arXiv subjects

Jiezhong Qiu

Publications and source records attributed to Jiezhong Qiu.

At least 19 recordsLinked to original sources

arXiv2026

Exploring the Alignment of Generation and Understanding in Protein Structure Modeling

Understanding and generation are often treated as two separate paradigms in training deep neural networks, despite the fact that both are trained with closely related objectives such as denoising and masked prediction. While prior studies have shown that generative models often learn suboptimal representations for understanding tasks in vision, it is less understood whether a similar gap exists in the protein domain. In this work, we systematically investigate this question by benchmarking state-of-the-art protein generative models on widely-used protein understanding tasks, and observe that these models exhibit consistently poor performance compared to existing protein encoders. Furthermore, inspired by the Representation Alignment (REPA) framework, we propose to explicitly align generative protein diffusion models with pretrained protein understanding models during training. Experiments on the MotifBench demonstrate that representation alignment significantly improves functional protein generation, boosting the MotifBench score of Protpardelle-1c from 39.2 to 47.1, corresponding to a 20% relative improvement. Our results suggest that representation alignment provides a general and effective mechanism for bridging understanding and generation in protein structure modeling.

cs.CE↗

arXiv2026

TensorCircuit-NG: A Universal, Composable, and Scalable Platform for Quantum Computing and Quantum Simulation

We present TensorCircuit-NG, a next-generation quantum software platform designed to bridge the gap between quantum physics, artificial intelligence, and high-performance computing. Moving beyond the scope of traditional circuit simulators, TensorCircuit-NG establishes a unified, tensor-native programming paradigm where quantum circuits, tensor networks, and neural networks fuse into a single, end-to-end differentiable computational graph. Built upon industry-standard machine learning backends (JAX, TensorFlow, PyTorch), the framework introduces comprehensive capabilities for approximate circuit simulation, analog dynamics, fermion Gaussian states, qudit systems, and scalable noise modeling. To tackle the exponential complexity of deep quantum circuits, TensorCircuit-NG implements advanced distributed computing strategies, including automated data parallelism and model-parallel tensor network slicing. We validate these capabilities on GPU clusters, demonstrating a near-linear speedup in distributed variational quantum algorithms. TensorCircuit-NG enables flagship applications, including end-to-end QML for CIFAR-100 computer vision, efficient pipelines from quantum states to neural networks via classical shadows, and differentiable optimization of tensor network states for many-body physics.

quant-ph↗

arXiv2026

InstructPLM-mu: 1-Hour Fine-Tuning of ESM2 Beats ESM3 in Protein Mutation Predictions

Multimodal protein language models deliver strong performance on mutation-effect prediction, but training such models from scratch demands substantial computational resources. In this paper, we propose a fine-tuning framework called InstructPLM-mu and try to answer a question: \textit{Can multimodal fine-tuning of a pretrained, sequence-only protein language model match the performance of models trained end-to-end? } Surprisingly, our experiments show that fine-tuning ESM2 with structural inputs can reach performance comparable to ESM3. To understand how this is achieved, we systematically compare three different feature-fusion designs and fine-tuning recipes. Our results reveal that both the fusion method and the tuning strategy strongly affect final accuracy, indicating that the fine-tuning process is not trivial. We hope this work offers practical guidance for injecting structure into pretrained protein language models and motivates further research on better fusion mechanisms and fine-tuning protocols.

q-bio.QM↗

arXiv2025

Kimi Linear: An Expressive, Efficient Attention Architecture

We introduce Kimi Linear, a hybrid linear attention architecture that, for the first time, outperforms full attention under fair comparisons across various scenarios -- including short-context, long-context, and reinforcement learning (RL) scaling regimes. At its core lies Kimi Delta Attention (KDA), an expressive linear attention module that extends Gated DeltaNet with a finer-grained gating mechanism, enabling more effective use of limited finite-state RNN memory. Our bespoke chunkwise algorithm achieves high hardware efficiency through a specialized variant of the Diagonal-Plus-Low-Rank (DPLR) transition matrices, which substantially reduces computation compared to the general DPLR formulation while remaining more consistent with the classical delta rule. We pretrain a Kimi Linear model with 3B activated parameters and 48B total parameters, based on a layerwise hybrid of KDA and Multi-Head Latent Attention (MLA). Our experiments show that with an identical training recipe, Kimi Linear outperforms full MLA with a sizeable margin across all evaluated tasks, while reducing KV cache usage by up to 75% and achieving up to 6 times decoding throughput for a 1M context. These results demonstrate that Kimi Linear can be a drop-in replacement for full attention architectures with superior performance and efficiency, including tasks with longer input and output lengths. To support further research, we open-source the KDA kernel and vLLM implementations, and release the pre-trained and instruction-tuned model checkpoints.

cs.CL↗

arXiv2025

ChemMiner: A Large Language Model Agent System for Chemical Literature Data Mining

The development of AI-assisted chemical synthesis tools requires comprehensive datasets covering diverse reaction types, yet current high-throughput experimental (HTE) approaches are expensive and limited in scope. Chemical literature represents a vast, underexplored data source containing thousands of reactions published annually. However, extracting reaction information from literature faces significant challenges including varied writing styles, complex coreference relationships, and multimodal information presentation. This paper proposes ChemMiner, a novel end-to-end framework leveraging multiple agents powered by large language models (LLMs) to extract high-fidelity chemical data from literature. ChemMiner incorporates three specialized agents: a text analysis agent for coreference mapping, a multimodal agent for non-textual information extraction, and a synthesis analysis agent for data generation. Furthermore, we developed a comprehensive benchmark with expert-annotated chemical literature to evaluate both extraction efficiency and precision. Experimental results demonstrate reaction identification rates comparable to human chemists while significantly reducing processing time, with high accuracy, recall, and F1 scores. Our open-sourced benchmark facilitates future research in chemical literature data mining.

cs.IR↗

arXiv2025

Kimi-VL Technical Report

We present Kimi-VL, an efficient open-source Mixture-of-Experts (MoE) vision-language model (VLM) that offers advanced multimodal reasoning, long-context understanding, and strong agent capabilities - all while activating only 2.8B parameters in its language decoder (Kimi-VL-A3B). Kimi-VL demonstrates strong performance across challenging domains: as a general-purpose VLM, Kimi-VL excels in multi-turn agent tasks (e.g., OSWorld), matching flagship models. Furthermore, it exhibits remarkable capabilities across diverse challenging vision language tasks, including college-level image and video comprehension, OCR, mathematical reasoning, and multi-image understanding. In comparative evaluations, it effectively competes with cutting-edge efficient VLMs such as GPT-4o-mini, Qwen2.5-VL-7B, and Gemma-3-12B-IT, while surpassing GPT-4o in several key domains. Kimi-VL also advances in processing long contexts and perceiving clearly. With a 128K extended context window, Kimi-VL can process diverse long inputs, achieving impressive scores of 64.5 on LongVideoBench and 35.1 on MMLongBench-Doc. Its native-resolution vision encoder, MoonViT, further allows it to see and understand ultra-high-resolution visual inputs, achieving 83.2 on InfoVQA and 34.5 on ScreenSpot-Pro, while maintaining lower computational cost for common tasks. Building upon Kimi-VL, we introduce an advanced long-thinking variant: Kimi-VL-Thinking-2506. Developed through long chain-of-thought (CoT) supervised fine-tuning (SFT) and reinforcement learning (RL), the latest model exhibits strong long-horizon reasoning capabilities (64.0 on MMMU, 46.3 on MMMU-Pro, 56.9 on MathVision, 80.1 on MathVista, 65.2 on VideoMMMU) while obtaining robust general abilities. Code and models are publicly accessible at https://github.com/MoonshotAI/Kimi-VL.

cs.CV↗

arXiv2025

Protein Inverse Folding From Structure Feedback

The inverse folding problem, aiming to design amino acid sequences that fold into desired three-dimensional structures, is pivotal for various biotechnological applications. Here, we introduce a novel approach leveraging Direct Preference Optimization (DPO) to fine-tune an inverse folding model using feedback from a protein folding model. Given a target protein structure, we begin by sampling candidate sequences from the inverse-folding model, then predict the three-dimensional structure of each sequence with the folding model to generate pairwise structural-preference labels. These labels are used to fine-tune the inverse-folding model under the DPO objective. Our results on the CATH 4.2 test set demonstrate that DPO fine-tuning not only improves sequence recovery of baseline models but also leads to a significant improvement in average TM-Score from 0.77 to 0.81, indicating enhanced structure similarity. Furthermore, iterative application of our DPO-based method on challenging protein structures yields substantial gains, with an average TM-Score increase of 79.5\% with regard to the baseline model. This work establishes a promising direction for enhancing protein sequence design ability from structure feedback by effectively utilizing preference optimization.

cs.LG↗

arXiv2025

Chemist-X: Large Language Model-empowered Agent for Reaction Condition Recommendation in Chemical Synthesis

Recent AI research plots a promising future of automatic chemical reactions within the chemistry society. This study proposes Chemist-X, a comprehensive AI agent that automates the reaction condition optimization (RCO) task in chemical synthesis with retrieval-augmented generation (RAG) technology and AI-controlled wet-lab experiment executions. To begin with, as an emulation on how chemical experts solve the RCO task, Chemist-X utilizes a novel RAG scheme to interrogate available molecular and literature databases to narrow the searching space for later processing. The agent then leverages a computer-aided design (CAD) tool we have developed through a large language model (LLM) supervised programming interface. With updated chemical knowledge obtained via RAG, as well as the ability in using CAD tools, our agent significantly outperforms conventional RCO AIs confined to the fixed knowledge within its training data. Finally, Chemist-X interacts with the physical world through an automated robotic system, which can validate the suggested chemical reaction condition without human interventions. The control of the robotic system was achieved with a novel algorithm we have developed for the equipment, which relies on LLMs for reliable script generation. Results of our automatic wet-lab experiments, achieved by fully LLM-supervised end-to-end operation with no human in the lope, prove Chemist-X's ability in self-driving laboratories.

cs.IR↗

arXiv2025

MoBA: Mixture of Block Attention for Long-Context LLMs

Scaling the effective context length is essential for advancing large language models (LLMs) toward artificial general intelligence (AGI). However, the quadratic increase in computational complexity inherent in traditional attention mechanisms presents a prohibitive overhead. Existing approaches either impose strongly biased structures, such as sink or window attention which are task-specific, or radically modify the attention mechanism into linear approximations, whose performance in complex reasoning tasks remains inadequately explored. In this work, we propose a solution that adheres to the ``less structure'' principle, allowing the model to determine where to attend autonomously, rather than introducing predefined biases. We introduce Mixture of Block Attention (MoBA), an innovative approach that applies the principles of Mixture of Experts (MoE) to the attention mechanism. This novel architecture demonstrates superior performance on long-context tasks while offering a key advantage: the ability to seamlessly transition between full and sparse attention, enhancing efficiency without the risk of compromising performance. MoBA has already been deployed to support Kimi's long-context requests and demonstrates significant advancements in efficient attention computation for LLMs. Our code is available at https://github.com/MoonshotAI/MoBA.

cs.LG↗

arXiv2024

Holmes: Towards Distributed Training Across Clusters with Heterogeneous NIC Environment

Large language models (LLMs) such as GPT-3, OPT, and LLaMA have demonstrated remarkable accuracy in a wide range of tasks. However, training these models can incur significant expenses, often requiring tens of thousands of GPUs for months of continuous operation. Typically, this training is carried out in specialized GPU clusters equipped with homogeneous high-speed Remote Direct Memory Access (RDMA) network interface cards (NICs). The acquisition and maintenance of such dedicated clusters is challenging. Current LLM training frameworks, like Megatron-LM and Megatron-DeepSpeed, focus primarily on optimizing training within homogeneous cluster settings. In this paper, we introduce Holmes, a training framework for LLMs that employs thoughtfully crafted data and model parallelism strategies over the heterogeneous NIC environment. Our primary technical contribution lies in a novel scheduling method that intelligently allocates distinct computational tasklets in LLM training to specific groups of GPU devices based on the characteristics of their connected NICs. Furthermore, our proposed framework, utilizing pipeline parallel techniques, demonstrates scalability to multiple GPU clusters, even in scenarios without high-speed interconnects between nodes in distinct clusters. We conducted comprehensive experiments that involved various scenarios in the heterogeneous NIC environment. In most cases, our framework achieves performance levels close to those achievable with homogeneous RDMA-capable networks (InfiniBand or RoCE), significantly exceeding training efficiency within the pure Ethernet environment. Additionally, we verified that our framework outperforms other mainstream LLM frameworks under heterogeneous NIC environment in terms of training efficiency and can be seamlessly integrated with them.

cs.CL↗

arXiv2024

Spatio-Temporal Contrastive Learning Enhanced GNNs for Session-based Recommendation

Session-based recommendation (SBR) systems aim to utilize the user's short-term behavior sequence to predict the next item without the detailed user profile. Most recent works try to model the user preference by treating the sessions as between-item transition graphs and utilize various graph neural networks (GNNs) to encode the representations of pair-wise relations among items and their neighbors. Some of the existing GNN-based models mainly focus on aggregating information from the view of spatial graph structure, which ignores the temporal relations within neighbors of an item during message passing and the information loss results in a sub-optimal problem. Other works embrace this challenge by incorporating additional temporal information but lack sufficient interaction between the spatial and temporal patterns. To address this issue, inspired by the uniformity and alignment properties of contrastive learning techniques, we propose a novel framework called Session-based Recommendation with Spatio-Temporal Contrastive Learning Enhanced GNNs (RESTC). The idea is to supplement the GNN-based main supervised recommendation task with the temporal representation via an auxiliary cross-view contrastive learning mechanism. Furthermore, a novel global collaborative filtering graph (CFG) embedding is leveraged to enhance the spatial view in the main task. Extensive experiments demonstrate the significant performance of RESTC compared with the state-of-the-art baselines e.g., with an improvement as much as 27.08% gain on HR@20 and 20.10% gain on MRR@20.

cs.IR↗

arXiv2024

SketchNE: Embedding Billion-Scale Networks Accurately in One Hour

We study large-scale network embedding with the goal of generating high-quality embeddings for networks with more than 1 billion vertices and 100 billion edges. Recent attempts LightNE and NetSMF propose to sparsify and factorize the (dense) NetMF matrix for embedding large networks, where NetMF is a theoretically-grounded network embedding method. However, there is a trade-off between their embeddings' quality and scalability due to their expensive memory requirements, making embeddings less effective under real-world memory constraints. Therefore, we present the SketchNE model, a scalable, effective, and memory-efficient network embedding solution developed for a single machine with CPU only. The main idea of SketchNE is to avoid the explicit construction and factorization of the NetMF matrix either sparsely or densely when producing the embeddings through the proposed sparse-sign randomized single-pass SVD algorithm. We conduct extensive experiments on nine datasets of various sizes for vertex classification and link prediction, demonstrating the consistent outperformance of SketchNE over state-of-the-art baselines in terms of both effectiveness and efficiency. SketchNE costs only 1.0 hours to embed the Hyperlink2012 network with 3.5 billion vertices and 225 billion edges on a CPU-only single machine with embedding superiority (e.g., a 282% relative HITS@10 gain over LightNE).

cs.SI↗

arXiv2023

Multi-task Bioassay Pre-training for Protein-ligand Binding Affinity Prediction

Protein-ligand binding affinity (PLBA) prediction is the fundamental task in drug discovery. Recently, various deep learning-based models predict binding affinity by incorporating the three-dimensional structure of protein-ligand complexes as input and achieving astounding progress. However, due to the scarcity of high-quality training data, the generalization ability of current models is still limited. In addition, different bioassays use varying affinity measurement labels (i.e., IC50, Ki, Kd), and different experimental conditions inevitably introduce systematic noise, which poses a significant challenge to constructing high-precision affinity prediction models. To address these issues, we (1) propose Multi-task Bioassay Pre-training (MBP), a pre-training framework for structure-based PLBA prediction; (2) construct a pre-training dataset called ChEMBL-Dock with more than 300k experimentally measured affinity labels and about 2.8M docked three-dimensional structures. By introducing multi-task pre-training to treat the prediction of different affinity labels as different tasks and classifying relative rankings between samples from the same bioassay, MBP learns robust and transferrable structural knowledge from our new ChEMBL-Dock dataset with varied and noisy labels. Experiments substantiate the capability of MBP as a general framework that can improve and be tailored to mainstream structure-based PLBA prediction tasks. To the best of our knowledge, MBP is the first affinity pre-training model and shows great potential for future development.

q-bio.BM↗

arXiv2023

Protein-Ligand Complex Generator & Drug Screening via Tiered Tensor Transform

The generation of small molecule candidate (ligand) binding poses in its target protein pocket is important for computer-aided drug discovery. Typical rigid-body docking methods ignore the pocket flexibility of protein, while the more accurate pose generation using molecular dynamics is hindered by slow protein dynamics. We develop a tiered tensor transform (3T) algorithm to rapidly generate diverse protein-ligand complex conformations for both pose and affinity estimation in drug screening, requiring neither machine learning training nor lengthy dynamics computation, while maintaining both coarse-grain-like coordinated protein dynamics and atomistic-level details of the complex pocket. The 3T conformation structures we generate achieve significantly higher accuracy in active ligand classification than traditional ensemble docking using hundreds of experimental protein conformations. Furthermore, we demonstrate that 3T can be used to explore distant protein-ligand binding poses within the protein pocket. 3T structure transformation is decoupled from the system physics, making future usage in other computational scientific domains possible.

cs.NE↗

arXiv2023

Towards Lightweight and Automated Representation Learning System for Networks

We propose LIGHTNE 2.0, a cost-effective, scalable, automated, and high-quality network embedding system that scales to graphs with hundreds of billions of edges on a single machine. In contrast to the mainstream belief that distributed architecture and GPUs are needed for large-scale network embedding with good quality, we prove that we can achieve higher quality, better scalability, lower cost, and faster runtime with shared-memory, CPU-only architecture. LIGHTNE 2.0 combines two theoretically grounded embedding methods NetSMF and ProNE. We introduce the following techniques to network embedding for the first time: (1) a newly proposed downsampling method to reduce the sample complexity of NetSMF while preserving its theoretical advantages; (2) a high-performance parallel graph processing stack GBBS to achieve high memory efficiency and scalability; (3) sparse parallel hash table to aggregate and maintain the matrix sparsifier in memory; (4) a fast randomized singular value decomposition (SVD) enhanced by power iteration and fast orthonormalization to improve vanilla randomized SVD in terms of both efficiency and effectiveness; (5) Intel MKL for proposed fast randomized SVD and spectral propagation; and (6) a fast and lightweight AutoML library FLAML for automated hyperparameter tuning. Experimental results show that LIGHTNE 2.0 can be up to 84X faster than GraphVite, 30X faster than PBG and 9X faster than NetSMF while delivering better performance. LIGHTNE 2.0 can embed very large graph with 1.7 billion nodes and 124 billion edges in half an hour on a CPU server, while other baselines cannot handle very large graphs of this scale.

cs.SI↗

arXiv2023

TensorCircuit: a Quantum Software Framework for the NISQ Era

TensorCircuit is an open source quantum circuit simulator based on tensor network contraction, designed for speed, flexibility and code efficiency. Written purely in Python, and built on top of industry-standard machine learning frameworks, TensorCircuit supports automatic differentiation, just-in-time compilation, vectorized parallelism and hardware acceleration. These features allow TensorCircuit to simulate larger and more complex quantum circuits than existing simulators, and are especially suited to variational algorithms based on parameterized quantum circuits. TensorCircuit enables orders of magnitude speedup for various quantum simulation tasks compared to other common quantum software, and can simulate up to 600 qubits with moderate circuit depth and low-dimensional connectivity. With its time and space efficiency, flexible and extensible architecture and compact, user-friendly API, TensorCircuit has been built to facilitate the design, simulation and analysis of quantum algorithms in the Noisy Intermediate-Scale Quantum (NISQ) era.

quant-ph↗

arXiv2023

Multi-Constraint Molecular Generation using Sparsely Labelled Training Data for Localized High-Concentration Electrolyte Diluent Screening

Recently, machine learning methods have been used to propose molecules with desired properties, which is especially useful for exploring large chemical spaces efficiently. However, these methods rely on fully labelled training data, and are not practical in situations where molecules with multiple property constraints are required. There is often insufficient training data for all those properties from publicly available databases, especially when ab-initio simulation or experimental property data is also desired for training the conditional molecular generative model. In this work, we show how to modify a semi-supervised variational auto-encoder (SSVAE) model which only works with fully labelled and fully unlabelled molecular property training data into the ConGen model, which also works on training data that have sparsely populated labels. We evaluate ConGen's performance in generating molecules with multiple constraints when trained on a dataset combined from multiple publicly available molecule property databases, and demonstrate an example application of building the virtual chemical space for potential Lithium-ion battery localized high-concentration electrolyte (LHCE) diluents.

physics.chem-ph↗

arXiv2022

Mask and Reason: Pre-Training Knowledge Graph Transformers for Complex Logical Queries

Knowledge graph (KG) embeddings have been a mainstream approach for reasoning over incomplete KGs. However, limited by their inherently shallow and static architectures, they can hardly deal with the rising focus on complex logical queries, which comprise logical operators, imputed edges, multiple source entities, and unknown intermediate entities. In this work, we present the Knowledge Graph Transformer (kgTransformer) with masked pre-training and fine-tuning strategies. We design a KG triple transformation method to enable Transformer to handle KGs, which is further strengthened by the Mixture-of-Experts (MoE) sparse activation. We then formulate the complex logical queries as masked prediction and introduce a two-stage masked pre-training strategy to improve transferability and generalizability. Extensive experiments on two benchmarks demonstrate that kgTransformer can consistently outperform both KG embedding-based baselines and advanced encoders on nine in-domain and out-of-domain reasoning tasks. Additionally, kgTransformer can reason with explainability via providing the full reasoning paths to interpret given answers.

cs.LG↗