structural prior-capturing when, where, and how rain develops. This shift, however, introduces two fundamental challenges: (i) translating high-resolution volumetric radar fields into sparse point-wise rainfall observations, and (ii) bridging the physical disconnect between aloft hydro-meteors and ground-level precipitation. RainSeer addresses these through a physics-informed two-stage architecture: a Structure-to-Point Mapper performs spatial alignment by projecting mesoscale radar structures into localized ground-level rainfall, through a bidirectional mapping, and a Geo-Aware Rain Decoder captures the semantic transformation of hydro-meteors through descent, melting, and evaporation via a causal spatiotemporal attention mechanism. We evaluate RainSeer on two public datasets-RAIN-F (Korea, 2017-2019) and MeteoNet (France, 2016-2018)-and observe consistent improvements over state-of-the-art baselines, reducing MAE by over 13.31% and significantly enhancing structural fidelity in reconstructed rainfall fields.

Rui Feng, Huan Tran, Aubrey Toland et al.

Polymer simulation with both accuracy and efficiency is a challenging task. Machine learning (ML) forcefields have been developed to achieve both the accuracy of ab initio methods and the efficiency of empirical force fields. However, existing ML force fields are usually limited to single-molecule settings, and their simulations are not robust enough. In this paper, we present PolyGET, a new framework for Polymer Forcefields with Generalizable Equivariant Transformers. PolyGET is designed to capture complex quantum interactions between atoms and generalize across various polymer families, using a deep learning model called Equivariant Transformers. We propose a new training paradigm that focuses exclusively on optimizing forces, which is different from existing methods that jointly optimize forces and energy. This simple force-centric objective function avoids competing objectives between energy and forces, thereby allowing for learning a unified forcefield ML model over different polymer families. We evaluated PolyGET on a large-scale dataset of 24 distinct polymer types and demonstrated state-of-the-art performance in force accuracy and robust MD simulations. Furthermore, PolyGET can simulate large polymers with high fidelity to the reference ab initio DFT method while being able to generalize to unseen polymers.

Karan Samel, Zelin Zhao, Binghong Chen et al.

Events across a timeline are a common data representation, seen in different temporal modalities. Individual atomic events can occur in a certain temporal ordering to compose higher level composite events. Examples of a composite event are a patient's medical symptom or a baseball player hitting a home run, caused distinct temporal orderings of patient vitals and player movements respectively. Such salient composite events are provided as labels in temporal datasets and most works optimize models to predict these composite event labels directly. We focus on uncovering the underlying atomic events and their relations that lead to the composite events within a noisy temporal data setting. We propose Neural Temporal Logic Programming (Neural TLP) which first learns implicit temporal relations between atomic events and then lifts logic rules for composite events, given only the composite events labels for supervision. This is done through efficiently searching through the combinatorial space of all temporal logic rules in an end-to-end differentiable manner. We evaluate our method on video and healthcare datasets where it outperforms the baseline methods for rule discovery.

Zelin Zhao, Karan Samel, Binghong Chen et al.

Programs, consisting of semantic and structural information, play an important role in the communication between humans and agents. Towards learning general program executors to unify perception, reasoning, and decision making, we formulate program-guided tasks which require learning to execute a given program on the observed task specification. Furthermore, we propose the Program-guided Transformer (ProTo), which integrates both semantic and structural guidance of a program by leveraging cross-attention and masked self-attention to pass messages between the specification and routines in the program. ProTo executes a program in a learned latent space and enjoys stronger representation ability than previous neural-symbolic approaches. We demonstrate that ProTo significantly outperforms the previous state-of-the-art methods on GQA visual reasoning and 2D Minecraft policy learning datasets. Additionally, ProTo demonstrates better generalization to unseen, complex, and human-written programs.

Zhaoyu Li, Binghong Chen, Xujie Si

Interactive theorem proving is a challenging and tedious process, which requires non-trivial expertise and detailed low-level instructions (or tactics) from human experts. Tactic prediction is a natural way to automate this process. Existing methods show promising results on tactic prediction by learning a deep neural network (DNN) based model from proofs written by human experts. In this paper, we propose NeuroTactic, a novel extension with a special focus on improving the representation learning for theorem proving. NeuroTactic leverages graph neural networks (GNNs) to represent the theorems and premises, and applies graph contrastive learning for pre-training. We demonstrate that the representation learning of theorems is essential to predict tactics. Compared with other methods, NeuroTactic achieves state-of-the-art performance on the CoqGym dataset.

Shuangjia Zheng, Tao Zeng, Chengtao Li et al.

Nature, a synthetic master, creates more than 300,000 natural products (NPs) which are the major constituents of FDA-proved drugs owing to the vast chemical space of NPs. To date, there are fewer than 30,000 validated NPs compounds involved in about 33,000 known enzyme catalytic reactions, and even fewer biosynthetic pathways are known with complete cascade-connected enzyme catalysis. Therefore, it is valuable to make computer-aided bio-retrosynthesis predictions. Here, we develop BioNavi-NP, a navigable and user-friendly toolkit, which is capable of predicting the biosynthetic pathways for NPs and NP-like compounds through a novel (AND-OR Tree)-based planning algorithm, an enhanced molecular Transformer neural network, and a training set that combines general organic transformations and biosynthetic steps. Extensive evaluations reveal that BioNavi-NP generalizes well to identifying the reported biosynthetic pathways for 90% of test compounds and recovering the verified building blocks for 73%, significantly outperforming conventional rule-based approaches. Moreover, BioNavi-NP also shows an outstanding capacity of biologically plausible pathways enumeration. In this sense, BioNavi-NP is a leading-edge toolkit to redesign complex biosynthetic pathways of natural products with applications to total or semi-synthesis and pathway elucidation or reconstruction.

Yuyu Zhang, Heng Chi, Binghong Chen et al.

A wide range of modern science and engineering applications are formulated as optimization problems with a system of partial differential equations (PDEs) as constraints. These PDE-constrained optimization problems are typically solved in a standard discretize-then-optimize approach. In many industry applications that require high-resolution solutions, the discretized constraints can easily have millions or even billions of variables, making it very slow for the standard iterative optimizer to solve the exact gradients. In this work, we propose a general framework to speed up PDE-constrained optimization using online neural synthetic gradients (ONSG) with a novel two-scale optimization scheme. We successfully apply our ONSG framework to computational morphogenesis, a representative and challenging class of PDE-constrained optimization problems. Extensive experiments have demonstrated that our method can significantly speed up computational morphogenesis (also known as topology optimization), and meanwhile maintain the quality of final solution compared to the standard optimizer. On a large-scale 3D optimal design problem with around 1,400,000 design variables, our method achieves up to 7.5x speedup while producing optimized designs with comparable objectives.

Karan Samel, Zelin Zhao, Binghong Chen et al.

In multi-modal reasoning tasks, such as visual question answering (VQA), there have been many modeling and training paradigms tested. Previous models propose different methods for the vision and language tasks, but which ones perform the best while being sample and computationally efficient? Based on our experiments, we find that representing the text as probabilistic programs and images as object-level scene graphs best satisfy these desiderata. We extend existing models to leverage these soft programs and scene graphs to train on question answer pairs in an end-to-end manner. Empirical results demonstrate that this differentiable end-to-end program executor is able to maintain state-of-the-art accuracy while being sample and computationally efficient.

Binghong Chen, Chengtao Li, Hanjun Dai et al.

Retrosynthetic planning is a critical task in organic chemistry which identifies a series of reactions that can lead to the synthesis of a target product. The vast number of possible chemical transformations makes the size of the search space very big, and retrosynthetic planning is challenging even for experienced chemists. However, existing methods either require expensive return estimation by rollout with high variance, or optimize for search speed rather than the quality. In this paper, we propose Retro*, a neural-based A*-like algorithm that finds high-quality synthetic routes efficiently. It maintains the search as an AND-OR tree, and learns a neural search bias with off-policy data. Then guided by this neural network, it performs best-first search efficiently during new planning episodes. Experiments on benchmark USPTO datasets show that, our proposed method outperforms existing state-of-the-art with respect to both the success rate and solution quality, while being more efficient at the same time.

Harsh Shrivastava, Xinshi Chen, Binghong Chen et al.

Recovering sparse conditional independence graphs from data is a fundamental problem in machine learning with wide applications. A popular formulation of the problem is an $\ell_1$ regularized maximum likelihood estimation. Many convex optimization algorithms have been designed to solve this formulation to recover the graph structure. Recently, there is a surge of interest to learn algorithms directly based on data, and in this case, learn to map empirical covariance to the sparse precision matrix. However, it is a challenging task in this case, since the symmetric positive definiteness (SPD) and sparsity of the matrix are not easy to enforce in learned algorithms, and a direct mapping from data to precision matrix may contain many parameters. We propose a deep learning architecture, GLAD, which uses an Alternating Minimization (AM) algorithm as our model inductive bias, and learns the model parameters via supervised learning. We show that GLAD learns a very compact and effective model for recovering sparse graphs from data.

Binghong Chen, Bo Dai, Qinjie Lin et al.

We propose a meta path planning algorithm named \emph{Neural Exploration-Exploitation Trees~(NEXT)} for learning from prior experience for solving new path planning problems in high dimensional continuous state and action spaces. Compared to more classical sampling-based methods like RRT, our approach achieves much better sample efficiency in high-dimensions and can benefit from prior experience of planning in similar environments. More specifically, NEXT exploits a novel neural architecture which can learn promising search directions from problem structures. The learned prior is then integrated into a UCB-type algorithm to achieve an online balance between \emph{exploration} and \emph{exploitation} when solving a new problem. We conduct thorough experiments to show that NEXT accomplishes new planning problems with more compact search trees and significantly outperforms state-of-the-art methods on several benchmarks.

Binghong Chen, Jun Zhu

Group-Lasso (gLasso) identifies important explanatory factors in predicting the response variable by considering the grouping structure over input variables. However, most existing algorithms for gLasso are not scalable to deal with large-scale datasets, which are becoming a norm in many applications. In this paper, we present a divide-and-conquer based parallel algorithm (DC-gLasso) to scale up gLasso in the tasks of regression with grouping structures. DC-gLasso only needs two iterations to collect and aggregate the local estimates on subsets of the data, and is provably correct to recover the true model under certain conditions. We further extend it to deal with overlappings between groups. Empirical results on a wide range of synthetic and real-world datasets show that DC-gLasso can significantly improve the time efficiency without sacrificing regression accuracy.