arXiv subjects

Nanning Zheng

Publications and source records attributed to Nanning Zheng.

At least 55 records · Page 3Linked to original sources

arXiv2024

Neural P$^3$M: A Long-Range Interaction Modeling Enhancer for Geometric GNNs

Geometric graph neural networks (GNNs) have emerged as powerful tools for modeling molecular geometry. However, they encounter limitations in effectively capturing long-range interactions in large molecular systems. To address this challenge, we introduce Neural P$^3$M, a versatile enhancer of geometric GNNs to expand the scope of their capabilities by incorporating mesh points alongside atoms and reimaging traditional mathematical operations in a trainable manner. Neural P$^3$M exhibits flexibility across a wide range of molecular systems and demonstrates remarkable accuracy in predicting energies and forces, outperforming on benchmarks such as the MD22 dataset. It also achieves an average improvement of 22% on the OE62 dataset while integrating with various architectures.

cs.LG↗

arXiv2024

PMT: Progressive Mean Teacher via Exploring Temporal Consistency for Semi-Supervised Medical Image Segmentation

Semi-supervised learning has emerged as a widely adopted technique in the field of medical image segmentation. The existing works either focuses on the construction of consistency constraints or the generation of pseudo labels to provide high-quality supervisory signals, whose main challenge mainly comes from how to keep the continuous improvement of model capabilities. In this paper, we propose a simple yet effective semi-supervised learning framework, termed Progressive Mean Teachers (PMT), for medical image segmentation, whose goal is to generate high-fidelity pseudo labels by learning robust and diverse features in the training process. Specifically, our PMT employs a standard mean teacher to penalize the consistency of the current state and utilizes two sets of MT architectures for co-training. The two sets of MT architectures are individually updated for prolonged periods to maintain stable model diversity established through performance gaps generated by iteration differences. Additionally, a difference-driven alignment regularizer is employed to expedite the alignment of lagging models with the representation capabilities of leading models. Furthermore, a simple yet effective pseudo-label filtering algorithm is employed for facile evaluation of models and selection of high-fidelity pseudo-labels outputted when models are operating at high performance for co-training purposes. Experimental results on two datasets with different modalities, i.e., CT and MRI, demonstrate that our method outperforms the state-of-the-art medical image segmentation approaches across various dimensions. The code is available at https://github.com/Axi404/PMT.

cs.CV↗

arXiv2024

Improving AlphaFlow for Efficient Protein Ensembles Generation

Investigating conformational landscapes of proteins is a crucial way to understand their biological functions and properties. AlphaFlow stands out as a sequence-conditioned generative model that introduces flexibility into structure prediction models by fine-tuning AlphaFold under the flow-matching framework. Despite the advantages of efficient sampling afforded by flow-matching, AlphaFlow still requires multiple runs of AlphaFold to finally generate one single conformation. Due to the heavy consumption of AlphaFold, its applicability is limited in sampling larger set of protein ensembles or the longer chains within a constrained timeframe. In this work, we propose a feature-conditioned generative model called AlphaFlow-Lit to realize efficient protein ensembles generation. In contrast to the full fine-tuning on the entire structure, we focus solely on the light-weight structure module to reconstruct the conformation. AlphaFlow-Lit performs on-par with AlphaFlow and surpasses its distilled version without pretraining, all while achieving a significant sampling acceleration of around 47 times. The advancement in efficiency showcases the potential of AlphaFlow-Lit in enabling faster and more scalable generation of protein ensembles.

cs.LG↗

arXiv2024

See Through Their Minds: Learning Transferable Neural Representation from Cross-Subject fMRI

Deciphering visual content from functional Magnetic Resonance Imaging (fMRI) helps illuminate the human vision system. However, the scarcity of fMRI data and noise hamper brain decoding model performance. Previous approaches primarily employ subject-specific models, sensitive to training sample size. In this paper, we explore a straightforward but overlooked solution to address data scarcity. We propose shallow subject-specific adapters to map cross-subject fMRI data into unified representations. Subsequently, a shared deeper decoding model decodes cross-subject features into the target feature space. During training, we leverage both visual and textual supervision for multi-modal brain decoding. Our model integrates a high-level perception decoding pipeline and a pixel-wise reconstruction pipeline guided by high-level perceptions, simulating bottom-up and top-down processes in neuroscience. Empirical experiments demonstrate robust neural representation learning across subjects for both pipelines. Moreover, merging high-level and low-level information improves both low-level and high-level reconstruction metrics. Additionally, we successfully transfer learned general knowledge to new subjects by training new adapters with limited training data. Compared to previous state-of-the-art methods, notably pre-training-based methods (Mind-Vis and fMRI-PTE), our approach achieves comparable or superior results across diverse tasks, showing promise as an alternative method for cross-subject fMRI data pre-training. Our code and pre-trained weights will be publicly released at https://github.com/YulongBonjour/See_Through_Their_Minds.

cs.CV↗

arXiv2024

Breaking through the learning plateaus of in-context learning in Transformer

In-context learning, i.e., learning from context examples, is an impressive ability of Transformer. Training Transformers to possess this in-context learning skill is computationally intensive due to the occurrence of learning plateaus, which are periods within the training process where there is minimal or no enhancement in the model's in-context learning capability. To study the mechanism behind the learning plateaus, we conceptually seperate a component within the model's internal representation that is exclusively affected by the model's weights. We call this the "weights component", and the remainder is identified as the "context component". By conducting meticulous and controlled experiments on synthetic tasks, we note that the persistence of learning plateaus correlates with compromised functionality of the weights component. Recognizing the impaired performance of the weights component as a fundamental behavior drives learning plateaus, we have developed three strategies to expedite the learning of Transformers. The effectiveness of these strategies is further confirmed in natural language processing tasks. In conclusion, our research demonstrates the feasibility of cultivating a powerful in-context learning ability within AI systems in an eco-friendly manner.

cs.LG↗

arXiv2024

Self-Consistency Training for Density-Functional-Theory Hamiltonian Prediction

Predicting the mean-field Hamiltonian matrix in density functional theory is a fundamental formulation to leverage machine learning for solving molecular science problems. Yet, its applicability is limited by insufficient labeled data for training. In this work, we highlight that Hamiltonian prediction possesses a self-consistency principle, based on which we propose self-consistency training, an exact training method that does not require labeled data. It distinguishes the task from predicting other molecular properties by the following benefits: (1) it enables the model to be trained on a large amount of unlabeled data, hence addresses the data scarcity challenge and enhances generalization; (2) it is more efficient than running DFT to generate labels for supervised training, since it amortizes DFT calculation over a set of queries. We empirically demonstrate the better generalization in data-scarce and out-of-distribution scenarios, and the better efficiency over DFT labeling. These benefits push forward the applicability of Hamiltonian prediction to an ever-larger scale.

cs.LG↗

arXiv2024

A General Theory for Compositional Generalization

Compositional Generalization (CG) embodies the ability to comprehend novel combinations of familiar concepts, representing a significant cognitive leap in human intellectual advancement. Despite its critical importance, the deep neural network (DNN) faces challenges in addressing the compositional generalization problem, prompting considerable research interest. However, existing theories often rely on task-specific assumptions, constraining the comprehensive understanding of CG. This study aims to explore compositional generalization from a task-agnostic perspective, offering a complementary viewpoint to task-specific analyses. The primary challenge is to define CG without overly restricting its scope, a feat achieved by identifying its fundamental characteristics and basing the definition on them. Using this definition, we seek to answer the question "what does the ultimate solution to CG look like?" through the following theoretical findings: 1) the first No Free Lunch theorem in CG, indicating the absence of general solutions; 2) a novel generalization bound applicable to any CG problem, specifying the conditions for an effective CG solution; and 3) the introduction of the generative effect to enhance understanding of CG problems and their solutions. This paper's significance lies in providing a general theory for CG problems, which, when combined with prior theorems under task-specific scenarios, can lead to a comprehensive understanding of CG.

cs.LG↗

arXiv2024

Text Grouping Adapter: Adapting Pre-trained Text Detector for Layout Analysis

Significant progress has been made in scene text detection models since the rise of deep learning, but scene text layout analysis, which aims to group detected text instances as paragraphs, has not kept pace. Previous works either treated text detection and grouping using separate models, or train a model from scratch while using a unified one. All of them have not yet made full use of the already well-trained text detectors and easily obtainable detection datasets. In this paper, we present Text Grouping Adapter (TGA), a module that can enable the utilization of various pre-trained text detectors to learn layout analysis, allowing us to adopt a well-trained text detector right off the shelf or just fine-tune it efficiently. Designed to be compatible with various text detector architectures, TGA takes detected text regions and image features as universal inputs to assemble text instance features. To capture broader contextual information for layout analysis, we propose to predict text group masks from text instance features by one-to-many assignment. Our comprehensive experiments demonstrate that, even with frozen pre-trained models, incorporating our TGA into various pre-trained text detectors and text spotters can achieve superior layout analysis performance, simultaneously inheriting generalized text detection ability from pre-training. In the case of full parameter fine-tuning, we can further improve layout analysis performance.

cs.CV↗

arXiv2024

F$^3$low: Frame-to-Frame Coarse-grained Molecular Dynamics with SE(3) Guided Flow Matching

Molecular dynamics (MD) is a crucial technique for simulating biological systems, enabling the exploration of their dynamic nature and fostering an understanding of their functions and properties. To address exploration inefficiency, emerging enhanced sampling approaches like coarse-graining (CG) and generative models have been employed. In this work, we propose a \underline{Frame-to-Frame} generative model with guided \underline{Flow}-matching (F$3$low) for enhanced sampling, which (a) extends the domain of CG modeling to the SE(3) Riemannian manifold; (b) retreating CGMD simulations as autoregressively sampling guided by the former frame via flow-matching models; (c) targets the protein backbone, offering improved insights into secondary structure formation and intricate folding pathways. Compared to previous methods, F$3$low allows for broader exploration of conformational space. The ability to rapidly generate diverse conformations via force-free generative paradigm on SE(3) paves the way toward efficient enhanced sampling methods.

q-bio.QM↗

arXiv2024

Make Your LLM Fully Utilize the Context

While many contemporary large language models (LLMs) can process lengthy input, they still struggle to fully utilize information within the long context, known as the lost-in-the-middle challenge. We hypothesize that it stems from insufficient explicit supervision during the long-context training, which fails to emphasize that any position in a long context can hold crucial information. Based on this intuition, our study presents information-intensive (IN2) training, a purely data-driven solution to overcome lost-in-the-middle. Specifically, IN2 training leverages a synthesized long-context question-answer dataset, where the answer requires (1) fine-grained information awareness on a short segment (~128 tokens) within a synthesized long context (4K-32K tokens), and (2) the integration and reasoning of information from two or more short segments. Through applying this information-intensive training on Mistral-7B, we present FILM-7B (FILl-in-the-Middle). To thoroughly assess the ability of FILM-7B for utilizing long contexts, we design three probing tasks that encompass various context styles (document, code, and structured-data context) and information retrieval patterns (forward, backward, and bi-directional retrieval). The probing results demonstrate that FILM-7B can robustly retrieve information from different positions in its 32K context window. Beyond these probing tasks, FILM-7B significantly improves the performance on real-world long-context tasks (e.g., 23.5->26.9 F1 score on NarrativeQA), while maintaining a comparable performance on short-context tasks (e.g., 59.3->59.2 accuracy on MMLU). Github Link: https://github.com/microsoft/FILM.

cs.CL↗

arXiv2024

Robust Noisy Label Learning via Two-Stream Sample Distillation

Noisy label learning aims to learn robust networks under the supervision of noisy labels, which plays a critical role in deep learning. Existing work either conducts sample selection or label correction to deal with noisy labels during the model training process. In this paper, we design a simple yet effective sample selection framework, termed Two-Stream Sample Distillation (TSSD), for noisy label learning, which can extract more high-quality samples with clean labels to improve the robustness of network training. Firstly, a novel Parallel Sample Division (PSD) module is designed to generate a certain training set with sufficient reliable positive and negative samples by jointly considering the sample structure in feature space and the human prior in loss space. Secondly, a novel Meta Sample Purification (MSP) module is further designed to mine adequate semi-hard samples from the remaining uncertain training set by learning a strong meta classifier with extra golden data. As a result, more and more high-quality samples will be distilled from the noisy training set to train networks robustly in every iteration. Extensive experiments on four benchmark datasets, including CIFAR-10, CIFAR-100, Tiny-ImageNet, and Clothing-1M, show that our method has achieved state-of-the-art results over its competitors.

cs.CV↗

arXiv2024

Learning From Mistakes Makes LLM Better Reasoner

Large language models (LLMs) recently exhibited remarkable reasoning capabilities on solving math problems. To further improve their reasoning capabilities, this work explores whether LLMs can LEarn from MistAkes (LEMA), akin to the human learning process. Consider a human student who failed to solve a math problem, he will learn from what mistake he has made and how to correct it. Mimicking this error-driven learning process, LEMA incorporates mistake-correction data pairs during fine-tuning LLMs. Specifically, we first collect inaccurate reasoning paths from various LLMs, and then employ GPT-4 as a ''corrector'' to identify the mistake step, explain the reason for the mistake, correct the mistake and generate the final answer. In addition, we apply a correction-centric evolution strategy that effectively expands the question set for generating correction data. Experiments across various LLMs and reasoning tasks show that LEMA effectively improves CoT-alone fine-tuning. Our further ablations shed light on the non-homogeneous effectiveness between CoT data and correction data. These results suggest a significant potential for LLMs to improve through learning from their mistakes. Our code, models and prompts are publicly available at https://github.com/microsoft/LEMA.

cs.CL↗

arXiv2024

Exploring Hardware Friendly Bottleneck Architecture in CNN for Embedded Computing Systems

In this paper, we explore how to design lightweight CNN architecture for embedded computing systems. We propose L-Mobilenet model for ZYNQ based hardware platform. L-Mobilenet can adapt well to the hardware computing and accelerating, and its network structure is inspired by the state-of-the-art work of Inception-ResnetV1 and MobilenetV2, which can effectively reduce parameters and delay while maintaining the accuracy of inference. We deploy our L-Mobilenet model to ZYNQ embedded platform for fully evaluating the performance of our design. By measuring in cifar10 and cifar100 datasets, L-Mobilenet model is able to gain 3x speed up and 3.7x fewer parameters than MobileNetV2 while maintaining a similar accuracy. It also can obtain 2x speed up and 1.5x fewer parameters than ShufflenetV2 while maintaining the same accuracy. Experiments show that our network model can obtain better performance because of the special considerations for hardware accelerating and software-hardware co-design strategies in our L-Mobilenet bottleneck architecture.

cs.CV↗

arXiv2024

Overcoming the Barrier of Orbital-Free Density Functional Theory for Molecular Systems Using Deep Learning

Orbital-free density functional theory (OFDFT) is a quantum chemistry formulation that has a lower cost scaling than the prevailing Kohn-Sham DFT, which is increasingly desired for contemporary molecular research. However, its accuracy is limited by the kinetic energy density functional, which is notoriously hard to approximate for non-periodic molecular systems. Here we propose M-OFDFT, an OFDFT approach capable of solving molecular systems using a deep learning functional model. We build the essential non-locality into the model, which is made affordable by the concise density representation as expansion coefficients under an atomic basis. With techniques to address unconventional learning challenges therein, M-OFDFT achieves a comparable accuracy with Kohn-Sham DFT on a wide range of molecules untouched by OFDFT before. More attractively, M-OFDFT extrapolates well to molecules much larger than those seen in training, which unleashes the appealing scaling of OFDFT for studying large molecules including proteins, representing an advancement of the accuracy-efficiency trade-off frontier in quantum chemistry.

stat.ML↗

arXiv2024

Common 7B Language Models Already Possess Strong Math Capabilities

Mathematical capabilities were previously believed to emerge in common language models only at a very large scale or require extensive math-related pre-training. This paper shows that the LLaMA-2 7B model with common pre-training already exhibits strong mathematical abilities, as evidenced by its impressive accuracy of 97.7% and 72.0% on the GSM8K and MATH benchmarks, respectively, when selecting the best response from 256 random generations. The primary issue with the current base model is the difficulty in consistently eliciting its inherent mathematical capabilities. Notably, the accuracy for the first answer drops to 49.5% and 7.9% on the GSM8K and MATH benchmarks, respectively. We find that simply scaling up the SFT data can significantly enhance the reliability of generating correct answers. However, the potential for extensive scaling is constrained by the scarcity of publicly available math questions. To overcome this limitation, we employ synthetic data, which proves to be nearly as effective as real data and shows no clear saturation when scaled up to approximately one million samples. This straightforward approach achieves an accuracy of 82.6% on GSM8K and 40.6% on MATH using LLaMA-2 7B models, surpassing previous models by 14.2% and 20.8%, respectively. We also provide insights into scaling behaviors across different reasoning complexities and error types.

cs.CL↗

arXiv2024

Leveraging Anchor-based LiDAR 3D Object Detection via Point Assisted Sample Selection

3D object detection based on LiDAR point cloud and prior anchor boxes is a critical technology for autonomous driving environment perception and understanding. Nevertheless, an overlooked practical issue in existing methods is the ambiguity in training sample allocation based on box Intersection over Union (IoU_box). This problem impedes further enhancements in the performance of anchor-based LiDAR 3D object detectors. To tackle this challenge, this paper introduces a new training sample selection method that utilizes point cloud distribution for anchor sample quality measurement, named Point Assisted Sample Selection (PASS). This method has undergone rigorous evaluation on two widely utilized datasets. Experimental results demonstrate that the application of PASS elevates the average precision of anchor-based LiDAR 3D object detectors to a novel state-of-the-art, thereby proving the effectiveness of the proposed approach. The codes will be made available at https://github.com/XJTU-Haolin/Point_Assisted_Sample_Selection.

cs.CV↗

arXiv2024

Voxel or Pillar: Exploring Efficient Point Cloud Representation for 3D Object Detection

Efficient representation of point clouds is fundamental for LiDAR-based 3D object detection. While recent grid-based detectors often encode point clouds into either voxels or pillars, the distinctions between these approaches remain underexplored. In this paper, we quantify the differences between the current encoding paradigms and highlight the limited vertical learning within. To tackle these limitations, we introduce a hybrid Voxel-Pillar Fusion network (VPF), which synergistically combines the unique strengths of both voxels and pillars. Specifically, we first develop a sparse voxel-pillar encoder that encodes point clouds into voxel and pillar features through 3D and 2D sparse convolutions respectively, and then introduce the Sparse Fusion Layer (SFL), facilitating bidirectional interaction between sparse voxel and pillar features. Our efficient, fully sparse method can be seamlessly integrated into both dense and sparse detectors. Leveraging this powerful yet straightforward framework, VPF delivers competitive performance, achieving real-time inference speeds on the nuScenes and Waymo Open Dataset. The code will be available.

cs.CV↗

arXiv2024

From Summary to Action: Enhancing Large Language Models for Complex Tasks with Open World APIs

The distinction between humans and animals lies in the unique ability of humans to use and create tools. Tools empower humans to overcome physiological limitations, fostering the creation of magnificent civilizations. Similarly, enabling foundational models like Large Language Models (LLMs) with the capacity to learn external tool usage may serve as a pivotal step toward realizing artificial general intelligence. Previous studies in this field have predominantly pursued two distinct approaches to augment the tool invocation capabilities of LLMs. The first approach emphasizes the construction of relevant datasets for model fine-tuning. The second approach, in contrast, aims to fully exploit the inherent reasoning abilities of LLMs through in-context learning strategies. In this work, we introduce a novel tool invocation pipeline designed to control massive real-world APIs. This pipeline mirrors the human task-solving process, addressing complicated real-life user queries. At each step, we guide LLMs to summarize the achieved results and determine the next course of action. We term this pipeline `from Summary to action', Sum2Act for short. Empirical evaluations of our Sum2Act pipeline on the ToolBench benchmark show significant performance improvements, outperforming established methods like ReAct and DFSDT. This highlights Sum2Act's effectiveness in enhancing LLMs for complex real-world tasks.

cs.AI↗