arXiv subjects

Binjie Hong

Publications and source records attributed to Binjie Hong.

6 recordsLinked to original sources

arXiv2026

BCIJelly: An integrated ecosystem for brain-computer interface research

Brain-computer interface (BCI) research relies on multistage computational pipelines, yet progress remains constrained by fragmented data formats, heterogeneous decoder implementations and hardware-specific deployment toolchains, and researchers lack an integrated workflow. Here, we fill this gap with BCIJelly, a unified computational ecosystem that integrates 18 curated BCI datasets, 15 benchmark decoders and an algorithmic library of 80 reusable modules, an automated architecture search (AAS) procedure, and hardware-aware deployment through the toChip pipeline within a single Python framework. AAS constructs task-specific decoders without manual architecture design. It is further extended into a closed-loop mode guided by a large language model (LLM), which uses task specifications, module descriptions and search history to support multitask and cross-species decoding. The toChip pipeline compiles trained decoders for execution on neuromorphic chips, enabling energy-efficient deployment for BCI systems. An accompanying visualization software provides a graphical interface to the full workflow, making BCIJelly accessible without programming. We validate BCIJelly across five BCI paradigms (motor, visual, speech, emotion and auditory) with recordings from humans, macaques and mice, and single-task, multitask and cross-species decoding settings. BCIJelly establishes a unified and extensible infrastructure that bridges decoder development and hardware-aware deployment for BCI research.

cs.HC↗

arXiv2026

UniBCI: Towards a Unified Pretrained Model for Invasive Brain-Computer Interfaces

Modeling invasive neural spike data is fundamental to advancing high-performance brain-computer interfaces (BCIs). However, existing approaches face critical challenges, including limited-scale heterogeneous data, cross-domain distribution shift, and the intrinsic spatiotemporal complexity of invasive neural signals. In this work, we propose UniBCI, a unified pretrained model for invasive Brain-Computer Interfaces. The model integrates three key components: (1) a context-conditioned spatio-temporal tokenization (CST) scheme that embeds neural signals together with metadata into a shared representation space; (2) a hierarchical Interval-Area Attention (IAA) mechanism that captures patterns of spike dynamics in slots via linear attention and locality dependencies via sliding-window attention; and (3) a scalable self-supervised masked signals reconstruction objective for learning generalizable neural representations from large-scale unlabeled data. We construct a pretraining corpus spanning multiple species, subjects, brain regions, and behavioral experiment paradigms. These heterogeneous recordings are standardize via our proposed unified normalization and tokenization. Comprehensive experiments demonstrate that UniBCI achieves SOTA performance across diverse downstream tasks while improving generalization. Moreover, the model achieves a strong balance between accuracy and efficiency, with fewer trainable parameters and lower inference latency. These results suggest that UniBCI provides a practical step toward general-purpose neural foundation models, enabling robust, scalable, and transferable representation learning for invasive neural data. The code for this paper is available at: https://anonymous.4open.science/r/UniBCI-C805.

cs.NE↗

arXiv2024

Retrosynthesis Prediction via Search in (Hyper) Graph

Predicting reactants from a specified core product stands as a fundamental challenge within organic synthesis, termed retrosynthesis prediction. Recently, semi-template-based methods and graph-edits-based methods have achieved good performance in terms of both interpretability and accuracy. However, due to their mechanisms these methods cannot predict complex reactions, e.g., reactions with multiple reaction center or attaching the same leaving group to more than one atom. In this study we propose a semi-template-based method, the \textbf{Retro}synthesis via \textbf{S}earch \textbf{i}n (Hyper) \textbf{G}raph (RetroSiG) framework to alleviate these limitations. In the proposed method, we turn the reaction center identification and the leaving group completion tasks as tasks of searching in the product molecular graph and leaving group hypergraph respectively. As a semi-template-based method RetroSiG has several advantages. First, RetroSiG is able to handle the complex reactions mentioned above by its novel search mechanism. Second, RetroSiG naturally exploits the hypergraph to model the implicit dependencies between leaving groups. Third, RetroSiG makes full use of the prior, i.e., one-hop constraint. It reduces the search space and enhances overall performance. Comprehensive experiments demonstrated that RetroSiG achieved competitive results. Furthermore, we conducted experiments to show the capability of RetroSiG in predicting complex reactions. Ablation experiments verified the efficacy of specific elements, such as the one-hop constraint and the leaving group hypergraph.

q-bio.QM↗

arXiv2023

Use neural networks to recognize students' handwritten letters and incorrect symbols

Correcting students' multiple-choice answers is a repetitive and mechanical task that can be considered an image multi-classification task. Assuming possible options are 'abcd' and the correct option is one of the four, some students may write incorrect symbols or options that do not exist. In this paper, five classifications were set up - four for possible correct options and one for other incorrect writing. This approach takes into account the possibility of non-standard writing options.

cs.CV↗

arXiv2023

RCsearcher: Reaction Center Identification in Retrosynthesis via Deep Q-Learning

The reaction center consists of atoms in the product whose local properties are not identical to the corresponding atoms in the reactants. Prior studies on reaction center identification are mainly on semi-templated retrosynthesis methods. Moreover, they are limited to single reaction center identification. However, many reaction centers are comprised of multiple bonds or atoms in reality. We refer to it as the multiple reaction center. This paper presents RCsearcher, a unified framework for single and multiple reaction center identification that combines the advantages of the graph neural network and deep reinforcement learning. The critical insight in this framework is that the single or multiple reaction center must be a node-induced subgraph of the molecular product graph. At each step, it considers choosing one node in the molecular product graph and adding it to the explored node-induced subgraph as an action. Comprehensive experiments demonstrate that RCsearcher consistently outperforms other baselines and can extrapolate the reaction center patterns that have not appeared in the training set. Ablation experiments verify the effectiveness of individual components, including the beam search and one-hop constraint of action space.

cs.LG↗

arXiv2022

More Interpretable Graph Similarity Computation via Maximum Common Subgraph Inference

Graph similarity measurement, which computes the distance/similarity between two graphs, arises in various graph-related tasks. Recent learning-based methods lack interpretability, as they directly transform interaction information between two graphs into one hidden vector and then map it to similarity. To cope with this problem, this study proposes a more interpretable end-to-end paradigm for graph similarity learning, named Similarity Computation via Maximum Common Subgraph Inference (INFMCS). Our critical insight into INFMCS is the strong correlation between similarity score and Maximum Common Subgraph (MCS). We implicitly infer MCS to obtain the normalized MCS size, with the supervision information being only the similarity score during training. To capture more global information, we also stack some vanilla transformer encoder layers with graph convolution layers and propose a novel permutation-invariant node Positional Encoding. The entire model is quite simple yet effective. Comprehensive experiments demonstrate that INFMCS consistently outperforms state-of-the-art baselines for graph-graph classification and regression tasks. Ablation experiments verify the effectiveness of the proposed computation paradigm and other components. Also, visualization and statistics of results reveal the interpretability of INFMCS.

cs.LG↗