Daily Papers

Code understanding models increasingly rely on pretrained language models (PLMs) and graph neural networks (GNNs), which capture complementary semantic and structural information. We conduct a controlled empirical study of PLM-GNN hybrids for code classification and vulnerability detection tasks by systematically pairing three code-specialized PLMs with three foundational GNN architectures. We compare these hybrids against PLM-only and GNN-only baselines on Java250 and Devign, including an identifier-obfuscation setting. Across both tasks, hybrids consistently outperform GNN-only baselines and often improve ranking quality over frozen PLMs. On Devign, performance and robustness are more sensitive to the PLM feature source than to the GNN backbone. We also find that larger PLMs are not necessarily better feature extractors in this pipeline, and that the PLM choice has more impact than the GNN choice. Finally, we distill these findings into practical guidelines for PLM-GNN design choices in code classification and vulnerability detection.

Hybrid model architectures that combine computational primitives (e.g., Attention, MLP) in different ratios have shown promising performance beyond Transformers. Some studies have shown that different interleavings of primitives can affect model quality as well. However, prior works explore the hybrid model architecture design space manually. Due to the large design space and training costs, discovering hybrid models that combine key computational primitives for pre-training is challenging. In this work, we take a principled approach in designing a modular hybrid model architecture search framework -- Composer. Composer explores model architectures at a small scale and extrapolates the top-performing model architectures to a larger scale using our proposed scaling strategies. Using Composer, we discover new hybrid LLM architectures that outperform Llama 3.2. Compared to Llama 3.2 and previous state-of-the-art baselines, the new model architectures consistently reduce validation loss at parameter scales of 350M-3B and improve evaluation accuracy on the downstream tasks by up to 2.8-8.3% (1.1-3.1% on average) while improving both training and inference efficiency.

This paper presents a novel hybrid model that integrates long-short-term memory (LSTM) networks and Graph Neural Networks (GNNs) to significantly enhance the accuracy of stock market predictions. The LSTM component adeptly captures temporal patterns in stock price data, effectively modeling the time series dynamics of financial markets. Concurrently, the GNN component leverages Pearson correlation and association analysis to model inter-stock relational data, capturing complex nonlinear polyadic dependencies influencing stock prices. The model is trained and evaluated using an expanding window validation approach, enabling continuous learning from increasing amounts of data and adaptation to evolving market conditions. Extensive experiments conducted on historical stock data demonstrate that our hybrid LSTM-GNN model achieves a mean square error (MSE) of 0.00144, representing a substantial reduction of 10.6% compared to the MSE of the standalone LSTM model of 0.00161. Furthermore, the hybrid model outperforms traditional and advanced benchmarks, including linear regression, convolutional neural networks (CNN), and dense networks. These compelling results underscore the significant potential of combining temporal and relational data through a hybrid approach, offering a powerful tool for real-time trading and financial analysis.

Transformers have become the de facto architecture for a wide range of machine learning tasks, particularly in large language models (LLMs). Despite their remarkable performance, challenges remain in training deep transformer networks, especially regarding the location of layer normalization. While Pre-Norm structures facilitate easier training due to their more prominent identity path, they often yield suboptimal performance compared to Post-Norm. In this paper, we propose HybridNorm, a straightforward yet effective hybrid normalization strategy that integrates the advantages of both Pre-Norm and Post-Norm approaches. Specifically, HybridNorm employs QKV normalization within the attention mechanism and Post-Norm in the feed-forward network (FFN) of each transformer block. This design not only stabilizes training but also enhances performance, particularly in the context of LLMs. Comprehensive experiments in both dense and sparse architectures show that HybridNorm consistently outperforms both Pre-Norm and Post-Norm approaches, achieving state-of-the-art results across various benchmarks. These findings highlight the potential of HybridNorm as a more stable and effective technique for improving the training and performance of deep transformer models. %Code will be made publicly available. Code is available at https://github.com/BryceZhuo/HybridNorm.

Convolutional Neural Networks (CNN) are known to exhibit poor generalization performance under distribution shifts. Their generalization have been studied extensively, and one line of work approaches the problem from a frequency-centric perspective. These studies highlight the fact that humans and CNNs might focus on different frequency components of an image. First, inspired by these observations, we propose a simple yet effective data augmentation method HybridAugment that reduces the reliance of CNNs on high-frequency components, and thus improves their robustness while keeping their clean accuracy high. Second, we propose HybridAugment++, which is a hierarchical augmentation method that attempts to unify various frequency-spectrum augmentations. HybridAugment++ builds on HybridAugment, and also reduces the reliance of CNNs on the amplitude component of images, and promotes phase information instead. This unification results in competitive to or better than state-of-the-art results on clean accuracy (CIFAR-10/100 and ImageNet), corruption benchmarks (ImageNet-C, CIFAR-10-C and CIFAR-100-C), adversarial robustness on CIFAR-10 and out-of-distribution detection on various datasets. HybridAugment and HybridAugment++ are implemented in a few lines of code, does not require extra data, ensemble models or additional networks.

Recent progress in large language models demonstrates that hybrid architectures--combining self-attention mechanisms with structured state space models like Mamba--can achieve a compelling balance between modeling quality and computational efficiency, particularly for long-context tasks. While these hybrid models show promising performance, systematic comparisons of hybridization strategies and analyses on the key factors behind their effectiveness have not been clearly shared to the community. In this work, we present a holistic evaluation of hybrid architectures based on inter-layer (sequential) or intra-layer (parallel) fusion. We evaluate these designs from a variety of perspectives: language modeling performance, long-context capabilities, scaling analysis, and training and inference efficiency. By investigating the core characteristics of their computational primitive, we identify the most critical elements for each hybridization strategy and further propose optimal design recipes for both hybrid models. Our comprehensive analysis provides practical guidance and valuable insights for developing hybrid language models, facilitating the optimization of architectural configurations.

The consensus that GCN, GraphSAGE, GAT, and EvolveGCN outperform feature-only baselines on the Elliptic Bitcoin Dataset is widely cited but has not been rigorously stress-tested under a leakage-free evaluation protocol. We perform a seed-matched inductive-versus-transductive comparison and find that this consensus does not hold. Under a strictly inductive protocol, Random Forest on raw features achieves F1 = 0.821 and outperforms all evaluated GNNs, while GraphSAGE reaches F1 = 0.689 +/- 0.017. A paired controlled experiment reveals a 39.5-point F1 gap attributable to training-time exposure to test-period adjacency. Additionally, edge-shuffle ablations show that randomly wired graphs outperform the real transaction graph, indicating that the dataset's topology can be misleading under temporal distribution shift. Hybrid models combining GNN embeddings with raw features provide only marginal gains and remain substantially below feature-only baselines. We release code, checkpoints, and a strict-inductive protocol to enable reproducible, leakage-free evaluation.

Recent research on integrating Large Language Models (LLMs) with Graph Neural Networks (GNNs) typically follows two approaches: LLM-centered models, which convert graph data into tokens for LLM processing, and GNN-centered models, which use LLMs to encode text features into node and edge representations for GNN input. LLM-centered models often struggle to capture graph structures effectively, while GNN-centered models compress variable-length textual data into fixed-size vectors, limiting their ability to understand complex semantics. Additionally, GNN-centered approaches require converting tasks into a uniform, manually-designed format, restricting them to classification tasks and preventing language output. To address these limitations, we introduce a new architecture that deeply integrates GNN with LLM, featuring three key innovations: (1) Structure-Aware Transformers, which incorporate GNN's message-passing capabilities directly into LLM's transformer layers, allowing simultaneous processing of textual and structural information and generating outputs from both GNN and LLM; (2) Graph-Text Cross-Attention, which processes full, uncompressed text from graph nodes and edges, ensuring complete semantic integration; and (3) GNN-LLM Twin Predictor, enabling LLM's flexible autoregressive generation alongside GNN's scalable one-pass prediction. GL-Fusion achieves outstand performance on various tasks. Notably, it achieves state-of-the-art performance on OGBN-Arxiv and OGBG-Code2.

Prediction of protein-ligand (PL) binding affinity remains the key to drug discovery. Popular approaches in recent years involve graph neural networks (GNNs), which are used to learn the topology and geometry of PL complexes. However, GNNs are computationally heavy and have poor scalability to graph sizes. On the other hand, traditional machine learning (ML) approaches, such as gradient-boosted decision trees (GBDTs), are lightweight yet extremely efficient for tabular data. We propose to use PL interaction features along with PL graph-level features in GBDT. We show that this combination outperforms the existing solutions.

Fine-tuning a pre-trained language model (PLM) emerges as the predominant strategy in many natural language processing applications. However, even fine-tuning the PLMs and doing inference are expensive, especially on edge devices with low computing power. Some general approaches (e.g. quantization and distillation) have been widely studied to reduce the compute/memory of PLM fine-tuning, while very few one-shot compression techniques are explored. In this paper, we investigate the neural tangent kernel (NTK)--which reveals the gradient descent dynamics of neural networks--of the multilayer perceptrons (MLP) modules in a PLM and propose to coin a lightweight PLM through NTK-approximating MLP fusion. To achieve this, we reconsider the MLP as a bundle of sub-MLPs, and cluster them into a given number of centroids, which can then be restored as a compressed MLP and surprisingly shown to well approximate the NTK of the original PLM. Extensive experiments of PLM fine-tuning on both natural language understanding (NLU) and generation (NLG) tasks are provided to verify the effectiveness of the proposed method MLP fusion. Our code is available at https://github.com/weitianxin/MLP_Fusion.

Large language models (LLMs) mark a key shift in natural language processing (NLP), having advanced text generation, translation, and domain-specific reasoning. Closed-source models like GPT-4, powered by proprietary datasets and extensive computational resources, lead with state-of-the-art performance today. However, they face criticism for their "black box" nature and for limiting accessibility in a manner that hinders reproducibility and equitable AI development. By contrast, open-source initiatives like LLaMA and BLOOM prioritize democratization through community-driven development and computational efficiency. These models have significantly reduced performance gaps, particularly in linguistic diversity and domain-specific applications, while providing accessible tools for global researchers and developers. Notably, both paradigms rely on foundational architectural innovations, such as the Transformer framework by Vaswani et al. (2017). Closed-source models excel by scaling effectively, while open-source models adapt to real-world applications in underrepresented languages and domains. Techniques like Low-Rank Adaptation (LoRA) and instruction-tuning datasets enable open-source models to achieve competitive results despite limited resources. To be sure, the tension between closed-source and open-source approaches underscores a broader debate on transparency versus proprietary control in AI. Ethical considerations further highlight this divide. Closed-source systems restrict external scrutiny, while open-source models promote reproducibility and collaboration but lack standardized auditing documentation frameworks to mitigate biases. Hybrid approaches that leverage the strengths of both paradigms are likely to shape the future of LLM innovation, ensuring accessibility, competitive technical performance, and ethical deployment.

Data generation-based zero-shot learning, although effective in training Small Task-specific Models (STMs) via synthetic datasets generated by Pre-trained Language Models (PLMs), is often limited by the low quality of such synthetic datasets. Previous solutions have primarily focused on single PLM settings, where synthetic datasets are typically restricted to specific sub-spaces and often deviate from real-world distributions, leading to severe distribution bias. To mitigate such bias, we propose FuseGen, a novel data generation-based zero-shot learning framework that introduces a new criteria for subset selection from synthetic datasets via utilizing multiple PLMs and trained STMs. The chosen subset provides in-context feedback to each PLM, enhancing dataset quality through iterative data generation. Trained STMs are then used for sample re-weighting as well, further improving data quality. Extensive experiments across diverse tasks demonstrate that FuseGen substantially outperforms existing methods, highly effective in boosting STM performance in a PLM-agnostic way. Code is provided in https://github.com/LindaLydia/FuseGen.

As a branch of advanced artificial intelligence, dialogue systems are prospering. Multi-turn response selection is a general research problem in dialogue systems. With the assistance of background information and pre-trained language models, the performance of state-of-the-art methods on this problem gains impressive improvement. However, existing studies neglect the importance of external commonsense knowledge. Hence, we design a Siamese network where a pre-trained Language model merges with a Graph neural network (SinLG). SinLG takes advantage of Pre-trained Language Models (PLMs) to catch the word correlations in the context and response candidates and utilizes a Graph Neural Network (GNN) to reason helpful common sense from an external knowledge graph. The GNN aims to assist the PLM in fine-tuning, and arousing its related memories to attain better performance. Specifically, we first extract related concepts as nodes from an external knowledge graph to construct a subgraph with the context response pair as a super node for each sample. Next, we learn two representations for the context response pair via both the PLM and GNN. A similarity loss between the two representations is utilized to transfer the commonsense knowledge from the GNN to the PLM. Then only the PLM is used to infer online so that efficiency can be guaranteed. Finally, we conduct extensive experiments on two variants of the PERSONA-CHAT dataset, which proves that our solution can not only improve the performance of the PLM but also achieve an efficient inference.

Recent prevailing works on graph machine learning typically follow a similar methodology that involves designing advanced variants of graph neural networks (GNNs) to maintain the superior performance of GNNs on different graphs. In this paper, we aim to streamline the GNN design process and leverage the advantages of Large Language Models (LLMs) to improve the performance of GNNs on downstream tasks. We formulate a new paradigm, coined "LLMs-as-Consultants," which integrates LLMs with GNNs in an interactive manner. A framework named LOGIN (LLM Consulted GNN training) is instantiated, empowering the interactive utilization of LLMs within the GNN training process. First, we attentively craft concise prompts for spotted nodes, carrying comprehensive semantic and topological information, and serving as input to LLMs. Second, we refine GNNs by devising a complementary coping mechanism that utilizes the responses from LLMs, depending on their correctness. We empirically evaluate the effectiveness of LOGIN on node classification tasks across both homophilic and heterophilic graphs. The results illustrate that even basic GNN architectures, when employed within the proposed LLMs-as-Consultants paradigm, can achieve comparable performance to advanced GNNs with intricate designs. Our codes are available at https://github.com/QiaoYRan/LOGIN.

Graph mining is an important area in data mining and machine learning that involves extracting valuable information from graph-structured data. In recent years, significant progress has been made in this field through the development of graph neural networks (GNNs). However, GNNs are still deficient in generalizing to diverse graph data. Aiming to this issue, Large Language Models (LLMs) could provide new solutions for graph mining tasks with their superior semantic understanding. In this review, we systematically review the combination and application techniques of LLMs and GNNs and present a novel taxonomy for research in this interdisciplinary field, which involves three main categories: GNN-driving-LLM, LLM-driving-GNN, and GNN-LLM-co-driving. Within this framework, we reveal the capabilities of LLMs in enhancing graph feature extraction as well as improving the effectiveness of downstream tasks such as node classification, link prediction, and community detection. Although LLMs have demonstrated their great potential in handling graph-structured data, their high computational requirements and complexity remain challenges. Future research needs to continue to explore how to efficiently fuse LLMs and GNNs to achieve more powerful graph learning and reasoning capabilities and provide new impetus for the development of graph mining techniques.

This study presents a systematic comparison between hybrid quantum-classical neural networks and purely classical models across three benchmark datasets (MNIST, CIFAR100, and STL10) to evaluate their performance, efficiency, and robustness. The hybrid models integrate parameterized quantum circuits with classical deep learning architectures, while the classical counterparts use conventional convolutional neural networks (CNNs). Experiments were conducted over 50 training epochs for each dataset, with evaluations on validation accuracy, test accuracy, training time, computational resource usage, and adversarial robustness (tested with epsilon=0.1 perturbations).Key findings demonstrate that hybrid models consistently outperform classical models in final accuracy, achieving {99.38\% (MNIST), 41.69\% (CIFAR100), and 74.05\% (STL10) validation accuracy, compared to classical benchmarks of 98.21\%, 32.25\%, and 63.76\%, respectively. Notably, the hybrid advantage scales with dataset complexity, showing the most significant gains on CIFAR100 (+9.44\%) and STL10 (+10.29\%). Hybrid models also train 5--12times faster (e.g., 21.23s vs. 108.44s per epoch on MNIST) and use 6--32\% fewer parameters} while maintaining superior generalization to unseen test data.Adversarial robustness tests reveal that hybrid models are significantly more resilient on simpler datasets (e.g., 45.27\% robust accuracy on MNIST vs. 10.80\% for classical) but show comparable fragility on complex datasets like CIFAR100 (sim1\% robustness for both). Resource efficiency analyses indicate that hybrid models consume less memory (4--5GB vs. 5--6GB for classical) and lower CPU utilization (9.5\% vs. 23.2\% on average).These results suggest that hybrid quantum-classical architectures offer compelling advantages in accuracy, training efficiency, and parameter scalability, particularly for complex vision tasks.

Neural fields have become widely used in various fields, from shape representation to neural rendering, and for solving partial differential equations (PDEs). With the advent of hybrid neural field representations like Instant NGP that leverage small MLPs and explicit representations, these models train quickly and can fit large scenes. Yet in many applications like rendering and simulation, hybrid neural fields can cause noticeable and unreasonable artifacts. This is because they do not yield accurate spatial derivatives needed for these downstream applications. In this work, we propose two ways to circumvent these challenges. Our first approach is a post hoc operator that uses local polynomial fitting to obtain more accurate derivatives from pre-trained hybrid neural fields. Additionally, we also propose a self-supervised fine-tuning approach that refines the hybrid neural field to yield accurate derivatives directly while preserving the initial signal. We show applications of our method to rendering, collision simulation, and solving PDEs. We observe that using our approach yields more accurate derivatives, reducing artifacts and leading to more accurate simulations in downstream applications.

Planning is a fundamental property of human intelligence. Reasoning about asynchronous plans is challenging since it requires sequential and parallel planning to optimize time costs. Can large language models (LLMs) succeed at this task? Here, we present the first large-scale study investigating this question. We find that a representative set of closed and open-source LLMs, including GPT-4 and LLaMA-2, behave poorly when not supplied with illustrations about the task-solving process in our benchmark AsyncHow. We propose a novel technique called Plan Like a Graph (PLaG) that combines graphs with natural language prompts and achieves state-of-the-art results. We show that although PLaG can boost model performance, LLMs still suffer from drastic degradation when task complexity increases, highlighting the limits of utilizing LLMs for simulating digital devices. We see our study as an exciting step towards using LLMs as efficient autonomous agents. Our code and data are available at https://github.com/fangru-lin/graph-llm-asynchow-plan.

In recent years, there have been remarkable advancements in node classification achieved by Graph Neural Networks (GNNs). However, they necessitate abundant high-quality labels to ensure promising performance. In contrast, Large Language Models (LLMs) exhibit impressive zero-shot proficiency on text-attributed graphs. Yet, they face challenges in efficiently processing structural data and suffer from high inference costs. In light of these observations, this work introduces a label-free node classification on graphs with LLMs pipeline, LLM-GNN. It amalgamates the strengths of both GNNs and LLMs while mitigating their limitations. Specifically, LLMs are leveraged to annotate a small portion of nodes and then GNNs are trained on LLMs' annotations to make predictions for the remaining large portion of nodes. The implementation of LLM-GNN faces a unique challenge: how can we actively select nodes for LLMs to annotate and consequently enhance the GNN training? How can we leverage LLMs to obtain annotations of high quality, representativeness, and diversity, thereby enhancing GNN performance with less cost? To tackle this challenge, we develop an annotation quality heuristic and leverage the confidence scores derived from LLMs to advanced node selection. Comprehensive experimental results validate the effectiveness of LLM-GNN. In particular, LLM-GNN can achieve an accuracy of 74.9% on a vast-scale dataset \products with a cost less than 1 dollar.

Large Language Models (LLMs) have shown remarkable generalization capability with exceptional performance in various language modeling tasks. However, they still exhibit inherent limitations in precisely capturing and returning grounded knowledge. While existing work has explored utilizing knowledge graphs to enhance language modeling via joint training and customized model architectures, applying this to LLMs is problematic owing to their large number of parameters and high computational cost. In addition, how to leverage the pre-trained LLMs and avoid training a customized model from scratch remains an open question. In this work, we propose Graph Neural Prompting (GNP), a novel plug-and-play method to assist pre-trained LLMs in learning beneficial knowledge from KGs. GNP encompasses various designs, including a standard graph neural network encoder, a cross-modality pooling module, a domain projector, and a self-supervised link prediction objective. Extensive experiments on multiple datasets demonstrate the superiority of GNP on both commonsense and biomedical reasoning tasks across different LLM sizes and settings.

Hybrid systems are prevalent in robotics. However, ensuring the stability of hybrid systems is challenging due to sophisticated continuous and discrete dynamics. A system with all its system modes stable can still be unstable. Hence special treatments are required at mode switchings to stabilize the system. In this work, we propose a hierarchical, neural network (NN)-based method to control general hybrid systems. For each system mode, we first learn an NN Lyapunov function and an NN controller to ensure the states within the region of attraction (RoA) can be stabilized. Then an RoA NN estimator is learned across different modes. Upon mode switching, we propose a differentiable planner to ensure the states after switching can land in next mode's RoA, hence stabilizing the hybrid system. We provide novel theoretical stability guarantees and conduct experiments in car tracking control, pogobot navigation, and bipedal walker locomotion. Our method only requires 0.25X of the training time as needed by other learning-based methods. With low running time (10-50X faster than model predictive control (MPC)), our controller achieves a higher stability/success rate over other baselines such as MPC, reinforcement learning (RL), common Lyapunov methods (CLF), linear quadratic regulator (LQR), quadratic programming (QP) and Hamilton-Jacobian-based methods (HJB). The project page is on https://mit-realm.github.io/hybrid-clf.

Graph Neural Networks (GNNs) have shown great potential in the field of graph representation learning. Standard GNNs define a local message-passing mechanism which propagates information over the whole graph domain by stacking multiple layers. This paradigm suffers from two major limitations, over-squashing and poor long-range dependencies, that can be solved using global attention but significantly increases the computational cost to quadratic complexity. In this work, we propose an alternative approach to overcome these structural limitations by leveraging the ViT/MLP-Mixer architectures introduced in computer vision. We introduce a new class of GNNs, called Graph ViT/MLP-Mixer, that holds three key properties. First, they capture long-range dependency and mitigate the issue of over-squashing as demonstrated on Long Range Graph Benchmark and TreeNeighbourMatch datasets. Second, they offer better speed and memory efficiency with a complexity linear to the number of nodes and edges, surpassing the related Graph Transformer and expressive GNN models. Third, they show high expressivity in terms of graph isomorphism as they can distinguish at least 3-WL non-isomorphic graphs. We test our architecture on 4 simulated datasets and 7 real-world benchmarks, and show highly competitive results on all of them. The source code is available for reproducibility at: https://github.com/XiaoxinHe/Graph-ViT-MLPMixer.

While scaling laws have been continuously validated in large language models (LLMs) with increasing model parameters, the inherent tension between the inference demands of LLMs and the limited resources of edge devices poses a critical challenge to the development of edge intelligence. Recently, numerous small language models have emerged, aiming to distill the capabilities of LLMs into smaller footprints. However, these models often retain the fundamental architectural principles of their larger counterparts, still imposing considerable strain on the storage and bandwidth capacities of edge devices. In this paper, we introduce the PLM, a Peripheral Language Model, developed through a co-design process that jointly optimizes model architecture and edge system constraints. The PLM utilizes a Multi-head Latent Attention mechanism and employs the squared ReLU activation function to encourage sparsity, thereby reducing peak memory footprint during inference. During training, we collect and reorganize open-source datasets, implement a multi-phase training strategy, and empirically investigate the Warmup-Stable-Decay-Constant (WSDC) learning rate scheduler. Additionally, we incorporate Reinforcement Learning from Human Feedback (RLHF) by adopting the ARIES preference learning approach. Following a two-phase SFT process, this method yields performance gains of 2% in general tasks, 9% in the GSM8K task, and 11% in coding tasks. In addition to its novel architecture, evaluation results demonstrate that PLM outperforms existing small language models trained on publicly available data while maintaining the lowest number of activated parameters. Furthermore, deployment across various edge devices, including consumer-grade GPUs, mobile phones, and Raspberry Pis, validates PLM's suitability for peripheral applications. The PLM series models are publicly available at https://github.com/plm-team/PLM.

Hybrid LLM architectures that combine Attention and State Space Models (SSMs) achieve state-of-the-art accuracy and runtime performance. Recent work has demonstrated that applying compression and distillation to Attention-only models yields smaller, more accurate models at a fraction of the training cost. In this work, we explore the effectiveness of compressing Hybrid architectures. We introduce a novel group-aware pruning strategy that preserves the structural integrity of SSM blocks and their sequence modeling capabilities. Furthermore, we demonstrate the necessity of such SSM pruning to achieve improved accuracy and inference speed compared to traditional approaches. Our compression recipe combines SSM, FFN, embedding dimension, and layer pruning, followed by knowledge distillation-based retraining, similar to the MINITRON technique. Using this approach, we compress the Nemotron-H 8B Hybrid model down to 4B parameters with up to 40x fewer training tokens. The resulting model surpasses the accuracy of similarly-sized models while achieving 2x faster inference, significantly advancing the Pareto frontier.

Combining different models is a widely used paradigm in machine learning applications. While the most common approach is to form an ensemble of models and average their individual predictions, this approach is often rendered infeasible by given resource constraints in terms of memory and computation, which grow linearly with the number of models. We present a layer-wise model fusion algorithm for neural networks that utilizes optimal transport to (soft-) align neurons across the models before averaging their associated parameters. We show that this can successfully yield "one-shot" knowledge transfer (i.e, without requiring any retraining) between neural networks trained on heterogeneous non-i.i.d. data. In both i.i.d. and non-i.i.d. settings , we illustrate that our approach significantly outperforms vanilla averaging, as well as how it can serve as an efficient replacement for the ensemble with moderate fine-tuning, for standard convolutional networks (like VGG11), residual networks (like ResNet18), and multi-layer perceptrons on CIFAR10, CIFAR100, and MNIST. Finally, our approach also provides a principled way to combine the parameters of neural networks with different widths, and we explore its application for model compression. The code is available at the following link, https://github.com/sidak/otfusion.

Recent work has demonstrated the potential of non-transformer language models, especially linear recurrent neural networks (RNNs) and hybrid models that mix recurrence and attention. Yet there is no consensus on whether the potential benefits of these new architectures justify the risk and effort of scaling them up. To address this, we provide evidence for the advantages of hybrid models over pure transformers on several fronts. First, theoretically, we show that hybrid models do not merely inherit the expressivity of transformers and linear RNNs, but can express tasks beyond both, such as code execution. Putting this theory to practice, we train Olmo Hybrid, a 7B-parameter model largely comparable to Olmo 3 7B but with the sliding window layers replaced by Gated DeltaNet layers. We show that Olmo Hybrid outperforms Olmo 3 across standard pretraining and mid-training evaluations, demonstrating the benefit of hybrid models in a controlled, large-scale setting. We find that the hybrid model scales significantly more efficiently than the transformer, explaining its higher performance. However, its unclear why greater expressivity on specific formal problems should result in better scaling or superior performance on downstream tasks unrelated to those problems. To explain this apparent gap, we return to theory and argue why increased expressivity should translate to better scaling efficiency, completing the loop. Overall, our results suggest that hybrid models mixing attention and recurrent layers are a powerful extension to the language modeling paradigm: not merely to reduce memory during inference, but as a fundamental way to obtain more expressive models that scale better during pretraining.

In this work, we consider the problem of deriving and incorporating accurate dynamic models for model predictive control (MPC) with an application to quadrotor control. MPC relies on precise dynamic models to achieve the desired closed-loop performance. However, the presence of uncertainties in complex systems and the environments they operate in poses a challenge in obtaining sufficiently accurate representations of the system dynamics. In this work, we make use of a deep learning tool, knowledge-based neural ordinary differential equations (KNODE), to augment a model obtained from first principles. The resulting hybrid model encompasses both a nominal first-principle model and a neural network learnt from simulated or real-world experimental data. Using a quadrotor, we benchmark our hybrid model against a state-of-the-art Gaussian Process (GP) model and show that the hybrid model provides more accurate predictions of the quadrotor dynamics and is able to generalize beyond the training data. To improve closed-loop performance, the hybrid model is integrated into a novel MPC framework, known as KNODE-MPC. Results show that the integrated framework achieves 60.2% improvement in simulations and more than 21% in physical experiments, in terms of trajectory tracking performance.

Recent years have witnessed the great success of Graph Neural Networks (GNNs) in handling graph-related tasks. However, MLPs remain the primary workhorse for practical industrial applications due to their desirable inference efficiency and scalability. To reduce their gaps, one can directly distill knowledge from a well-designed teacher GNN to a student MLP, which is termed as GNN-to-MLP distillation. However, the process of distillation usually entails a loss of information, and ``which knowledge patterns of GNNs are more likely to be left and distilled into MLPs?" becomes an important question. In this paper, we first factorize the knowledge learned by GNNs into low- and high-frequency components in the spectral domain and then derive their correspondence in the spatial domain. Furthermore, we identified a potential information drowning problem for existing GNN-to-MLP distillation, i.e., the high-frequency knowledge of the pre-trained GNNs may be overwhelmed by the low-frequency knowledge during distillation; we have described in detail what it represents, how it arises, what impact it has, and how to deal with it. In this paper, we propose an efficient Full-Frequency GNN-to-MLP (FF-G2M) distillation framework, which extracts both low-frequency and high-frequency knowledge from GNNs and injects it into MLPs. Extensive experiments show that FF-G2M improves over the vanilla MLPs by 12.6% and outperforms its corresponding teacher GNNs by 2.6% averaged over six graph datasets and three common GNN architectures.

Graph Neural Architecture Search (GNAS) facilitates the automatic design of Graph Neural Networks (GNNs) tailored to specific downstream graph learning tasks. However, existing GNAS approaches often require manual adaptation to new graph search spaces, necessitating substantial code optimization and domain-specific knowledge. To address this challenge, we present LLM4GNAS, a toolkit for GNAS that leverages the generative capabilities of Large Language Models (LLMs). LLM4GNAS includes an algorithm library for graph neural architecture search algorithms based on LLMs, enabling the adaptation of GNAS methods to new search spaces through the modification of LLM prompts. This approach reduces the need for manual intervention in algorithm adaptation and code modification. The LLM4GNAS toolkit is extensible and robust, incorporating LLM-enhanced graph feature engineering, LLM-enhanced graph neural architecture search, and LLM-enhanced hyperparameter optimization. Experimental results indicate that LLM4GNAS outperforms existing GNAS methods on tasks involving both homogeneous and heterogeneous graphs.

To understand the learning process in brains, biologically plausible algorithms have been explored by modeling the detailed neuron properties and dynamics. On the other hand, simplified multi-layer models of neural networks have shown great success on computational tasks such as image classification and speech recognition. However, the computational models that can achieve good accuracy for these learning applications are very different from the bio-plausible models. This paper studies whether a bio-plausible model of a in vitro living neural network can be used to perform machine learning tasks and achieve good inference accuracy. A novel two-layer bio-hardware hybrid neural network is proposed. The biological layer faithfully models variations of synapses, neurons, and network sparsity in in vitro living neural networks. The hardware layer is a computational fully-connected layer that tunes parameters to optimize for accuracy. Several techniques are proposed to improve the inference accuracy of the proposed hybrid neural network. For instance, an adaptive pre-processing technique helps the proposed neural network to achieve good learning accuracy for different living neural network sparsity. The proposed hybrid neural network with realistic neuron parameters and variations achieves a 98.3% testing accuracy for the handwritten digit recognition task on the full MNIST dataset.

Integrating first-order logic constraints (FOLCs) with neural networks is a crucial but challenging problem since it involves modeling intricate correlations to satisfy the constraints. This paper proposes a novel neural layer, LogicMP, whose layers perform mean-field variational inference over an MLN. It can be plugged into any off-the-shelf neural network to encode FOLCs while retaining modularity and efficiency. By exploiting the structure and symmetries in MLNs, we theoretically demonstrate that our well-designed, efficient mean-field iterations effectively mitigate the difficulty of MLN inference, reducing the inference from sequential calculation to a series of parallel tensor operations. Empirical results in three kinds of tasks over graphs, images, and text show that LogicMP outperforms advanced competitors in both performance and efficiency.

Breast cancer is a common cancer for women. Early detection of breast cancer can considerably increase the survival rate of women. This paper mainly focuses on transfer learning process to detect breast cancer. Modified VGG (MVGG), residual network, mobile network is proposed and implemented in this paper. DDSM dataset is used in this paper. Experimental results show that our proposed hybrid transfers learning model (Fusion of MVGG16 and ImageNet) provides an accuracy of 88.3% where the number of epoch is 15. On the other hand, only modified VGG 16 architecture (MVGG 16) provides an accuracy 80.8% and MobileNet provides an accuracy of 77.2%. So, it is clearly stated that the proposed hybrid pre-trained network outperforms well compared to single architecture. This architecture can be considered as an effective tool for the radiologists in order to reduce the false negative and false positive rate. Therefore, the efficiency of mammography analysis will be improved.

Hybrid RL is the setting where an RL agent has access to both offline data and online data by interacting with the real-world environment. In this work, we propose a new hybrid RL algorithm that combines an on-policy actor-critic method with offline data. On-policy methods such as policy gradient and natural policy gradient (NPG) have shown to be more robust to model misspecification, though sometimes it may not be as sample efficient as methods that rely on off-policy learning. On the other hand, offline methods that depend on off-policy training often require strong assumptions in theory and are less stable to train in practice. Our new approach integrates a procedure of off-policy training on the offline data into an on-policy NPG framework. We show that our approach, in theory, can obtain a best-of-both-worlds type of result -- it achieves the state-of-art theoretical guarantees of offline RL when offline RL-specific assumptions hold, while at the same time maintaining the theoretical guarantees of on-policy NPG regardless of the offline RL assumptions' validity. Experimentally, in challenging rich-observation environments, we show that our approach outperforms a state-of-the-art hybrid RL baseline which only relies on off-policy policy optimization, demonstrating the empirical benefit of combining on-policy and off-policy learning. Our code is publicly available at https://github.com/YifeiZhou02/HNPG.

Neural networks efficiently encode learned information within their parameters. Consequently, many tasks can be unified by treating neural networks themselves as input data. When doing so, recent studies demonstrated the importance of accounting for the symmetries and geometry of parameter spaces. However, those works developed architectures tailored to specific networks such as MLPs and CNNs without normalization layers, and generalizing such architectures to other types of networks can be challenging. In this work, we overcome these challenges by building new metanetworks - neural networks that take weights from other neural networks as input. Put simply, we carefully build graphs representing the input neural networks and process the graphs using graph neural networks. Our approach, Graph Metanetworks (GMNs), generalizes to neural architectures where competing methods struggle, such as multi-head attention layers, normalization layers, convolutional layers, ResNet blocks, and group-equivariant linear layers. We prove that GMNs are expressive and equivariant to parameter permutation symmetries that leave the input neural network functions unchanged. We validate the effectiveness of our method on several metanetwork tasks over diverse neural network architectures.

Computational materials discovery is limited by the high cost of first-principles calculations. Machine learning (ML) potentials that predict energies from crystal structures are promising, but existing methods face computational bottlenecks. Steerable graph neural networks (GNNs) encode geometry with spherical harmonics, respecting atomic symmetries -- permutation, rotation, and translation -- for physically realistic predictions. Yet maintaining equivariance is difficult: activation functions must be modified, and each layer must handle multiple data types for different harmonic orders. We present Facet, a GNN architecture for efficient ML potentials, developed through systematic analysis of steerable GNNs. Our innovations include replacing expensive multi-layer perceptrons (MLPs) for interatomic distances with splines, which match performance while cutting computational and memory demands. We also introduce a general-purpose equivariant layer that mixes node information via spherical grid projection followed by standard MLPs -- faster than tensor products and more expressive than linear or gate layers. On the MPTrj dataset, Facet matches leading models with far fewer parameters and under 10% of their training compute. On a crystal relaxation task, it runs twice as fast as MACE models. We further show SevenNet-0's parameters can be reduced by over 25% with no accuracy loss. These techniques enable more than 10x faster training of large-scale foundation models for ML potentials, potentially reshaping computational materials discovery.

Spatial-temporal forecasting and imputation are important for real-world intelligent systems. Most existing methods are tailored for individual forecasting or imputation tasks but are not designed for both. Additionally, they are less effective for zero-shot and few-shot learning. While pre-trained language model (PLM) have exhibited strong pattern recognition and reasoning abilities across various tasks, including few-shot and zero-shot learning, their applications in spatial-temporal data understanding has been constrained by insufficient modeling of complex correlations such as the temporal correlations, spatial connectivity, non-pairwise and high-order spatial-temporal correlations within data. In this paper, we propose STD-PLM for understanding both spatial and temporal properties of Spatial-Temporal Data with PLM, which is capable of implementing both spatial-temporal forecasting and imputation tasks. STD-PLM understands spatial-temporal correlations via explicitly designed spatial and temporal tokenizers. Topology-aware node embeddings are designed for PLM to comprehend and exploit the topology structure of data in inductive manner. Furthermore, to mitigate the efficiency issues introduced by the PLM, we design a sandglass attention module (SGA) combined with a specific constrained loss function, which significantly improves the model's efficiency while ensuring performance. Extensive experiments demonstrate that STD-PLM exhibits competitive performance and generalization capabilities across the forecasting and imputation tasks on various datasets. Moreover, STD-PLM achieves promising results on both few-shot and zero-shot tasks.The code is made available at https://anonymous.4open.science/r/STD-PLM-F3BA{https://anonymous.4open.science/r/STD-PLM-F3BA}

The numerical solution of partial differential equations (PDEs) is difficult, having led to a century of research so far. Recently, there have been pushes to build neural--numerical hybrid solvers, which piggy-backs the modern trend towards fully end-to-end learned systems. Most works so far can only generalize over a subset of properties to which a generic solver would be faced, including: resolution, topology, geometry, boundary conditions, domain discretization regularity, dimensionality, etc. In this work, we build a solver, satisfying these properties, where all the components are based on neural message passing, replacing all heuristically designed components in the computation graph with backprop-optimized neural function approximators. We show that neural message passing solvers representationally contain some classical methods, such as finite differences, finite volumes, and WENO schemes. In order to encourage stability in training autoregressive models, we put forward a method that is based on the principle of zero-stability, posing stability as a domain adaptation problem. We validate our method on various fluid-like flow problems, demonstrating fast, stable, and accurate performance across different domain topologies, equation parameters, discretizations, etc., in 1D and 2D.

Unlike cloud-based deep learning models that are often large and uniform, edge-deployed models usually demand customization for domain-specific tasks and resource-limited environments. Such customization processes can be costly and time-consuming due to the diversity of edge scenarios and the training load for each scenario. Although various approaches have been proposed for rapid resource-oriented customization and task-oriented customization respectively, achieving both of them at the same time is challenging. Drawing inspiration from the generative AI and the modular composability of neural networks, we introduce NN-Factory, an one-for-all framework to generate customized lightweight models for diverse edge scenarios. The key idea is to use a generative model to directly produce the customized models, instead of training them. The main components of NN-Factory include a modular supernet with pretrained modules that can be conditionally activated to accomplish different tasks and a generative module assembler that manipulate the modules according to task and sparsity requirements. Given an edge scenario, NN-Factory can efficiently customize a compact model specialized in the edge task while satisfying the edge resource constraints by searching for the optimal strategy to assemble the modules. Based on experiments on image classification and object detection tasks with different edge devices, NN-Factory is able to generate high-quality task- and resource-specific models within few seconds, faster than conventional model customization approaches by orders of magnitude.

Transformers are highly parallel but are limited to computations in the TC^0 complexity class, excluding tasks such as entity tracking and code execution that provably require greater expressive power. Motivated by this limitation, we revisit non-linear Recurrent Neural Networks (RNNs) for language modeling and introduce Matrix-to-Matrix RNN (M^2RNN): an architecture with matrix-valued hidden states and expressive non-linear state transitions. We demonstrate that the language modeling performance of non-linear RNNs is limited by their state size. We also demonstrate how the state size expansion mechanism enables efficient use of tensor cores. Empirically, M^2RNN achieves perfect state tracking generalization at sequence lengths not seen during training. These benefits also translate to large-scale language modeling. In hybrid settings that interleave recurrent layers with attention, Hybrid M^2RNN outperforms equivalent Gated DeltaNet hybrids by 0.4-0.5 perplexity points on a 7B MoE model, while using 3times smaller state sizes for the recurrent layers. Notably, replacing even a single recurrent layer with M^2RNN in an existing hybrid architecture yields accuracy gains comparable to Hybrid M^2RNN with minimal impact on training throughput. Further, the Hybrid Gated DeltaNet models with a single M^2RNN layer also achieve superior long-context generalization, outperforming state-of-the-art hybrid linear attention architectures by up to 8 points on LongBench. Together, these results establish non-linear RNN layers as a compelling building block for efficient and scalable language models.

Pre-trained large language models (PLMs) underlie most new developments in natural language processing. They have shifted the field from application-specific model pipelines to a single model that is adapted to a wide range of tasks. Autoregressive PLMs like GPT-3 or PaLM, alongside techniques like few-shot learning, have additionally shifted the output modality to generation instead of classification or regression. Despite their ubiquitous use, the generation quality of language models is rarely evaluated when these models are introduced. Additionally, it is unclear how existing generation tasks--while they can be used to compare systems at a high level--relate to the real world use cases for which people have been adopting them. In this work, we discuss how to adapt existing application-specific generation benchmarks to PLMs and provide an in-depth, empirical study of the limitations and capabilities of PLMs in natural language generation tasks along dimensions such as scale, architecture, input and output language. Our results show that PLMs differ in their applicability to different data regimes and their generalization to multiple languages and inform which PLMs to use for a given generation task setup. We share best practices to be taken into consideration when benchmarking generation capabilities during the development of upcoming PLMs.

Neural models that do not rely on pre-training have excelled in the keyphrase generation task with large annotated datasets. Meanwhile, new approaches have incorporated pre-trained language models (PLMs) for their data efficiency. However, there lacks a systematic study of how the two types of approaches compare and how different design choices can affect the performance of PLM-based models. To fill in this knowledge gap and facilitate a more informed use of PLMs for keyphrase extraction and keyphrase generation, we present an in-depth empirical study. Formulating keyphrase extraction as sequence labeling and keyphrase generation as sequence-to-sequence generation, we perform extensive experiments in three domains. After showing that PLMs have competitive high-resource performance and state-of-the-art low-resource performance, we investigate important design choices including in-domain PLMs, PLMs with different pre-training objectives, using PLMs with a parameter budget, and different formulations for present keyphrases. Further results show that (1) in-domain BERT-like PLMs can be used to build strong and data-efficient keyphrase generation models; (2) with a fixed parameter budget, prioritizing model depth over width and allocating more layers in the encoder leads to better encoder-decoder models; and (3) introducing four in-domain PLMs, we achieve a competitive performance in the news domain and the state-of-the-art performance in the scientific domain.

Graph neural networks (GNNs) have become an indispensable tool for analyzing relational data. In the literature, classical GNNs may be classified into three variants: convolutional, attentional, and message-passing. While the standard message-passing variant is highly expressive, its typical pair-wise messages nevertheless only consider the features of the center node and each neighboring node individually. This design fails to incorporate the rich contextual information contained within the broader local neighborhood, potentially hindering its ability to learn complex relationships within the entire set of neighboring nodes. To address this limitation, this work first formalizes the concept of neighborhood-contextualization, rooted in a key property of the attentional variant. This then serves as the foundation for generalizing the message-passing variant to the proposed neighborhood-contextualized message-passing (NCMP) framework. To demonstrate its utility, a simple, practical, and efficient method to parametrize and operationalize NCMP is presented, leading to the development of the proposed Soft-Isomorphic Neighborhood-Contextualized Graph Convolution Network (SINC-GCN). A preliminary analysis on a synthetic binary node classification problem then underscores both the expressivity and efficiency of the proposed GNN architecture. Overall, the paper lays the foundation for the novel NCMP framework as a practical path toward further enhancing the graph representational power of classical GNNs.

Relational graph neural networks (RGNNs) are graph neural networks (GNNs) with dedicated structures for modeling the different types of nodes and/or edges in heterogeneous graphs. While RGNNs have been increasingly adopted in many real-world applications due to their versatility and accuracy, they pose performance and system design challenges due to their inherent computation patterns, gap between the programming interface and kernel APIs, and heavy programming efforts in optimizing kernels caused by their coupling with data layout and heterogeneity. To systematically address these challenges, we propose Pigeon, a novel two-level intermediate representation (IR) and its code generator framework, that (a) represents the key properties of the RGNN models to bridge the gap between the programming interface and kernel APIs, (b) decouples model semantics, data layout, and operators-specific optimization from each other to reduce programming efforts, (c) expresses and leverages optimization opportunities in inter-operator transforms, data layout, and operator-specific schedules. By building on one general matrix multiply (GEMM) template and a node/edge traversal template, Pigeon achieves up to 7.8x speed-up in inference and 5.6x speed-up in training compared with the state-of-the-art public systems in select models, i.e., RGCN, RGAT, HGT, when running heterogeneous graphs provided by Deep Graph Library (DGL) and Open Graph Benchmark (OGB). Pigeon also triggers fewer out-of-memory (OOM) errors. In addition, we propose linear operator fusion and compact materialization to further accelerate the system by up to 2.2x.

Large Generative Models (LGMs) such as GPT, Stable Diffusion, Sora, and Suno are trained on a huge amount of language corpus, images, videos, and audio that are extremely diverse from numerous domains. This training paradigm over diverse well-curated data lies at the heart of generating creative and sensible content. However, all previous graph generative models (e.g., GraphRNN, MDVAE, MoFlow, GDSS, and DiGress) have been trained only on one dataset each time, which cannot replicate the revolutionary success achieved by LGMs in other fields. To remedy this crucial gap, we propose a new class of graph generative model called Large Graph Generative Model (LGGM) that is trained on a large corpus of graphs (over 5000 graphs) from 13 different domains. We empirically demonstrate that the pre-trained LGGM has superior zero-shot generative capability to existing graph generative models. Furthermore, our pre-trained LGGM can be easily fine-tuned with graphs from target domains and demonstrate even better performance than those directly trained from scratch, behaving as a solid starting point for real-world customization. Inspired by Stable Diffusion, we further equip LGGM with the capability to generate graphs given text prompts (Text-to-Graph), such as the description of the network name and domain (i.e., "The power-1138-bus graph represents a network of buses in a power distribution system."), and network statistics (i.e., "The graph has a low average degree, suitable for modeling social media interactions."). This Text-to-Graph capability integrates the extensive world knowledge in the underlying language model, offering users fine-grained control of the generated graphs. We release the code, the model checkpoint, and the datasets at https://lggm-lg.github.io/.

Neural networks adapt very well to distributed and continuous representations, but struggle to generalize from small amounts of data. Symbolic systems commonly achieve data efficient generalization by exploiting modularity to benefit from local and discrete features of a representation. These features allow symbolic programs to be improved one module at a time and to experience combinatorial growth in the values they can successfully process. However, it is difficult to design a component that can be used to form symbolic abstractions and which is adequately overparametrized to learn arbitrary high-dimensional transformations. I present Graph-based Symbolically Synthesized Neural Networks (G-SSNNs), a class of neural modules that operate on representations modified with synthesized symbolic programs to include a fixed set of local and discrete features. I demonstrate that the choice of injected features within a G-SSNN module modulates the data efficiency and generalization of baseline neural models, creating predictable patterns of both heightened and curtailed generalization. By training G-SSNNs, we also derive information about desirable semantics of symbolic programs without manual engineering. This information is compact and amenable to abstraction, but can also be flexibly recontextualized for other high-dimensional settings. In future work, I will investigate data efficient generalization and the transferability of learned symbolic representations in more complex G-SSNN designs based on more complex classes of symbolic programs. Experimental code and data are available at https://github.com/shlomenu/symbolically_synthesized_networks .

With the increase of data in day-to-day life, businesses and different stakeholders need to analyze the data for better predictions. Traditionally, relational data has been a source of various insights, but with the increase in computational power and the need to understand deeper relationships between entities, the need to design new techniques has arisen. For this graph data analysis has become an extraordinary tool for understanding the data, which reveals more realistic and flexible modelling of complex relationships. Recently, Graph Neural Networks (GNNs) have shown great promise in various applications, such as social network analysis, recommendation systems, drug discovery, and more. However, many adversarial attacks can happen over the data, whether during training (poisoning attack) or during testing (evasion attack), which can adversely manipulate the desired outcome from the GNN model. Therefore, it is crucial to make the GNNs robust to such attacks. The existing robustness methods are computationally demanding and perform poorly when the intensity of attack increases. This paper presents a computationally efficient framework, namely, pLapGNN, based on weighted p-Laplacian for making GNNs robust. Empirical evaluation on real datasets establishes the efficacy and efficiency of the proposed method.

Protein language models (PLMs) encode rich biological information, yet their internal neuron representations are poorly understood. We introduce the first automated framework for labeling every neuron in a PLM with biologically grounded natural language descriptions. Unlike prior approaches relying on sparse autoencoders or manual annotation, our method scales to hundreds of thousands of neurons, revealing individual neurons are selectively sensitive to diverse biochemical and structural properties. We then develop a novel neuron activation-guided steering method to generate proteins with desired traits, enabling convergence to target biochemical properties like molecular weight and instability index as well as secondary and tertiary structural motifs, including alpha helices and canonical Zinc Fingers. We finally show that analysis of labeled neurons in different model sizes reveals PLM scaling laws and a structured neuron space distribution.

Graph Neural Networks (GNNs) have already been widely applied in various graph mining tasks. However, they suffer from the shallow architecture issue, which is the key impediment that hinders the model performance improvement. Although several relevant approaches have been proposed, none of the existing studies provides an in-depth understanding of the root causes of performance degradation in deep GNNs. In this paper, we conduct the first systematic experimental evaluation to present the fundamental limitations of shallow architectures. Based on the experimental results, we answer the following two essential questions: (1) what actually leads to the compromised performance of deep GNNs; (2) when we need and how to build deep GNNs. The answers to the above questions provide empirical insights and guidelines for researchers to design deep and well-performed GNNs. To show the effectiveness of our proposed guidelines, we present Deep Graph Multi-Layer Perceptron (DGMLP), a powerful approach (a paradigm in its own right) that helps guide deep GNN designs. Experimental results demonstrate three advantages of DGMLP: 1) high accuracy -- it achieves state-of-the-art node classification performance on various datasets; 2) high flexibility -- it can flexibly choose different propagation and transformation depths according to graph size and sparsity; 3) high scalability and efficiency -- it supports fast training on large-scale graphs. Our code is available in https://github.com/zwt233/DGMLP.

Property prediction plays an important role in material discovery. As an initial step to eventually develop a foundation model for material science, we introduce a new autoencoder called the MHG-GNN, which combines graph neural network (GNN) with Molecular Hypergraph Grammar (MHG). Results on a variety of property prediction tasks with diverse materials show that MHG-GNN is promising.

Pre-trained language models (PLMs) have revolutionized scientific research, yet their application to single-cell analysis remains limited. Text PLMs cannot process single-cell RNA sequencing data, while cell PLMs lack the ability to handle free text, restricting their use in multimodal tasks. Existing efforts to bridge these modalities often suffer from information loss or inadequate single-modal pre-training, leading to suboptimal performances. To address these challenges, we propose Single-Cell MultiModal Generative Pre-trained Transformer (scMMGPT), a unified PLM for joint cell and text modeling. scMMGPT effectively integrates the state-of-the-art cell and text PLMs, facilitating cross-modal knowledge sharing for improved performance. To bridge the text-cell modality gap, scMMGPT leverages dedicated cross-modal projectors, and undergoes extensive pre-training on 27 million cells -- the largest dataset for multimodal cell-text PLMs to date. This large-scale pre-training enables scMMGPT to excel in joint cell-text tasks, achieving an 84\% relative improvement of textual discrepancy for cell description generation, 20.5\% higher accuracy for cell type annotation, and 4\% improvement in k-NN accuracy for text-conditioned pseudo-cell generation, outperforming baselines.

Advances in natural language processing and large language models have sparked growing interest in modeling DNA, often referred to as the "language of life". However, DNA modeling poses unique challenges. First, it requires the ability to process ultra-long DNA sequences while preserving single-nucleotide resolution, as individual nucleotides play a critical role in DNA function. Second, success in this domain requires excelling at both generative and understanding tasks: generative tasks hold potential for therapeutic and industrial applications, while understanding tasks provide crucial insights into biological mechanisms and diseases. To address these challenges, we propose HybriDNA, a decoder-only DNA language model that incorporates a hybrid Transformer-Mamba2 architecture, seamlessly integrating the strengths of attention mechanisms with selective state-space models. This hybrid design enables HybriDNA to efficiently process DNA sequences up to 131kb in length with single-nucleotide resolution. HybriDNA achieves state-of-the-art performance across 33 DNA understanding datasets curated from the BEND, GUE, and LRB benchmarks, and demonstrates exceptional capability in generating synthetic cis-regulatory elements (CREs) with desired properties. Furthermore, we show that HybriDNA adheres to expected scaling laws, with performance improving consistently as the model scales from 300M to 3B and 7B parameters. These findings underscore HybriDNA's versatility and its potential to advance DNA research and applications, paving the way for innovations in understanding and engineering the "language of life".

Graph Drawing techniques have been developed in the last few years with the purpose of producing aesthetically pleasing node-link layouts. Recently, the employment of differentiable loss functions has paved the road to the massive usage of Gradient Descent and related optimization algorithms. In this paper, we propose a novel framework for the development of Graph Neural Drawers (GND), machines that rely on neural computation for constructing efficient and complex maps. GNDs are Graph Neural Networks (GNNs) whose learning process can be driven by any provided loss function, such as the ones commonly employed in Graph Drawing. Moreover, we prove that this mechanism can be guided by loss functions computed by means of Feedforward Neural Networks, on the basis of supervision hints that express beauty properties, like the minimization of crossing edges. In this context, we show that GNNs can nicely be enriched by positional features to deal also with unlabelled vertexes. We provide a proof-of-concept by constructing a loss function for the edge-crossing and provide quantitative and qualitative comparisons among different GNN models working under the proposed framework.

Self-supervised training of language models (LMs) has seen great success for protein sequences in learning meaningful representations and for generative drug design. Most protein LMs are based on the Transformer architecture trained on individual proteins with short context lengths. Such protein LMs cannot extrapolate to longer proteins and protein complexes well. They also fail to account for the underlying biological mechanisms carried out by biomolecular interactions and dynamics i.e., proteins often interact with other proteins, molecules, and pathways in complex biological systems. In this work, we propose LC-PLM based on an alternative protein LM architecture, BiMamba-S, built off selective structured state-space models, to learn high-quality universal protein representations at the amino acid token level using masked language modeling. We also introduce its graph-contextual variant, LC-PLM-G, which contextualizes protein-protein interaction (PPI) graphs for a second stage of training. LC-PLM demonstrates favorable neural scaling laws, better length extrapolation capability, and a 7% to 34% improvement on protein downstream tasks than Transformer-based ESM-2. LC-PLM-G further trained within the context of PPI graphs shows promising results on protein structure and function prediction tasks. Our study demonstrates the benefit of increasing the context size with computationally efficient LM architecture (e.g. structured state space models) in learning universal protein representations and incorporating molecular interaction context contained in biological graphs.

As Chile's electric power sector advances toward a future powered by renewable energy, accurate forecasting of renewable generation is essential for managing grid operations. The integration of renewable energy sources is particularly challenging due to the operational difficulties of managing their power generation, which is highly variable compared to fossil fuel sources, delaying the availability of clean energy. To mitigate this, we quantify the impact of increasing intermittent generation from wind and solar on thermal power plants in Chile and introduce a hybrid wind speed forecasting methodology which combines two custom ML models for Chile. The first model is based on TiDE, an MLP-based ML model for short-term forecasts, and the second is based on a graph neural network, GraphCast, for medium-term forecasts up to 10 days. Our hybrid approach outperforms the most accurate operational deterministic systems by 4-21% for short-term forecasts and 5-23% for medium-term forecasts and can directly lower the impact of wind generation on thermal ramping, curtailment, and system-level emissions in Chile.

Predictive modeling on web-scale tabular data with billions of instances and hundreds of heterogeneous numerical features faces significant scalability challenges. These features exhibit anisotropy, heavy-tailed distributions, and non-stationarity, creating bottlenecks for models like Gradient Boosting Decision Trees and requiring laborious manual feature engineering. We introduce KMLP, a hybrid deep architecture integrating a shallow Kolmogorov-Arnold Network (KAN) front-end with a Gated Multilayer Perceptron (gMLP) backbone. The KAN front-end uses learnable activation functions to automatically model complex non-linear transformations for each feature, while the gMLP backbone captures high-order interactions. Experiments on public benchmarks and an industrial dataset with billions of samples show KMLP achieves state-of-the-art performance, with advantages over baselines like GBDTs increasing at larger scales, validating KMLP as a scalable deep learning paradigm for large-scale web tabular data.

Learning effective protein representations is critical in a variety of tasks in biology such as predicting protein functions. Recent sequence representation learning methods based on Protein Language Models (PLMs) excel in sequence-based tasks, but their direct adaptation to tasks involving protein structures remains a challenge. In contrast, structure-based methods leverage 3D structural information with graph neural networks and geometric pre-training methods show potential in function prediction tasks, but still suffers from the limited number of available structures. To bridge this gap, our study undertakes a comprehensive exploration of joint protein representation learning by integrating a state-of-the-art PLM (ESM-2) with distinct structure encoders (GVP, GearNet, CDConv). We introduce three representation fusion strategies and explore different pre-training techniques. Our method achieves significant improvements over existing sequence- and structure-based methods, setting new state-of-the-art for function annotation. This study underscores several important design choices for fusing protein sequence and structure information. Our implementation is available at https://github.com/DeepGraphLearning/ESM-GearNet.

Recent advances in neural algorithmic reasoning with graph neural networks (GNNs) are propped up by the notion of algorithmic alignment. Broadly, a neural network will be better at learning to execute a reasoning task (in terms of sample complexity) if its individual components align well with the target algorithm. Specifically, GNNs are claimed to align with dynamic programming (DP), a general problem-solving strategy which expresses many polynomial-time algorithms. However, has this alignment truly been demonstrated and theoretically quantified? Here we show, using methods from category theory and abstract algebra, that there exists an intricate connection between GNNs and DP, going well beyond the initial observations over individual algorithms such as Bellman-Ford. Exposing this connection, we easily verify several prior findings in the literature, produce better-grounded GNN architectures for edge-centric tasks, and demonstrate empirical results on the CLRS algorithmic reasoning benchmark. We hope our exposition will serve as a foundation for building stronger algorithmically aligned GNNs.

Graph Neural Networks (GNNs) have shown promising potential in graph representation learning. The majority of GNNs define a local message-passing mechanism, propagating information over the graph by stacking multiple layers. These methods, however, are known to suffer from two major limitations: over-squashing and poor capturing of long-range dependencies. Recently, Graph Transformers (GTs) emerged as a powerful alternative to Message-Passing Neural Networks (MPNNs). GTs, however, have quadratic computational cost, lack inductive biases on graph structures, and rely on complex Positional/Structural Encodings (SE/PE). In this paper, we show that while Transformers, complex message-passing, and SE/PE are sufficient for good performance in practice, neither is necessary. Motivated by the recent success of State Space Models (SSMs), such as Mamba, we present Graph Mamba Networks (GMNs), a general framework for a new class of GNNs based on selective SSMs. We discuss and categorize the new challenges when adopting SSMs to graph-structured data, and present four required and one optional steps to design GMNs, where we choose (1) Neighborhood Tokenization, (2) Token Ordering, (3) Architecture of Bidirectional Selective SSM Encoder, (4) Local Encoding, and dispensable (5) PE and SE. We further provide theoretical justification for the power of GMNs. Experiments demonstrate that despite much less computational cost, GMNs attain an outstanding performance in long-range, small-scale, large-scale, and heterophilic benchmark datasets.

Mixed-Integer Linear Programming (MILP) is a cornerstone of combinatorial optimization, yet solving large-scale instances remains a significant computational challenge. Recently, Graph Neural Networks (GNNs) have shown promise in accelerating MILP solvers by predicting high-quality solutions. However, we identify that existing methods misalign with the intrinsic structure of MILP problems at two levels. At the leaning objective level, the Binary Cross-Entropy (BCE) loss treats variables independently, neglecting their relative priority and yielding plausible logits. At the model architecture level, standard GNN message passing inherently smooths the representations across variables, missing the natural competitive relationships within constraints. To address these challenges, we propose CoCo-MILP, which explicitly models inter-variable Contrast and intra-constraint Competition for advanced MILP solution prediction. At the objective level, CoCo-MILP introduces the Inter-Variable Contrastive Loss (VCL), which explicitly maximizes the embedding margin between variables assigned one versus zero. At the architectural level, we design an Intra-Constraint Competitive GNN layer that, instead of homogenizing features, learns to differentiate representations of competing variables within a constraint, capturing their exclusionary nature. Experimental results on standard benchmarks demonstrate that CoCo-MILP significantly outperforms existing learning-based approaches, reducing the solution gap by up to 68.12% compared to traditional solvers. Our code is available at https://github.com/happypu326/CoCo-MILP.

Hybrid methods have been shown to outperform pure statistical and pure deep learning methods at forecasting tasks and quantifying the associated uncertainty with those forecasts (prediction intervals). One example is Exponential Smoothing Recurrent Neural Network (ES-RNN), a hybrid between a statistical forecasting model and a recurrent neural network variant. ES-RNN achieves a 9.4\% improvement in absolute error in the Makridakis-4 Forecasting Competition. This improvement and similar outperformance from other hybrid models have primarily been demonstrated only on univariate datasets. Difficulties with applying hybrid forecast methods to multivariate data include (i) the high computational cost involved in hyperparameter tuning for models that are not parsimonious, (ii) challenges associated with auto-correlation inherent in the data, as well as (iii) complex dependency (cross-correlation) between the covariates that may be hard to capture. This paper presents Multivariate Exponential Smoothing Long Short Term Memory (MES-LSTM), a generalized multivariate extension to ES-RNN, that overcomes these challenges. MES-LSTM utilizes a vectorized implementation. We test MES-LSTM on several aggregated coronavirus disease of 2019 (COVID-19) morbidity datasets and find our hybrid approach shows consistent, significant improvement over pure statistical and deep learning methods at forecast accuracy and prediction interval construction.

Protein language models (PLMs) face a fundamental divide: masked language models (MLMs) excel at fitness prediction while causal models enable generation, forcing practitioners to maintain separate architectures. We introduce Proust, a 309M-parameter causal PLM that bridges this gap through architectural innovations adapted from recent LLM research, including grouped-query attention with shared K/V projections, cross-layer value residuals, and depthwise causal convolutions. Trained on 33B tokens in 40 B200 GPU-hours, Proust achieves Spearman ρ= 0.390 on ProteinGym substitutions, competitive with MLMs requiring 50--200times the compute. On indels, Proust sets a new state-of-the-art, outperforming models up to 20times larger. On EVEREST viral fitness benchmarks, it approaches structure-aware methods using sequence alone. These powerful representations position Proust in a sweet spot as it also retains native generative capabilities that MLMs lack by design. Interpretability analysis reveals that per-position entropy variance predicts, to an extent, when retrieval augmentation helps and hurts. Such insights can grow in both quantity and quality at scale and inform capabilities such as test-time scaling. Code and weights are available at https://github.com/Furkan9015/proust-inference

The application of Large Language Models (LLMs) in Computer-Aided Design (CAD) remains an underexplored area, despite their remarkable advancements in other domains. In this paper, we present BlenderLLM, a novel framework for training LLMs specifically for CAD tasks leveraging a self-improvement methodology. To support this, we developed a bespoke training dataset, BlendNet, and introduced a comprehensive evaluation suite, CADBench. Our results reveal that existing models demonstrate significant limitations in generating accurate CAD scripts. However, through minimal instruction-based fine-tuning and iterative self-improvement, BlenderLLM significantly surpasses these models in both functionality and accuracy of CAD script generation. This research establishes a strong foundation for the application of LLMs in CAD while demonstrating the transformative potential of self-improving models in advancing CAD automation. We encourage further exploration and adoption of these methodologies to drive innovation in the field. The dataset, model, benchmark, and source code are publicly available at https://github.com/FreedomIntelligence/BlenderLLM

Transformers excel at sequence modeling but face quadratic complexity, while linear attention offers improved efficiency but often compromises recall accuracy over long contexts. In this work, we introduce Native Hybrid Attention (NHA), a novel hybrid architecture of linear and full attention that integrates both intra \& inter-layer hybridization into a unified layer design. NHA maintains long-term context in key-value slots updated by a linear RNN, and augments them with short-term tokens from a sliding window. A single softmax attention operation is then applied over all keys and values, enabling per-token and per-head context-dependent weighting without requiring additional fusion parameters. The inter-layer behavior is controlled through a single hyperparameter, the sliding window size, which allows smooth adjustment between purely linear and full attention while keeping all layers structurally uniform. Experimental results show that NHA surpasses Transformers and other hybrid baselines on recall-intensive and commonsense reasoning tasks. Furthermore, pretrained LLMs can be structurally hybridized with NHA, achieving competitive accuracy while delivering significant efficiency gains. Code is available at https://github.com/JusenD/NHA.

Machine learning (ML) and deep learning (DL) techniques have gained significant attention as reduced order models (ROMs) to computationally expensive structural analysis methods, such as finite element analysis (FEA). Graph neural network (GNN) is a particular type of neural network which processes data that can be represented as graphs. This allows for efficient representation of complex geometries that can change during conceptual design of a structure or a product. In this study, we propose a novel graph embedding technique for efficient representation of 3D stiffened panels by considering separate plate domains as vertices. This approach is considered using Graph Sampling and Aggregation (GraphSAGE) to predict stress distributions in stiffened panels with varying geometries. A comparison between a finite-element-vertex graph representation is conducted to demonstrate the effectiveness of the proposed approach. A comprehensive parametric study is performed to examine the effect of structural geometry on the prediction performance. Our results demonstrate the immense potential of graph neural networks with the proposed graph embedding method as robust reduced-order models for 3D structures.

We present a Morphology-Informed Heterogeneous Graph Neural Network (MI-HGNN) for learning-based contact perception. The architecture and connectivity of the MI-HGNN are constructed from the robot morphology, in which nodes and edges are robot joints and links, respectively. By incorporating the morphology-informed constraints into a neural network, we improve a learning-based approach using model-based knowledge. We apply the proposed MI-HGNN to two contact perception problems, and conduct extensive experiments using both real-world and simulated data collected using two quadruped robots. Our experiments demonstrate the superiority of our method in terms of effectiveness, generalization ability, model efficiency, and sample efficiency. Our MI-HGNN improved the performance of a state-of-the-art model that leverages robot morphological symmetry by 8.4% with only 0.21% of its parameters. Although MI-HGNN is applied to contact perception problems for legged robots in this work, it can be seamlessly applied to other types of multi-body dynamical systems and has the potential to improve other robot learning frameworks. Our code is made publicly available at https://github.com/lunarlab-gatech/Morphology-Informed-HGNN.

Pre-trained language models (PLMs) have become a prevalent technique in deep learning for code, utilizing a two-stage pre-training and fine-tuning procedure to acquire general knowledge about code and specialize in a variety of downstream tasks. However, the dynamic nature of software codebases poses a challenge to the effectiveness and robustness of PLMs. In particular, world-realistic scenarios potentially lead to significant differences between the distribution of the pre-training and test data, i.e., distribution shift, resulting in a degradation of the PLM's performance on downstream tasks. In this paper, we stress the need for adapting PLMs of code to software data whose distribution changes over time, a crucial problem that has been overlooked in previous works. The motivation of this work is to consider the PLM in a non-stationary environment, where fine-tuning data evolves over time according to a software evolution scenario. Specifically, we design a scenario where the model needs to learn from a stream of programs containing new, unseen APIs over time. We study two widely used PLM architectures, i.e., a GPT2 decoder and a RoBERTa encoder, on two downstream tasks, API call and API usage prediction. We demonstrate that the most commonly used fine-tuning technique from prior work is not robust enough to handle the dynamic nature of APIs, leading to the loss of previously acquired knowledge i.e., catastrophic forgetting. To address these issues, we implement five continual learning approaches, including replay-based and regularization-based methods. Our findings demonstrate that utilizing these straightforward methods effectively mitigates catastrophic forgetting in PLMs across both downstream tasks while achieving comparable or superior performance.

The enduring challenge in the field of artificial intelligence has been the control of systems to achieve desired behaviours. While for systems governed by straightforward dynamics equations, methods like Linear Quadratic Regulation (LQR) have historically proven highly effective, most real-world tasks, which require a general problem-solver, demand world models with dynamics that cannot be easily described by simple equations. Consequently, these models must be learned from data using neural networks. Most model predictive control (MPC) algorithms designed for visual world models have traditionally explored gradient-free population-based optimisation methods, such as Cross Entropy and Model Predictive Path Integral (MPPI) for planning. However, we present an exploration of a gradient-based alternative that fully leverages the differentiability of the world model. In our study, we conduct a comparative analysis between our method and other MPC-based alternatives, as well as policy-based algorithms. In a sample-efficient setting, our method achieves on par or superior performance compared to the alternative approaches in most tasks. Additionally, we introduce a hybrid model that combines policy networks and gradient-based MPC, which outperforms pure policy based methods thereby holding promise for Gradient-based planning with world models in complex real-world tasks.

Graph Neural Networks (GNNs) extend basic Neural Networks (NNs) by using graph structures based on the relational inductive bias (homophily assumption). While GNNs have been commonly believed to outperform NNs in real-world tasks, recent work has identified a non-trivial set of datasets where their performance compared to NNs is not satisfactory. Heterophily has been considered the main cause of this empirical observation and numerous works have been put forward to address it. In this paper, we first revisit the widely used homophily metrics and point out that their consideration of only graph-label consistency is a shortcoming. Then, we study heterophily from the perspective of post-aggregation node similarity and define new homophily metrics, which are potentially advantageous compared to existing ones. Based on this investigation, we prove that some harmful cases of heterophily can be effectively addressed by local diversification operation. Then, we propose the Adaptive Channel Mixing (ACM), a framework to adaptively exploit aggregation, diversification and identity channels node-wisely to extract richer localized information for diverse node heterophily situations. ACM is more powerful than the commonly used uni-channel framework for node classification tasks on heterophilic graphs and is easy to be implemented in baseline GNN layers. When evaluated on 10 benchmark node classification tasks, ACM-augmented baselines consistently achieve significant performance gain, exceeding state-of-the-art GNNs on most tasks without incurring significant computational burden.

In recent years, significant efforts have been directed toward adapting modern neural network architectures for tabular data. However, despite their larger number of parameters and longer training and inference times, these models often fail to consistently outperform vanilla multilayer perceptron (MLP) neural networks. Moreover, MLP-based ensembles have recently demonstrated superior performance and efficiency compared to advanced deep learning methods. Therefore, rather than focusing on building deeper and more complex deep learning models, we propose investigating whether MLP neural networks can be replaced with more efficient architectures without sacrificing performance. In this paper, we first introduce GG MoE, a mixture-of-experts (MoE) model with a Gumbel-Softmax gating function. We then demonstrate that GG MoE with an embedding layer achieves the highest performance across 38 datasets compared to standard MoE and MLP models. Finally, we show that both MoE and GG MoE utilize significantly fewer parameters than MLPs, making them a promising alternative for scaling and ensemble methods.

The study of biological materials and bio-inspired materials science is well established; however, surprisingly little knowledge has been systematically translated to engineering solutions. To accelerate discovery and guide insights, an open-source autoregressive transformer large language model (LLM), BioinspiredLLM, is reported. The model was finetuned with a corpus of over a thousand peer-reviewed articles in the field of structural biological and bio-inspired materials and can be prompted to recall information, assist with research tasks, and function as an engine for creativity. The model has proven that it is able to accurately recall information about biological materials and is further enhanced with enhanced reasoning ability, as well as with retrieval-augmented generation to incorporate new data during generation that can also help to traceback sources, update the knowledge base, and connect knowledge domains. BioinspiredLLM also has been shown to develop sound hypotheses regarding biological materials design and remarkably so for materials that have never been explicitly studied before. Lastly, the model showed impressive promise in collaborating with other generative artificial intelligence models in a workflow that can reshape the traditional materials design process. This collaborative generative artificial intelligence method can stimulate and enhance bio-inspired materials design workflows. Biological materials are at a critical intersection of multiple scientific fields and models like BioinspiredLLM help to connect knowledge domains.

The rise of Deep Generative Models (DGM) has enabled the generation of high-quality synthetic data. When used to augment authentic data in Deep Metric Learning (DML), these synthetic samples enhance intra-class diversity and improve the performance of downstream DML tasks. We introduce BLenDeR, a diffusion sampling method designed to increase intra-class diversity for DML in a controllable way by leveraging set-theory inspired union and intersection operations on denoising residuals. The union operation encourages any attribute present across multiple prompts, while the intersection extracts the common direction through a principal component surrogate. These operations enable controlled synthesis of diverse attribute combinations within each class, addressing key limitations of existing generative approaches. Experiments on standard DML benchmarks demonstrate that BLenDeR consistently outperforms state-of-the-art baselines across multiple datasets and backbones. Specifically, BLenDeR achieves 3.7% increase in Recall@1 on CUB-200 and a 1.8% increase on Cars-196, compared to state-of-the-art baselines under standard experimental settings.

While training large language models (LLMs) from scratch can generate models with distinct functionalities and strengths, it comes at significant costs and may result in redundant capabilities. Alternatively, a cost-effective and compelling approach is to merge existing pre-trained LLMs into a more potent model. However, due to the varying architectures of these LLMs, directly blending their weights is impractical. In this paper, we introduce the notion of knowledge fusion for LLMs, aimed at combining the capabilities of existing LLMs and transferring them into a single LLM. By leveraging the generative distributions of source LLMs, we externalize their collective knowledge and unique strengths, thereby potentially elevating the capabilities of the target model beyond those of any individual source LLM. We validate our approach using three popular LLMs with different architectures--Llama-2, MPT, and OpenLLaMA--across various benchmarks and tasks. Our findings confirm that the fusion of LLMs can improve the performance of the target model across a range of capabilities such as reasoning, commonsense, and code generation. Our code, model weights, and data are public at https://github.com/fanqiwan/FuseLLM.

Expanding the long-context capabilities of Multi-modal Large Language Models~(MLLMs) is crucial for video understanding, high-resolution image understanding, and multi-modal agents. This involves a series of systematic optimizations, including model architecture, data construction and training strategy, particularly addressing challenges such as degraded performance with more images and high computational costs. In this paper, we adapt the model architecture to a hybrid of Mamba and Transformer blocks, approach data construction with both temporal and spatial dependencies among multiple images and employ a progressive training strategy. The released model LongLLaVA~(Long-Context Large Language and Vision Assistant) is the first hybrid MLLM, which achieved a better balance between efficiency and effectiveness. LongLLaVA not only achieves competitive results across various benchmarks, but also maintains high throughput and low memory consumption. Especially, it could process nearly a thousand images on a single A100 80GB GPU, showing promising application prospects for a wide range of tasks.

A major challenge of AI + Science lies in their inherent incompatibility: today's AI is primarily based on connectionism, while science depends on symbolism. To bridge the two worlds, we propose a framework to seamlessly synergize Kolmogorov-Arnold Networks (KANs) and science. The framework highlights KANs' usage for three aspects of scientific discovery: identifying relevant features, revealing modular structures, and discovering symbolic formulas. The synergy is bidirectional: science to KAN (incorporating scientific knowledge into KANs), and KAN to science (extracting scientific insights from KANs). We highlight major new functionalities in the pykan package: (1) MultKAN: KANs with multiplication nodes. (2) kanpiler: a KAN compiler that compiles symbolic formulas into KANs. (3) tree converter: convert KANs (or any neural networks) to tree graphs. Based on these tools, we demonstrate KANs' capability to discover various types of physical laws, including conserved quantities, Lagrangians, symmetries, and constitutive laws.

The complex nature of big biological systems pushed some scientists to classify its understanding under the inconceivable missions. Different leveled challenges complicated this task, one of is the prediction of a protein's function. In recent years, significant progress has been made in this field through the development of various machine learning approaches. However, most existing methods formulate the task as a multi-classification problem, i.e assigning predefined labels to proteins. In this work, we propose a novel approach, Prot2Text, which predicts a protein function's in a free text style, moving beyond the conventional binary or categorical classifications. By combining Graph Neural Networks(GNNs) and Large Language Models(LLMs), in an encoder-decoder framework, our model effectively integrates diverse data types including proteins' sequences, structures, and textual annotations. This multimodal approach allows for a holistic representation of proteins' functions, enabling the generation of detailed and accurate descriptions. To evaluate our model, we extracted a multimodal protein dataset from SwissProt, and demonstrate empirically the effectiveness of Prot2Text. These results highlight the transformative impact of multimodal models, specifically the fusion of GNNs and LLMs, empowering researchers with powerful tools for more accurate prediction of proteins' functions. The code, the models and a demo will be publicly released.

Optimization problems are prevalent across various scenarios. Formulating and then solving optimization problems described by natural language often requires highly specialized human expertise, which could block the widespread application of optimization-based decision making. To automate problem formulation and solving, leveraging large language models (LLMs) has emerged as a potential way. However, this kind of approach suffers from the issue of optimization generalization. Namely, the accuracy of most current LLM-based methods and the generality of optimization problem types that they can model are still limited. In this paper, we propose a unified learning-based framework called LLMOPT to boost optimization generalization. Starting from the natural language descriptions of optimization problems and a pre-trained LLM, LLMOPT constructs the introduced five-element formulation as a universal model for learning to define diverse optimization problem types. Then, LLMOPT employs the multi-instruction tuning to enhance both problem formalization and solver code generation accuracy and generality. After that, to prevent hallucinations in LLMs, such as sacrificing solving accuracy to avoid execution errors, the model alignment and self-correction mechanism are adopted in LLMOPT. We evaluate the optimization generalization ability of LLMOPT and compared methods across six real-world datasets covering roughly 20 fields such as health, environment, energy and manufacturing, etc. Extensive experiment results show that LLMOPT is able to model various optimization problem types such as linear/nonlinear programming, mixed integer programming, and combinatorial optimization, and achieves a notable 11.08% average solving accuracy improvement compared with the state-of-the-art methods. The code is available at https://github.com/caigaojiang/LLMOPT.

Recent advances in Graph Neural Networks (GNNs) and Graph Transformers (GTs) have been driven by innovations in architectures and Positional Encodings (PEs), which are critical for augmenting node features and capturing graph topology. PEs are essential for GTs, where topological information would otherwise be lost without message-passing. However, PEs are often tested alongside novel architectures, making it difficult to isolate their effect on established models. To address this, we present a comprehensive benchmark of PEs in a unified framework that includes both message-passing GNNs and GTs. We also establish theoretical connections between MPNNs and GTs and introduce a sparsified GRIT attention mechanism to examine the influence of global connectivity. Our findings demonstrate that previously untested combinations of GNN architectures and PEs can outperform existing methods and offer a more comprehensive picture of the state-of-the-art. To support future research and experimentation in our framework, we make the code publicly available.

Vision graph neural networks (ViG) offer a new avenue for exploration in computer vision. A major bottleneck in ViGs is the inefficient k-nearest neighbor (KNN) operation used for graph construction. To solve this issue, we propose a new method for designing ViGs, Dynamic Axial Graph Construction (DAGC), which is more efficient than KNN as it limits the number of considered graph connections made within an image. Additionally, we propose a novel CNN-GNN architecture, GreedyViG, which uses DAGC. Extensive experiments show that GreedyViG beats existing ViG, CNN, and ViT architectures in terms of accuracy, GMACs, and parameters on image classification, object detection, instance segmentation, and semantic segmentation tasks. Our smallest model, GreedyViG-S, achieves 81.1% top-1 accuracy on ImageNet-1K, 2.9% higher than Vision GNN and 2.2% higher than Vision HyperGraph Neural Network (ViHGNN), with less GMACs and a similar number of parameters. Our largest model, GreedyViG-B obtains 83.9% top-1 accuracy, 0.2% higher than Vision GNN, with a 66.6% decrease in parameters and a 69% decrease in GMACs. GreedyViG-B also obtains the same accuracy as ViHGNN with a 67.3% decrease in parameters and a 71.3% decrease in GMACs. Our work shows that hybrid CNN-GNN architectures not only provide a new avenue for designing efficient models, but that they can also exceed the performance of current state-of-the-art models.

Spiking neural networks (SNNs) have ultra-low energy consumption and high biological plausibility due to their binary and bio-driven nature compared with artificial neural networks (ANNs). While previous research has primarily focused on enhancing the performance of SNNs in classification tasks, the generative potential of SNNs remains relatively unexplored. In our paper, we put forward Spiking Denoising Diffusion Probabilistic Models (SDDPM), a new class of SNN-based generative models that achieve high sample quality. To fully exploit the energy efficiency of SNNs, we propose a purely Spiking U-Net architecture, which achieves comparable performance to its ANN counterpart using only 4 time steps, resulting in significantly reduced energy consumption. Extensive experimental results reveal that our approach achieves state-of-the-art on the generative tasks and substantially outperforms other SNN-based generative models, achieving up to 12x and 6x improvement on the CIFAR-10 and the CelebA datasets, respectively. Moreover, we propose a threshold-guided strategy that can further improve the performances by 2.69% in a training-free manner. The SDDPM symbolizes a significant advancement in the field of SNN generation, injecting new perspectives and potential avenues of exploration. Our code is available at https://github.com/AndyCao1125/SDDPM.

Pretrained language models (PLMs) have demonstrated remarkable performance in various natural language processing tasks: Unidirectional PLMs (e.g., GPT) are well known for their superior text generation capabilities; bidirectional PLMs (e.g., BERT) have been the prominent choice for natural language understanding (NLU) tasks. While both types of models have achieved promising few-shot learning performance, their potential for zero-shot learning has been underexplored. In this paper, we present a simple approach that uses both types of PLMs for fully zero-shot learning of NLU tasks without requiring any task-specific data: A unidirectional PLM generates class-conditioned texts guided by prompts, which are used as the training data for fine-tuning a bidirectional PLM. With quality training data selected based on the generation probability and regularization techniques (label smoothing and temporal ensembling) applied to the fine-tuning stage for better generalization and stability, our approach demonstrates strong performance across seven classification tasks of the GLUE benchmark (e.g., 72.3/73.8 on MNLI-m/mm and 92.8 on SST-2), significantly outperforming zero-shot prompting methods and achieving even comparable results to strong few-shot approaches using 32 training samples per class.

Efficient deployment of small language models (SLMs) is essential for numerous real-world applications with stringent latency constraints. While previous work on SLM design has primarily focused on reducing the number of parameters to achieve parameter-optimal SLMs, parameter efficiency does not necessarily translate into proportional real-device speed-ups. This work aims to identify the key determinants of SLMs' real-device latency and offer generalizable principles and methodologies for SLM design and training when real-device latency is the primary consideration. Specifically, we identify two central architectural factors: depth-width ratios and operator choices. The former is crucial for small-batch-size latency, while the latter affects both latency and large-batch-size throughput. In light of this, we first study latency-optimal depth-width ratios, with the key finding that although deep-thin models generally achieve better accuracy under the same parameter budget, they may not lie on the accuracy-latency trade-off frontier. Next, we explore emerging efficient attention alternatives to evaluate their potential as candidate building operators. Using the identified promising operators, we construct an evolutionary search framework to automatically discover latency-optimal combinations of these operators within hybrid SLMs, thereby advancing the accuracy-latency frontier. In addition to architectural improvements, we further enhance SLM training using a weight normalization technique that enables more effective weight updates and improves final convergence. Combining these methods, we introduce a new family of hybrid SLMs, called Nemotron-Flash, which significantly advances the accuracy-efficiency frontier of state-of-the-art SLMs, e.g., achieving over +5.5% average accuracy, 1.3x/1.9x lower latency, and 18.7x/45.6x higher throughput compared to Qwen3-1.7B/0.6B, respectively.

With the advancement of RNN models with linear complexity, the quadratic complexity challenge of transformers has the potential to be overcome. Notably, the emerging Mamba-2 has demonstrated competitive performance, bridging the gap between RNN models and transformers. However, due to sequential processing and vanishing gradients, RNN models struggle to capture long-range dependencies, limiting contextual understanding. This results in slow convergence, high resource demands, and poor performance on downstream understanding and complex reasoning tasks. In this work, we present a hybrid model MaTVLM by substituting a portion of the transformer decoder layers in a pre-trained VLM with Mamba-2 layers. Leveraging the inherent relationship between attention and Mamba-2, we initialize Mamba-2 with corresponding attention weights to accelerate convergence. Subsequently, we employ a single-stage distillation process, using the pre-trained VLM as the teacher model to transfer knowledge to the MaTVLM, further enhancing convergence speed and performance. Furthermore, we investigate the impact of differential distillation loss within our training framework. We evaluate the MaTVLM on multiple benchmarks, demonstrating competitive performance against the teacher model and existing VLMs while surpassing both Mamba-based VLMs and models of comparable parameter scales. Remarkably, the MaTVLM achieves up to 3.6x faster inference than the teacher model while reducing GPU memory consumption by 27.5%, all without compromising performance. Code and models are released at http://github.com/hustvl/MaTVLM.

Recovering Computer-Aided Design (CAD) programs from 3D geometries is a widely studied problem. Recent advances in large language models (LLMs) have enabled progress in CAD program synthesis, but existing methods rely on supervised training with paired shape-program data, which is often unavailable. We introduce PLLM, a self-training framework for CAD program synthesis from unlabeled 3D shapes. Given a pre-trained CAD-capable LLM and a shape dataset, PLLM iteratively samples candidate programs, selects high-fidelity executions, and augments programs to construct synthetic program-shape pairs for fine-tuning. We experiment on adapting CAD-Recode from DeepCAD to the unlabeled ABC dataset show consistent improvements in geometric fidelity and program diversity.

Message-passing Graph Neural Networks (GNNs) are often criticized for their limited expressiveness, issues like over-smoothing and over-squashing, and challenges in capturing long-range dependencies. Conversely, Graph Transformers (GTs) are regarded as superior due to their employment of global attention mechanisms, which potentially mitigate these challenges. Literature frequently suggests that GTs outperform GNNs in graph-level tasks, especially for graph classification and regression on small molecular graphs. In this study, we explore the untapped potential of GNNs through an enhanced framework, GNN+, which integrates six widely used techniques: edge feature integration, normalization, dropout, residual connections, feed-forward networks, and positional encoding, to effectively tackle graph-level tasks. We conduct a systematic re-evaluation of three classic GNNs (GCN, GIN, and GatedGCN) enhanced by the GNN+ framework across 14 well-known graph-level datasets. Our results reveal that, contrary to prevailing beliefs, these classic GNNs consistently match or surpass the performance of GTs, securing top-three rankings across all datasets and achieving first place in eight. Furthermore, they demonstrate greater efficiency, running several times faster than GTs on many datasets. This highlights the potential of simple GNN architectures, challenging the notion that complex mechanisms in GTs are essential for superior graph-level performance. Our source code is available at https://github.com/LUOyk1999/GNNPlus.

This paper introduces the Point Cloud Network (PCN) architecture, a novel implementation of linear layers in deep learning networks, and provides empirical evidence to advocate for its preference over the Multilayer Perceptron (MLP) in linear layers. We train several models, including the original AlexNet, using both MLP and PCN architectures for direct comparison of linear layers (Krizhevsky et al., 2012). The key results collected are model parameter count and top-1 test accuracy over the CIFAR-10 and CIFAR-100 datasets (Krizhevsky, 2009). AlexNet-PCN16, our PCN equivalent to AlexNet, achieves comparable efficacy (test accuracy) to the original architecture with a 99.5% reduction of parameters in its linear layers. All training is done on cloud RTX 4090 GPUs, leveraging pytorch for model construction and training. Code is provided for anyone to reproduce the trials from this paper.

Pre-trained language models (PLMs) have achieved remarkable success in natural language generation (NLG) tasks. Up to now, most NLG-oriented PLMs are pre-trained in an unsupervised manner using the large-scale general corpus. In the meanwhile, an increasing number of models pre-trained with labeled data (i.e., ``supervised pre-training'') showcase superior performance compared to unsupervised pre-trained models. Motivated by the success of supervised pre-training, we propose Multi-task superVised Pre-training~(MVP) for natural language generation. We collect a large-scale natural language generation corpus, MVPCorpus, from 77 datasets over 11 diverse NLG tasks. Then we unify these examples into a general text-to-text format to pre-train the text generation model MVP in a supervised manner. For each task, we further pre-train specific soft prompts to stimulate the model's capacity to perform a specific task. Extensive experiments have demonstrated the effectiveness and generality of our MVP model in a number of NLG tasks, which achieves state-of-the-art performance on 13 out of 17 datasets.

Modular neural networks without additional training have recently been shown to surpass end-to-end neural networks on challenging vision-language tasks. The latest such methods simultaneously introduce LLM-based code generation to build programs and a number of skill-specific, task-oriented modules to execute them. In this paper, we focus on ViperGPT and ask where its additional performance comes from and how much is due to the (state-of-art, end-to-end) BLIP-2 model it subsumes vs. additional symbolic components. To do so, we conduct a controlled study (comparing end-to-end, modular, and prompting-based methods across several VQA benchmarks). We find that ViperGPT's reported gains over BLIP-2 can be attributed to its selection of task-specific modules, and when we run ViperGPT using a more task-agnostic selection of modules, these gains go away. Additionally, ViperGPT retains much of its performance if we make prominent alterations to its selection of modules: e.g. removing or retaining only BLIP-2. Finally, we compare ViperGPT against a prompting-based decomposition strategy and find that, on some benchmarks, modular approaches significantly benefit by representing subtasks with natural language, instead of code.

Realistic graphs contain both (1) rich self-features of nodes and (2) informative structures of neighborhoods, jointly handled by a Graph Neural Network (GNN) in the typical setup. We propose to decouple the two modalities by Mixture of weak and strong experts (Mowst), where the weak expert is a light-weight Multi-layer Perceptron (MLP), and the strong expert is an off-the-shelf GNN. To adapt the experts' collaboration to different target nodes, we propose a "confidence" mechanism based on the dispersion of the weak expert's prediction logits. The strong expert is conditionally activated in the low-confidence region when either the node's classification relies on neighborhood information, or the weak expert has low model quality. We reveal interesting training dynamics by analyzing the influence of the confidence function on loss: our training algorithm encourages the specialization of each expert by effectively generating soft splitting of the graph. In addition, our "confidence" design imposes a desirable bias toward the strong expert to benefit from GNN's better generalization capability. Mowst is easy to optimize and achieves strong expressive power, with a computation cost comparable to a single GNN. Empirically, Mowst on 4 backbone GNN architectures show significant accuracy improvement on 6 standard node classification benchmarks, including both homophilous and heterophilous graphs (https://github.com/facebookresearch/mowst-gnn).

The number of groups (g) in group convolution (GConv) is selected to boost the predictive performance of deep neural networks (DNNs) in a compute and parameter efficient manner. However, we show that naive selection of g in GConv creates an imbalance between the computational complexity and degree of data reuse, which leads to suboptimal energy efficiency in DNNs. We devise an optimum group size model, which enables a balance between computational cost and data movement cost, thus, optimize the energy-efficiency of DNNs. Based on the insights from this model, we propose an "energy-efficient group convolution" (E2GC) module where, unlike the previous implementations of GConv, the group size (G) remains constant. Further, to demonstrate the efficacy of the E2GC module, we incorporate this module in the design of MobileNet-V1 and ResNeXt-50 and perform experiments on two GPUs, P100 and P4000. We show that, at comparable computational complexity, DNNs with constant group size (E2GC) are more energy-efficient than DNNs with a fixed number of groups (FgGC). For example, on P100 GPU, the energy-efficiency of MobileNet-V1 and ResNeXt-50 is increased by 10.8% and 4.73% (respectively) when E2GC modules substitute the FgGC modules in both the DNNs. Furthermore, through our extensive experimentation with ImageNet-1K and Food-101 image classification datasets, we show that the E2GC module enables a trade-off between generalization ability and representational power of DNN. Thus, the predictive performance of DNNs can be optimized by selecting an appropriate G. The code and trained models are available at https://github.com/iithcandle/E2GC-release.

Graph neural networks (GNN) has been successfully applied to operate on the graph-structured data. Given a specific scenario, rich human expertise and tremendous laborious trials are usually required to identify a suitable GNN architecture. It is because the performance of a GNN architecture is significantly affected by the choice of graph convolution components, such as aggregate function and hidden dimension. Neural architecture search (NAS) has shown its potential in discovering effective deep architectures for learning tasks in image and language modeling. However, existing NAS algorithms cannot be directly applied to the GNN search problem. First, the search space of GNN is different from the ones in existing NAS work. Second, the representation learning capacity of GNN architecture changes obviously with slight architecture modifications. It affects the search efficiency of traditional search methods. Third, widely used techniques in NAS such as parameter sharing might become unstable in GNN. To bridge the gap, we propose the automated graph neural networks (AGNN) framework, which aims to find an optimal GNN architecture within a predefined search space. A reinforcement learning based controller is designed to greedily validate architectures via small steps. AGNN has a novel parameter sharing strategy that enables homogeneous architectures to share parameters, based on a carefully-designed homogeneity definition. Experiments on real-world benchmark datasets demonstrate that the GNN architecture identified by AGNN achieves the best performance, comparing with existing handcrafted models and tradistional search methods.

The 2021 NeurIPS Machine Learning for Combinatorial Optimization (ML4CO) competition was designed with the goal of improving state-of-the-art combinatorial optimization solvers by replacing key heuristic components with machine learning models. The competition's main scientific question was the following: is machine learning a viable option for improving traditional combinatorial optimization solvers on specific problem distributions, when historical data is available? This was motivated by the fact that in many practical scenarios, the data changes only slightly between the repetitions of a combinatorial optimization problem, and this is an area where machine learning models are particularly powerful at. This paper summarizes the solution and lessons learned by the Huawei EI-OROAS team in the dual task of the competition. The submission of our team achieved the second place in the final ranking, with a very close distance to the first spot. In addition, our solution was ranked first consistently for several weekly leaderboard updates before the final evaluation. We provide insights gained from a large number of experiments, and argue that a simple Graph Convolutional Neural Network (GCNNs) can achieve state-of-the-art results if trained and tuned properly.

Obtaining high-quality generations in modern LLMs has largely been framed as a selection problem: identifying a single winning generation from a diverse pool of N samples, the Best-of-N (BoN). Yet, this approach is inherently zero-sum, discarding diverse and potentially useful information from the pool. Instead, we explore a collaborative setup, where all candidates can potentially contribute to the final winning generation. To this end, we propose Fusion-of-N (FusioN): a method that uses a general LLM judge to synthesize the most informative elements of each sample into a single final answer. We compare FusioN to BoN in two settings, (i) test-time scaling, where we sample and aggregate from a single model at test-time (ii) synthetic data generation, where we fuse samples from a pool of diverse teachers to improve a student model. We extensively benchmark both setups across 11 languages, 3 diverse tasks and varying model scales. Across the bench, FusioN consistently outperforms BoN showing versatility and robustness both in test-time scaling and in downstream gains from synthetic data generation. We also perform extensive analysis on FusioN, where it shows surprising strengths and robustness under challenging settings. These results show that we should shift how we think about evaluating and utilizing LLM generations from a monolithic measure of quality, to embracing their polylithic nature. This shift allows us to integrate diverse strengths, unlock latent potential, and achieve improvements that were previously inaccessible through selection alone.

Recent advancements in both representation learning and function learning have demonstrated substantial promise across diverse domains of artificial intelligence. However, the effective integration of these paradigms poses a significant challenge, particularly in cases where users must manually decide whether to apply a representation learning or function learning model based on dataset characteristics. To address this issue, we introduce MLP-KAN, a unified method designed to eliminate the need for manual model selection. By integrating Multi-Layer Perceptrons (MLPs) for representation learning and Kolmogorov-Arnold Networks (KANs) for function learning within a Mixture-of-Experts (MoE) architecture, MLP-KAN dynamically adapts to the specific characteristics of the task at hand, ensuring optimal performance. Embedded within a transformer-based framework, our work achieves remarkable results on four widely-used datasets across diverse domains. Extensive experimental evaluation demonstrates its superior versatility, delivering competitive performance across both deep representation and function learning tasks. These findings highlight the potential of MLP-KAN to simplify the model selection process, offering a comprehensive, adaptable solution across various domains. Our code and weights are available at https://github.com/DLYuanGod/MLP-KAN.

Graph Neural Networks (GNNs) are popular models for graph learning problems. GNNs show strong empirical performance in many practical tasks. However, the theoretical properties have not been completely elucidated. In this paper, we investigate whether GNNs can exploit the graph structure from the perspective of the expressive power of GNNs. In our analysis, we consider graph generation processes that are controlled by hidden (or latent) node features, which contain all information about the graph structure. A typical example of this framework is kNN graphs constructed from the hidden features. In our main results, we show that GNNs can recover the hidden node features from the input graph alone, even when all node features, including the hidden features themselves and any indirect hints, are unavailable. GNNs can further use the recovered node features for downstream tasks. These results show that GNNs can fully exploit the graph structure by themselves, and in effect, GNNs can use both the hidden and explicit node features for downstream tasks. In the experiments, we confirm the validity of our results by showing that GNNs can accurately recover the hidden features using a GNN architecture built based on our theoretical analysis.

We address the problem of performing backpropagation for computation graphs involving 3D transformation groups SO(3), SE(3), and Sim(3). 3D transformation groups are widely used in 3D vision and robotics, but they do not form vector spaces and instead lie on smooth manifolds. The standard backpropagation approach, which embeds 3D transformations in Euclidean spaces, suffers from numerical difficulties. We introduce a new library, which exploits the group structure of 3D transformations and performs backpropagation in the tangent spaces of manifolds. We show that our approach is numerically more stable, easier to implement, and beneficial to a diverse set of tasks. Our plug-and-play PyTorch library is available at https://github.com/princeton-vl/lietorch.

Model merging is a powerful technique for integrating the specialized knowledge of multiple machine learning models into a single model. However, existing methods require manually partitioning model parameters into fixed groups for merging, which restricts the exploration of potential combinations and limits performance. To overcome these limitations, we propose Model Merging of Natural Niches (M2N2), an evolutionary algorithm with three key features: (1) dynamic adjustment of merging boundaries to progressively explore a broader range of parameter combinations; (2) a diversity preservation mechanism inspired by the competition for resources in nature, to maintain a population of diverse, high-performing models that are particularly well-suited for merging; and (3) a heuristicbased attraction metric to identify the most promising pairs of models for fusion. Our experimental results demonstrate, for the first time, that model merging can be used to evolve models entirely from scratch. Specifically, we apply M2N2 to evolve MNIST classifiers from scratch and achieve performance comparable to CMA-ES, while being computationally more efficient. Furthermore, M2N2 scales to merge specialized language and image generation models, achieving state-of-the-art performance. Notably, it preserves crucial model capabilities beyond those explicitly optimized by the fitness function, highlighting its robustness and versatility. Our code is available at https://github.com/SakanaAI/natural_niches

Simultaneously achieving robust classification and high-fidelity generative modeling within a single framework presents a significant challenge. Hybrid approaches, such as Joint Energy-Based Models (JEM), interpret classifiers as EBMs but are often limited by the instability and poor sample quality inherent in SGLD-based training. We address these limitations by proposing a novel training framework that integrates adversarial training (AT) principles for both discriminative robustness and stable generative learning. The proposed method introduces three key innovations: (1) the replacement of SGLD-based JEM learning with a stable, AT-based approach that optimizes the energy function by discriminating between real data and PGD-generated contrastive samples using the BCE loss; (2) synergistic adversarial training for the discriminative component that enhances classification robustness while eliminating the need for explicit gradient penalties; and (3) a two-stage training procedure to resolve the incompatibility between batch normalization and EBM training. Experiments on CIFAR-10, CIFAR-100, and ImageNet demonstrate that our method substantially improves adversarial robustness over existing hybrid models while maintaining competitive generative performance. On ImageNet, when optimized for generative modeling, our model's generative fidelity surpasses that of BigGAN and approaches diffusion models, representing the first MCMC-based EBM approach to achieve high-quality generation on complex, high-resolution datasets. Our approach addresses key stability issues that have limited JEM scaling and demonstrates that adversarial training can serve as an effective foundation for unified frameworks capable of generating and robustly classifying visual data.

Graph neural networks (GNNs) have achieved remarkable success across a wide range of applications, such as recommendation, drug discovery, and question answering. Behind the success of GNNs lies the backpropagation (BP) algorithm, which is the de facto standard for training deep neural networks (NNs). However, despite its effectiveness, BP imposes several constraints, which are not only biologically implausible, but also limit the scalability, parallelism, and flexibility in learning NNs. Examples of such constraints include storage of neural activities computed in the forward pass for use in the subsequent backward pass, and the dependence of parameter updates on non-local signals. To address these limitations, the forward-forward algorithm (FF) was recently proposed as an alternative to BP in the image classification domain, which trains NNs by performing two forward passes over positive and negative data. Inspired by this advance, we propose ForwardGNN in this work, a new forward learning procedure for GNNs, which avoids the constraints imposed by BP via an effective layer-wise local forward training. ForwardGNN extends the original FF to deal with graph data and GNNs, and makes it possible to operate without generating negative inputs (hence no longer forward-forward). Further, ForwardGNN enables each layer to learn from both the bottom-up and top-down signals without relying on the backpropagation of errors. Extensive experiments on real-world datasets show the effectiveness and generality of the proposed forward graph learning framework. We release our code at https://github.com/facebookresearch/forwardgnn.

Neural Module Network (NMN) is a machine learning model for solving the visual question answering tasks. NMN uses programs to encode modules' structures, and its modularized architecture enables it to solve logical problems more reasonably. However, because of the non-differentiable procedure of module selection, NMN is hard to be trained end-to-end. To overcome this problem, existing work either included ground-truth program into training data or applied reinforcement learning to explore the program. However, both of these methods still have weaknesses. In consideration of this, we proposed a new learning framework for NMN. Graph-based Heuristic Search is the algorithm we proposed to discover the optimal program through a heuristic search on the data structure named Program Graph. Our experiments on FigureQA and CLEVR dataset show that our methods can realize the training of NMN without ground-truth programs and achieve superior efficiency over existing reinforcement learning methods in program exploration.

This paper demonstrates that language models are strong structure-based protein designers. We present LM-Design, a generic approach to reprogramming sequence-based protein language models (pLMs), that have learned massive sequential evolutionary knowledge from the universe of natural protein sequences, to acquire an immediate capability to design preferable protein sequences for given folds. We conduct a structural surgery on pLMs, where a lightweight structural adapter is implanted into pLMs and endows it with structural awareness. During inference, iterative refinement is performed to effectively optimize the generated protein sequences. Experiments show that LM-Design improves the state-of-the-art results by a large margin, leading to up to 4% to 12% accuracy gains in sequence recovery (e.g., 55.65%/56.63% on CATH 4.2/4.3 single-chain benchmarks, and >60% when designing protein complexes). We provide extensive and in-depth analyses, which verify that LM-Design can (1) indeed leverage both structural and sequential knowledge to accurately handle structurally non-deterministic regions, (2) benefit from scaling data and model size, and (3) generalize to other proteins (e.g., antibodies and de novo proteins)

Graph Neural Networks (GNNs), especially message-passing neural networks (MPNNs), have emerged as powerful architectures for learning on graphs in diverse applications. However, MPNNs face challenges when modeling non-local interactions in graphs such as large conjugated molecules, and social networks due to oversmoothing and oversquashing. Although Spectral GNNs and traditional neural networks such as recurrent neural networks and transformers mitigate these challenges, they often lack generalizability, or fail to capture detailed structural relationships or symmetries in the data. To address these concerns, we introduce Matrix Function Neural Networks (MFNs), a novel architecture that parameterizes non-local interactions through analytic matrix equivariant functions. Employing resolvent expansions offers a straightforward implementation and the potential for linear scaling with system size. The MFN architecture achieves stateof-the-art performance in standard graph benchmarks, such as the ZINC and TU datasets, and is able to capture intricate non-local interactions in quantum systems, paving the way to new state-of-the-art force fields.

Linear RNN architectures, like Mamba, can be competitive with Transformer models in language modeling while having advantageous deployment characteristics. Given the focus on training large-scale Transformer models, we consider the challenge of converting these pretrained models for deployment. We demonstrate that it is feasible to distill large Transformers into linear RNNs by reusing the linear projection weights from attention layers with academic GPU resources. The resulting hybrid model, which incorporates a quarter of the attention layers, achieves performance comparable to the original Transformer in chat benchmarks and outperforms open-source hybrid Mamba models trained from scratch with trillions of tokens in both chat benchmarks and general benchmarks. Moreover, we introduce a hardware-aware speculative decoding algorithm that accelerates the inference speed of Mamba and hybrid models. Overall we show how, with limited computation resources, we can remove many of the original attention layers and generate from the resulting model more efficiently. Our top-performing model, distilled from Llama3-8B-Instruct, achieves a 29.61 length-controlled win rate on AlpacaEval 2 against GPT-4 and 7.35 on MT-Bench, surpassing the best instruction-tuned linear RNN model.

This paper explores the advancements and applications of large-scale models in the medical field, with a particular focus on Medical Large Models (MedLMs). These models, encompassing Large Language Models (LLMs), Vision Models, 3D Large Models, and Multimodal Models, are revolutionizing healthcare by enhancing disease prediction, diagnostic assistance, personalized treatment planning, and drug discovery. The integration of graph neural networks in medical knowledge graphs and drug discovery highlights the potential of Large Graph Models (LGMs) in understanding complex biomedical relationships. The study also emphasizes the transformative role of Vision-Language Models (VLMs) and 3D Large Models in medical image analysis, anatomical modeling, and prosthetic design. Despite the challenges, these technologies are setting new benchmarks in medical innovation, improving diagnostic accuracy, and paving the way for personalized healthcare solutions. This paper aims to provide a comprehensive overview of the current state and future directions of large models in medicine, underscoring their significance in advancing global health.

Model merging combines multiple fine-tuned checkpoints into a single model without additional training, offering an attractive approach to reusing models and efficiently improving performance. However, it remains unclear whether the advantages reported for settings where all merged experts have distinct roles and are tuned on clearly separated tasks also hold in settings where the merged experts do not have clearly distinct roles, but are trained on overlapping or even conflicting objectives. To evaluate this setting, we present a large-scale, systematic evaluation of "in-the-wild" model merging of heterogeneous experts, that may have been trained on overlapping or conflicting objectives. Concretely, we evaluate six state-of-the-art merging methods, including recent subspace methods, across four open-weight LLMs, twelve fine-tuned checkpoints per base model, and sixteen standard LLM benchmarks. Evaluating through standardized benchmarks, we measure both the probability that a model merged from a heterogeneous set of experts outperforms the base model and we measure relative gains over the best individual checkpoint. Our results show that the oldest and simplest method, Task Arithmetic, is the only approach that reliably yields performance gains on LLMs in this "in-the-wild" setting. Other interference-aware and subspace merging methods typically do not result in notable improvements over the base model. Our findings indicate that current merging techniques mostly do not enable extracting useful weight updates from heterogeneous and potentially conflicting versions. This motivates the design of LLM-specific merging algorithms and merging-aware fine-tuning methods.

Protein language models (pLMs) pre-trained on vast protein sequence databases excel at various downstream tasks but lack the structural knowledge essential for many biological applications. To address this, we integrate structural insights from pre-trained protein graph neural networks (pGNNs) into pLMs through a latent-level contrastive learning task. This task aligns residue representations from pLMs with those from pGNNs across multiple proteins, enriching pLMs with inter-protein structural knowledge. Additionally, we incorporate a physical-level task that infuses intra-protein structural knowledge by optimizing pLMs to predict structural tokens. The proposed dual-task framework effectively incorporates both inter-protein and intra-protein structural knowledge into pLMs. Given the variability in the quality of protein structures in PDB, we further introduce a residue loss selection module, which uses a small model trained on high-quality structures to select reliable yet challenging residue losses for the pLM to learn. Applying our structure alignment method to the state-of-the-art ESM2 and AMPLIFY results in notable performance gains across a wide range of tasks, including a 12.7% increase in ESM2 contact prediction. The data, code, and resulting SaESM2 and SaAMPLIFY models will be released on Hugging Face.

Scaling language models to handle longer contexts introduces substantial memory challenges due to the growing cost of key-value (KV) caches. Motivated by the efficiency gains of hybrid models and the broad availability of pretrained large transformer backbones, we explore transitioning transformer models into hybrid architectures for a more efficient generation. In this work, we propose LightTransfer, a lightweight method that transforms models such as LLaMA into hybrid variants. Our approach identifies lazy layers -- those focusing on recent or initial tokens -- and replaces their full attention with streaming attention. This transformation can be performed without any training for long-context understanding tasks or with minimal fine-tuning for o1-like long reasoning generation tasks that require stronger reasoning capabilities. Experiments across diverse benchmarks and models (e.g., LLaMA, Mistral, QwQ-STILL) demonstrate that, even when half of the layers are identified as lazy, LightTransfer achieves up to 2.17times throughput improvement with minimal performance loss (<1.5% on LongBench) and achieves 53.3\% on math benchmark AIME24 of advanced o1-like long reasoning model QwQ-STILL.

Communication is a key bottleneck for distributed graph neural network (GNN) training. This paper proposes GNNPipe, a new approach that scales the distributed full-graph deep GNN training. Being the first to use layer-level model parallelism for GNN training, GNNPipe partitions GNN layers among GPUs, each device performs the computation for a disjoint subset of consecutive GNN layers on the whole graph. Compared to graph parallelism with each GPU handling a graph partition, GNNPipe reduces the communication volume by a factor of the number of GNN layers. GNNPipe overcomes the unique challenges for pipelined layer-level model parallelism on the whole graph by partitioning it into dependent chunks, allowing the use of historical vertex embeddings, and applying specific training techniques to ensure convergence. We also propose a hybrid approach by combining GNNPipe with graph parallelism to handle large graphs, achieve better computer resource utilization and ensure model convergence. We build a general GNN training system supporting all three parallelism setting. Extensive experiments show that our method reduces the per-epoch training time by up to 2.45x (on average 1.58x) and reduces the communication volume and overhead by up to 22.89x and 27.21x (on average 8.69x and 11.60x), respectively, while achieving a comparable level of model accuracy and convergence speed compared to graph parallelism.

This study introduces BrainTransformers, an innovative Large Language Model (LLM) implemented using Spiking Neural Networks (SNN). Our key contributions include: (1) designing SNN-compatible Transformer components such as SNNMatmul, SNNSoftmax, and SNNSiLU; (2) implementing an SNN approximation of the SiLU activation function; and (3) developing a Synapsis module to simulate synaptic plasticity. Our 3-billion parameter model, BrainTransformers-3B-Chat, demonstrates competitive performance across various benchmarks, including MMLU (63.2), BBH (54.1), ARC-C (54.3), and GSM8K (76.3), while potentially offering improved energy efficiency and biological plausibility. The model employs a three-stage training approach, including SNN-specific neuronal synaptic plasticity training. This research opens new avenues for brain-like AI systems in natural language processing and neuromorphic computing. Future work will focus on hardware optimization, developing specialized SNN fine-tuning tools, and exploring practical applications in energy-efficient computing environments.

Fine-tuning pre-trained Large Language Models (LLMs) for specialized tasks incurs substantial computational and data costs. While model merging offers a training-free solution to integrate multiple task-specific models, existing methods suffer from safety-utility conflicts where enhanced general capabilities degrade safety safeguards. We identify two root causes: neuron misidentification due to simplistic parameter magnitude-based selection, and cross-task neuron interference during merging. To address these challenges, we propose LED-Merging, a three-stage framework that Locates task-specific neurons via gradient-based attribution, dynamically Elects critical neurons through multi-model importance fusion, and Disjoints conflicting updates through parameter isolation. Extensive experiments on Llama-3-8B, Mistral-7B, and Llama2-13B demonstrate that LED-Merging effectively reduces harmful response rates, showing a 31.4\% decrease on Llama-3-8B-Instruct on HarmBench, while simultaneously preserving 95\% of utility performance, such as achieving 52.39\% accuracy on GSM8K. LED-Merging resolves safety-utility conflicts and provides a lightweight, training-free paradigm for constructing reliable multi-task LLMs. Code is available at https://github.com/MqLeet/LED-Merging{GitHub}.

In this paper, we present LiGNN, a deployed large-scale Graph Neural Networks (GNNs) Framework. We share our insight on developing and deployment of GNNs at large scale at LinkedIn. We present a set of algorithmic improvements to the quality of GNN representation learning including temporal graph architectures with long term losses, effective cold start solutions via graph densification, ID embeddings and multi-hop neighbor sampling. We explain how we built and sped up by 7x our large-scale training on LinkedIn graphs with adaptive sampling of neighbors, grouping and slicing of training data batches, specialized shared-memory queue and local gradient optimization. We summarize our deployment lessons and learnings gathered from A/B test experiments. The techniques presented in this work have contributed to an approximate relative improvements of 1% of Job application hearing back rate, 2% Ads CTR lift, 0.5% of Feed engaged daily active users, 0.2% session lift and 0.1% weekly active user lift from people recommendation. We believe that this work can provide practical solutions and insights for engineers who are interested in applying Graph neural networks at large scale.

Can we leverage LLMs to model the process of discovering novel language model (LM) architectures? Inspired by real research, we propose a multi-agent LLM approach that simulates the conventional stages of research, from ideation and literature search (proposal stage) to design implementation (code generation), generative pre-training, and downstream evaluation (verification). Using ideas from scaling laws, our system, Genesys, employs a Ladder of Scales approach; new designs are proposed, adversarially reviewed, implemented, and selectively verified at increasingly larger model scales (14Msim350M parameters) with a narrowing budget (the number of models we can train at each scale). To help make discovery efficient and factorizable, Genesys uses a novel genetic programming backbone, which we show has empirical advantages over commonly used direct prompt generation workflows (e.g., sim86\% percentage point improvement in successful design generation, a key bottleneck). We report experiments involving 1,162 newly discovered designs (1,062 fully verified through pre-training) and find the best designs to be highly competitive with known architectures (e.g., outperform GPT2, Mamba2, etc., on 6/9 common benchmarks). We couple these results with comprehensive system-level ablations and formal results, which give broader insights into the design of effective autonomous discovery systems.

Graph neural networks (GNNs) have been demonstrated to be powerful in modeling graph-structured data. However, training GNNs usually requires abundant task-specific labeled data, which is often arduously expensive to obtain. One effective way to reduce the labeling effort is to pre-train an expressive GNN model on unlabeled data with self-supervision and then transfer the learned model to downstream tasks with only a few labels. In this paper, we present the GPT-GNN framework to initialize GNNs by generative pre-training. GPT-GNN introduces a self-supervised attributed graph generation task to pre-train a GNN so that it can capture the structural and semantic properties of the graph. We factorize the likelihood of the graph generation into two components: 1) Attribute Generation and 2) Edge Generation. By modeling both components, GPT-GNN captures the inherent dependency between node attributes and graph structure during the generative process. Comprehensive experiments on the billion-scale Open Academic Graph and Amazon recommendation data demonstrate that GPT-GNN significantly outperforms state-of-the-art GNN models without pre-training by up to 9.1% across various downstream tasks.

Hybrid models that combine the language modeling capabilities of Attention layers with the efficiency of Recurrent layers (e.g., State Space Models) have gained traction in practically supporting long contexts in Large Language Model serving. Yet, the unique properties of these models complicate the usage of complementary efficiency optimizations such as prefix caching that skip redundant computations across requests. Most notably, their use of in-place state updates for recurrent layers precludes rolling back cache entries for partial sequence overlaps, and instead mandates only exact-match cache hits; the effect is a deluge of (large) cache entries per sequence, most of which yield minimal reuse opportunities. We present Marconi, the first system that supports efficient prefix caching with Hybrid LLMs. Key to Marconi are its novel admission and eviction policies that more judiciously assess potential cache entries based not only on recency, but also on (1) forecasts of their reuse likelihood across a taxonomy of different hit scenarios, and (2) the compute savings that hits deliver relative to memory footprints. Across diverse workloads and Hybrid models, Marconi achieves up to 34.4times higher token hit rates (71.1% or 617 ms lower TTFT) compared to state-of-the-art prefix caching systems.

Graph Neural Network (GNN) research is rapidly advancing due to GNNs' capacity to learn distributed representations from graph-structured data. However, centralizing large volumes of real-world graph data for GNN training is often impractical due to privacy concerns, regulatory restrictions, and commercial competition. Federated learning (FL), a distributed learning paradigm, offers a solution by preserving data privacy with collaborative model training. Despite progress in training huge vision and language models, federated learning for GNNs remains underexplored. To address this challenge, we present a novel method for federated learning on GNNs based on spectral GNNs equipped with neural ordinary differential equations (ODE) for better information capture, showing promising results across both homophilic and heterophilic graphs. Our approach effectively handles non-Independent and Identically Distributed (non-IID) data, while also achieving performance comparable to existing methods that only operate on IID data. It is designed to be privacy-preserving and bandwidth-optimized, making it suitable for real-world applications such as social network analysis, recommendation systems, and fraud detection, which often involve complex, non-IID, and heterophilic graph structures. Our results in the area of federated learning on non-IID heterophilic graphs demonstrate significant improvements, while also achieving better performance on homophilic graphs. This work highlights the potential of federated learning in diverse and challenging graph settings. Open-source code available on GitHub (https://github.com/SpringWiz11/Fed-GNODEFormer).

This paper introduces GLLM, an innovative tool that leverages Large Language Models (LLMs) to automatically generate G-code from natural language instructions for Computer Numerical Control (CNC) machining. GLLM addresses the challenges of manual G-code writing by bridging the gap between human-readable task descriptions and machine-executable code. The system incorporates a fine-tuned StarCoder-3B model, enhanced with domain-specific training data and a Retrieval-Augmented Generation (RAG) mechanism. GLLM employs advanced prompting strategies and a novel self-corrective code generation approach to ensure both syntactic and semantic correctness of the generated G-code. The architecture includes robust validation mechanisms, including syntax checks, G-code-specific verifications, and functional correctness evaluations using Hausdorff distance. By combining these techniques, GLLM aims to democratize CNC programming, making it more accessible to users without extensive programming experience while maintaining high accuracy and reliability in G-code generation.

Graph neural networks (GNNs) are a powerful architecture for tackling graph learning tasks, yet have been shown to be oblivious to eminent substructures such as cycles. We present TOGL, a novel layer that incorporates global topological information of a graph using persistent homology. TOGL can be easily integrated into any type of GNN and is strictly more expressive (in terms the Weisfeiler--Lehman graph isomorphism test) than message-passing GNNs. Augmenting GNNs with TOGL leads to improved predictive performance for graph and node classification tasks, both on synthetic data sets, which can be classified by humans using their topology but not by ordinary GNNs, and on real-world data.

Although pre-trained language models have exhibited great flexibility and versatility with prompt-based few-shot learning, they suffer from the extensive parameter size and limited applicability for inference. Recent studies have suggested that PLMs be used as dataset generators and a tiny task-specific model be trained to achieve efficient inference. However, their applicability to various domains is limited because they tend to generate domain-specific datasets. In this work, we propose a novel approach to universal domain generalization that generates a dataset regardless of the target domain. This allows for generalization of the tiny task model to any domain that shares the label space, thus enhancing the real-world applicability of the dataset generation paradigm. Our experiments indicate that the proposed method accomplishes generalizability across various domains while using a parameter set that is orders of magnitude smaller than PLMs.

Large language models (LLMs) have recently demonstrated their potential in clinical applications, providing valuable medical knowledge and advice. For example, a large dialog LLM like ChatGPT has successfully passed part of the US medical licensing exam. However, LLMs currently have difficulty processing images, making it challenging to interpret information from medical images, which are rich in information that supports clinical decisions. On the other hand, computer-aided diagnosis (CAD) networks for medical images have seen significant success in the medical field by using advanced deep-learning algorithms to support clinical decision-making. This paper presents a method for integrating LLMs into medical-image CAD networks. The proposed framework uses LLMs to enhance the output of multiple CAD networks, such as diagnosis networks, lesion segmentation networks, and report generation networks, by summarizing and reorganizing the information presented in natural language text format. The goal is to merge the strengths of LLMs' medical domain knowledge and logical reasoning with the vision understanding capability of existing medical-image CAD models to create a more user-friendly and understandable system for patients compared to conventional CAD systems. In the future, LLM's medical knowledge can be also used to improve the performance of vision-based medical-image CAD models.

In recent years, generative pre-trained paradigms such as Large Language Models (LLMs) and Large Vision Models (LVMs) have achieved revolutionary advancements and widespread real-world applications. Particularly, the emergence of pre-trained LLMs-based temporal works, compared to previous deep model approaches, has demonstrated superior generalization and robustness, showcasing the potential of generative pre-trained paradigms as foundation models for time series. However, those LLMs-based works mainly focus on cross-modal research, i.e., leveraging the language capabilities of LLMs in time series contexts. Although they have achieved impressive performance, there still exist the issues of concept drift caused by differences in data distribution and inflexibility caused by misalignment of dimensions. To this end, inspired by recent work on LVMs, we reconsider the paradigm of time series modeling. In this paper, we comprehensively explore, for the first time, the effectiveness and superiority of the Generative Pre-trained Diffusion (GPD) paradigm in real-world multivariate time series forecasting (TSF). Specifically, to mitigate performance bias introduced by sophisticated networks, we propose a straightforward MLP diffusion network for unconditional modeling of time series. Then we employ a zero-shot and tuning-free method to predict (generate) future data using historical data as prompts. The GPD paradigm is established on the time series modality, effectively preventing the phenomenon of concept drift, and enabling flexible forecasting of arbitrary lengths. We demonstrate that the GPD paradigm achieves comprehensive performance and generalization comparable to current SOTA LLM-based and deep model paradigms on mainstream benchmarks and various TSF tasks. Extensive experiments validate the potential of the GPD paradigm and its assistance in future related research.

Graph Neural Networks (GNNs) that are based on the message passing (MP) paradigm generally exchange information between 1-hop neighbors to build node representations at each layer. In principle, such networks are not able to capture long-range interactions (LRI) that may be desired or necessary for learning a given task on graphs. Recently, there has been an increasing interest in development of Transformer-based methods for graphs that can consider full node connectivity beyond the original sparse structure, thus enabling the modeling of LRI. However, MP-GNNs that simply rely on 1-hop message passing often fare better in several existing graph benchmarks when combined with positional feature representations, among other innovations, hence limiting the perceived utility and ranking of Transformer-like architectures. Here, we present the Long Range Graph Benchmark (LRGB) with 5 graph learning datasets: PascalVOC-SP, COCO-SP, PCQM-Contact, Peptides-func and Peptides-struct that arguably require LRI reasoning to achieve strong performance in a given task. We benchmark both baseline GNNs and Graph Transformer networks to verify that the models which capture long-range dependencies perform significantly better on these tasks. Therefore, these datasets are suitable for benchmarking and exploration of MP-GNNs and Graph Transformer architectures that are intended to capture LRI.