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Deep Learning · Graph Neural Networks

Dongzhuoran Zhou, Evgeny Kharlamov, Egor Kostylev

Learning on graphs is one of the most active research topics in machine learning (ML). Among the key challenges in this field, effectively learning long-range dependencies in graphs has been particularly difficult. It has been observed that, in practice, the performance of many ML approaches, including various types of graph neural networks (GNNs), degrades significantly when the learning task involves long-range dependencies—that is, when the answer is determined by the presence of a certain path of significant length in the graph. This issue has been attributed to several phenomena, including over-smoothing, over-squashing, and vanishing gradient. A number of solutions have been proposed to mitigate these causes. However, evaluation of these solutions is currently challenging because existing benchmarks do not effectively test systems for their ability to learn tasks based on long-range dependencies in a transparent manner. In this paper, we introduce GLoRa, a synthetic benchmark that allows testing of systems for this ability in a systematic way. We then evaluate state-of-the-art systems using GLoRa and conclude that none of them can confidently claim to learn long-range dependencies well. We also observe that this weak performance cannot be attributed to any of the three causes, highlighting the need for further investigation.

Deep Learning · Large Language Models

Minsung Kim, Jea Kwon, Dong-Kyum Kim, Meeyoung Cha

Large Language Models (LLMs) are enhancing our daily lives but also pose risks like spreading misinformation and violating privacy, highlighting the importance of understanding how they process and store information. This blogpost offers a fresh look into a neuroscience-inspired perspective of LLM's memory functions, based on the concept of engrams-the physical substrate of memory in living organism. We discuss a synergy between AI research and neuroscience, as both fields cover complexities of intelligent systems.

Applications · Computer Vision

Jea Kwon, Sungjun Lim, Kyungwoo Song, C. Lee

Convolutional Neural Networks (CNNs) have profoundly influenced the field of computer vision, drawing significant inspiration from the visual processing mechanisms inherent in the brain. Despite sharing fundamental structural and representational similarities with the biological visual system, differences in local connectivity patterns within CNNs open up an interesting area to explore. In this work, we explore whether integrating biologically observed receptive fields (RFs) can enhance model performance and foster alignment with brain representations. We introduce a novel methodology, termed $L_p$-convolution, which employs the multivariate $L_p$-generalized normal distribution as an adaptable $L_p$-masks, to reconcile disparities between artificial and biological RFs. $L_p$-masks finds the optimal RFs through task-dependent adaptation of conformation such as distortion, scale, and rotation. This allows $L_p$-convolution to excel in tasks that require flexible RF shapes, including not only square-shaped regular RFs but also horizontal and vertical ones. Furthermore, we demonstrate that $L_p$-convolution with biological RFs significantly enhances the performance of large kernel CNNs possibly by introducing structured sparsity inspired by $L_p$-generalized normal distribution in convolution. Lastly, we present that neural representations of CNNs align more closely with the visual cortex when -convolution is close to biological RFs.

Applications · Computer Vision

Maximilian Weiherer, Bernhard Egger

We propose to use the family of Matérn kernels for implicit surface reconstruction, building upon the recent success of kernel methods for 3D reconstruction of oriented point clouds. As we show from a theoretical and practical perspective, Matérn kernels have some appealing properties which make them particularly well suited for surface reconstruction---outperforming state-of-the-art methods based on the arc-cosine kernel while being significantly easier to implement, faster to compute, and scalable. Being stationary, we demonstrate that Matérn kernels allow for tunable surface reconstruction in the same way as Fourier feature mappings help coordinate-based MLPs overcome spectral bias. Moreover, we theoretically analyze Matérn kernels' connection to SIREN networks as well as their relation to previously employed arc-cosine kernels. Finally, based on recently introduced Neural Kernel Fields, we present data-dependent Matérn kernels and conclude that especially the Laplace kernel (being part of the Matérn family) is extremely competitive, performing almost on par with state-of-the-art methods in the noise-free case while having a more than five times shorter training time.

Deep Learning · Large Language Models

Jingwei Xu, Junyu Lai, Yunpeng Huang

The pretrain+fine-tune paradigm is foundational for deploying large language models (LLMs) across various downstream applications. Within this framework, Low-Rank Adaptation (LoRA) stands out for its parameter-efficient fine-tuning (PEFT), producing numerous reusable task-specific LoRA adapters. However, this approach requires explicit task intention selection, posing challenges for autonomous task sensing and switching during inference with multiple existing LoRA adapters embedded in a single LLM. In this work, we introduce MeteoRA (Multiple-Tasks embedded LoRA), a scalable and efficient framework that reuses multiple task-specific LoRA adapters into the base LLM via a full-mode Mixture-of-Experts (MoE) architecture. This framework also includes novel MoE forward acceleration strategies to address the efficiency challenges of traditional MoE implementations. Our evaluation, using the LlaMA2-13B and LlaMA3-8B base models equipped with 28 existing LoRA adapters through MeteoRA, demonstrates equivalent performance with the traditional PEFT method. Moreover, the LLM equipped with MeteoRA achieves superior performance in handling composite tasks, effectively solving ten sequential problems in a single inference pass, thereby demonstrating the framework's enhanced capability for timely adapter switching.

Theory · Game Theory

Wonjoon Chang, Myeongjin Lee, Jaesik Choi

We study causal interactions for payoff allocation in cooperative game theory, including quantifying feature attribution for deep learning models. Most feature attribution methods mainly stem from the criteria of the Shapley value, which assigns fair payoffs to players based on their expected contribution in a cooperative game. However, interactions between players in the game do not explicitly appear in the original formulation of the Shapley value. In this work, we reformulate the Shapley value to clarify the role of interactions and discuss implicit assumptions from a game-theoretical perspective. Our theoretical analysis demonstrates that when negative interactions exist—common in deep learning models—the efficiency axiom can lead to the undervaluation of attributions or payoffs. We suggest a new allocation rule that decomposes contributions into interactions and aggregates positive parts for non-convex games. Furthermore, we propose an approximation algorithm to reduce the cost of interaction computation which can be applied to differentiable functions such as deep learning models. Our approach mitigates counterintuitive attribution outcomes observed in existing methods, ensuring that features critical to a model’s decision receive appropriate attribution.

Deep Learning · Large Language Models

Zafeirios Fountas, Martin A Benfeghoul, Adnan Oomerjee, Fenia Christopoulou, Gerasimos Lampouras, Haitham Bou Ammar, Jun Wang

Large language models (LLMs) have shown remarkable capabilities, but still struggle with processing extensive contexts, limiting their ability to maintain coherence and accuracy over long sequences. In contrast, the human brain excels at organising and retrieving episodic experiences across vast temporal scales, spanning a lifetime. In this work, we introduce EM-LLM, a novel approach that integrates key aspects of human episodic memory and event cognition into LLMs with no fine-tuning, enabling them to handle practically infinite context lengths while maintaining computational efficiency. EM-LLM organises sequences of tokens into coherent episodic events using a combination of Bayesian surprise and graph-theoretic boundary refinement in an online fashion. When needed, these events are retrieved through a two-stage memory process, combining similarity-based and temporally contiguous retrieval for efficient, human-inspired access to relevant information. Experiments on the LongBench and $\infty$-Bench benchmarks demonstrate EM-LLM's superior performance, consistently outperforming the state-of-the-art retrieval model InfLLM across various baseline LLMs. In addition, EM-LLM outperforms its popular counterpart, RAG, in a wide range of tasks, while requiring similar resources. Notably, EM-LLM's performance even surpasses full-context models in most tasks, while successfully performing retrieval across 10 million tokens -- a scale computationally infeasible for such models. Finally, our analysis reveals strong correlations between EM-LLM's event segmentation and human-perceived events, suggesting parallels between this artificial system and its biological counterpart, thereby offering a novel computational framework for exploring human memory mechanisms.

Deep Learning · Large Language Models

Tanishq Kumar, Zachary Ankner, Benjamin Spector, Blake Bordelon, Niklas Muennighoff, Mansheej Paul, Cengiz Pehlevan, Christopher Re, Aditi Raghunathan

Low precision training and inference affect both the quality and cost of language models, but current scaling laws do not account for this. In this work, we devise "precision-aware" scaling laws for both training and inference. We propose that training in lower precision reduces the model's "effective parameter count," allowing us to predict the additional loss incurred from training in low precision and post-train quantization. For inference, we find that the degradation introduced by post-training quantization increases as models are trained on more data, eventually making additional pretraining data actively harmful. For training, our scaling laws allow us to predict the loss of a model with different parts in different precisions, and suggest that training larger models in lower precision can be compute optimal. We unify the scaling laws for post and pretraining quantization to arrive at a single functional form that predicts degradation from training and inference in varied precisions. We fit on over 465 pretraining runs and validate our predictions on model sizes up to 1.7B parameters trained on up to 26B tokens.

Deep Learning · Large Language Models

Tanishq Kumar, Zachary Ankner, Benjamin Spector, Blake Bordelon, Niklas Muennighoff, Mansheej Paul, Cengiz Pehlevan, Christopher Re, Aditi Raghunathan

Low precision training and inference affect both the quality and cost of language models, but current scaling laws do not account for this. In this work, we devise "precision-aware" scaling laws for both training and inference. We propose that training in lower precision reduces the model's "effective parameter count," allowing us to predict the additional loss incurred from training in low precision and post-train quantization. For inference, we find that the degradation introduced by post-training quantization increases as models are trained on more data, eventually making additional pretraining data actively harmful. For training, our scaling laws allow us to predict the loss of a model with different parts in different precisions, and suggest that training larger models in lower precision can be compute optimal. We unify the scaling laws for post and pretraining quantization to arrive at a single functional form that predicts degradation from training and inference in varied precisions. We fit on over 465 pretraining runs and validate our predictions on model sizes up to 1.7B parameters trained on up to 26B tokens.

Theory · Domain Adaptation and Transfer Learning

Yushu Li, Yongyi Su, Adam Goodge, Kui Jia, Xun Xu

Vision-language models (VLMs) have revolutionized machine learning by leveraging large pre-trained models to tackle various downstream tasks. Although label, training, and data efficiency have improved, many state-of-the-art VLMs still require task-specific hyperparameter tuning and fail to fully exploit test samples. To overcome these challenges, we propose a graph-based approach for label-efficient adaptation and inference. Our method dynamically constructs a graph over text prompts, few-shot examples, and test samples, using label propagation for inference without task-specific tuning. Unlike existing zero-shot label propagation techniques, our approach requires no additional unlabeled support set and effectively leverages the test sample manifold through dynamic graph expansion. We further introduce a context-aware feature re-weighting mechanism to improve task adaptation accuracy. Additionally, our method supports efficient graph expansion, enabling real-time inductive inference. Extensive evaluations on downstream tasks, such as fine-grained categorization and out-of-distribution generalization, demonstrate the effectiveness of our approach. The source code is available at https://github.com/Yushu-Li/ECALP.

Deep Learning · Large Language Models

Yang Qin, Chao Chen, Zhihang Fu, Ze Chen, Dezhong Peng, Peng Hu, Jieping Ye

Despite the significant advancements in Text-to-SQL (Text2SQL) facilitated by large language models (LLMs), the latest state-of-the-art techniques are still trapped in the in-context learning of closed-source LLMs (e.g., GPT-4), which limits their applicability in open scenarios. To address this challenge, we propose a novel RObust mUltitask Tuning and collaboration mEthod (ROUTE) to improve the comprehensive capabilities of open-source LLMs for Text2SQL, thereby providing a more practical solution. Our approach begins with multi-task supervised fine-tuning (SFT) using various synthetic training data related to SQL generation. Unlike existing SFT-based Text2SQL methods, we introduced several additional SFT tasks, including schema linking, noise correction, and continuation writing. Engaging in a variety of SQL generation tasks enhances the model's understanding of SQL syntax and improves its ability to generate high-quality SQL queries. Additionally, inspired by the collaborative modes of LLM agents, we introduce a Multitask Collaboration Prompting (MCP) strategy. This strategy leverages collaboration across several SQL-related tasks to reduce hallucinations during SQL generation, thereby maximizing the potential of enhancing Text2SQL performance through explicit multitask capabilities. Extensive experiments and in-depth analyses have been performed on eight open-source LLMs and five widely-used benchmarks. The results demonstrate that our proposal outperforms the latest Text2SQL methods and yields leading performance.

Deep Learning · Large Language Models

Zachary Ankner, Cody Blakeney, Kartik Sreenivasan, Max M Marion, Matthew Leavitt, Mansheej Paul

In this work, we investigate whether small language models can determine high-quality subsets of large-scale text datasets that improve the performance of larger language models. While existing work has shown that pruning based on the perplexity of a larger model can yield high-quality data, we investigate whether smaller models can be used for perplexity-based pruning and how pruning is affected by the domain composition of the data being pruned. We demonstrate that for multiple dataset compositions, perplexity-based pruning of pretraining data can significantly improve downstream task performance: pruning based on perplexities computed with a 125 million parameter model improves the average performance on downstream tasks of a 3 billion parameter model by up to 2.04 and achieves up to a 1.45× reduction in pretraining steps to reach commensurate baseline performance. Furthermore, we demonstrate that such perplexity-based data pruning also yields downstream performance gains in the over-trained and data-constrained regimes.

Applications · Neuroscience, Cognitive Science

Omer Moussa, Dietrich Klakow, Mariya Toneva

Speech language models align with human brain responses to natural language to an impressive degree. However, current models rely heavily on low-level speech features, indicating they lack brain-relevant semantics which limits their utility as model organisms of semantic processing in the brain. In this work, we address this limitation by inducing brain-relevant bias directly into the models via fine-tuning with fMRI recordings of people listening to natural stories--a process we name brain-tuning. After testing it on 3 different pretrained model families, we show that brain-tuning not only improves overall alignment with new brain recordings in semantic language regions, but also reduces the reliance on low-level speech features for this alignment. Excitingly, we further show that brain-tuning leads to 1) consistent improvements in performance on semantic downstream tasks and 2) a representational space with increased semantic preference. Our results provide converging evidence, for the first time, that incorporating brain signals into the training of language models improves the models’ semantic understanding.

Deep Learning · Graph Neural Networks

Tuo Xu

Designing expressive Graph neural networks (GNNs) is an important topic in graph machine learning fields. Traditionally, the Weisfeiler-Lehman (WL) test has been the primary measure for evaluating GNN expressiveness. However, high-order WL tests can be obscure, making it challenging to discern the specific graph patterns captured by them. Given the connection between WL tests and first-order logic, some have explored the logical expressiveness of Message Passing Neural Networks. This paper aims to establish a comprehensive and systematic relationship between GNNs and logic. We propose a framework for identifying the equivalent logical formulas for arbitrary GNN architectures, which not only explains existing models, but also provides inspiration for future research. As case studies, we analyze multiple classes of prominent GNNs within this framework, unifying different subareas of the field. Additionally, we conduct a detailed examination of homomorphism expressivity from a logical perspective and present a general method for determining the homomorphism expressivity of arbitrary GNN models, as well as addressing several open problems.

Deep Learning · Graph Neural Networks

Najwa Laabid, Severi Rissanen, Markus Heinonen, Arno Solin, Vikas Garg

Graph diffusion models, dominant in graph generative modeling, remain underexplored for graph-to-graph translation tasks like chemical reaction prediction. We demonstrate that standard permutation equivariant denoisers face fundamental limitations in these tasks due to their inability to break symmetries in noisy inputs. To address this, we propose \emph{aligning} input and target graphs to break input symmetries while preserving permutation equivariance in non-matching graph portions. Using retrosynthesis (i.e., the task of predicting precursors for synthesis of a given target molecule) as our application domain, we show how alignment dramatically improves discrete diffusion model performance from $5$\% to a SOTA-matching $54.7$\% top-1 accuracy. Code is available at https://github.com/Aalto-QuML/DiffAlign.

Miscellaneous Aspects of Machine Learning · Representation Learning

Tarun Suresh, Revanth Gangi Reddy, Yifei Xu, Zach Nussbaum, Andriy Mulyar, Brandon Duderstadt, Heng Ji

Effective code retrieval plays a crucial role in advancing code generation, bug fixing, and software maintenance, particularly as software systems increase in complexity. While current code embedding models have demonstrated promise in retrieving code snippets for small-scale, well-defined tasks, they often underperform in more demanding real-world applications such as bug localization within GitHub repositories. We hypothesize that a key issue is their reliance on noisy and inconsistent datasets for training, which impedes their ability to generalize to more complex retrieval scenarios. To address these limitations, we introduce CoRNStack, a large-scale, high-quality contrastive training dataset for code that spans multiple programming languages. This dataset is curated using consistency filtering to eliminate noisy positives and is further enriched with mined hard negatives, thereby facilitating more effective learning. We demonstrate that contrastive training of embedding models using CoRNStack leads to state-of-the-art performance across a variety of code retrieval tasks. Furthermore, the dataset can be leveraged for training code reranking models, a largely underexplored area compared to text reranking. Our finetuned code reranking model significantly improves the ranking quality over the retrieved results. Finally, by employing our code retriever and reranker together, we demonstrate significant improvements in function localization for GitHub issues, an importantcomponent of real-world software development.

Tiago Silva, Rodrigo Alves, Eliezer de Souza da Silva, Amauri Souza, Vikas Garg, Samuel Kaski, Diego Mesquita

Generative Flow Networks (GFlowNets) are an emerging class of sampling methods for distributions over discrete and compositional objects, e.g., graphs. In spite of their remarkable success in problems such as drug discovery and phylogenetic inference, the question of when and whether GFlowNets learn to sample from the target distribution remains underexplored. To tackle this issue, we first assess the extent to which a violation of the detailed balance of the underlying flow network might hamper the correctness of GFlowNet's sampling distribution. In particular, we demonstrate that the impact of an imbalanced edge on the model's accuracy is influenced by the total amount of flow passing through it and, as a consequence, is unevenly distributed across the network. We also argue that, depending on the parameterization, imbalance may be inevitable. In this regard, we consider the problem of sampling from distributions over graphs with GFlowNets parameterized by graph neural networks (GNNs) and show that the representation limits of GNNs delineate which distributions these GFlowNets can approximate. Lastly, we address these limitations by proposing a theoretically sound and computationally tractable metric for assessing GFlowNets, experimentally showing it is a better proxy for correctness than popular evaluation protocols.

Optimization · Optimization and Learning under Uncertainty

Kai Jungel, Dario Paccagnan, Axel Parmentier, Maximilian Schiffer

When optimizing transportation systems, anticipating traffic flows is a central element. Yet, computing such traffic equilibria remains computationally expensive. Against this background, we introduce a novel combinatorial optimization augmented neural network pipeline that allows for fast and accurate traffic flow predictions. We propose WardropNet, a neural network that combines classical layers with a subsequent equilibrium layer: the first ones inform the latter by predicting the parameterization of the equilibrium problem's latency functions. Using supervised learning we minimize the difference between the actual traffic flow and the predicted output. We show how to leverage a Bregman divergence fitting the geometry of the equilibria, which allows for end-to-end learning. WardropNet outperforms pure learning-based approaches in predicting traffic equilibria for realistic and stylized traffic scenarios. On realistic scenarios, WardropNet improves on average for time-invariant predictions by up to 72\% and for time-variant predictions by up to 23\% over pure learning-based approaches.

Deep Learning · Everything Else

George Wang, Jesse Hoogland, Stan van Wingerden, Zach Furman, Daniel Murfet

We introduce refined variants of the Local Learning Coefficient (LLC), a measure of model complexity grounded in singular learning theory, to study the development of internal structure in transformer language models during training. By applying these refined LLCs (rLLCs) to individual components of a two-layer attention-only transformer, we gain novel insights into the progressive differentiation and specialization of attention heads. Our methodology reveals how attention heads differentiate into distinct functional roles over the course of training, analyzes the types of data these heads specialize to process, and discovers a previously unidentified multigram circuit. These findings demonstrate that rLLCs provide a principled, quantitative toolkit for developmental interpretability, which aims to understand models through their evolution across the learning process. This work advances the field of developmental interpretability by providing a mathematically rigorous approach to understanding neural networks through the lens of their learning process. More broadly, this work takes a step towards establishing the correspondence between data distributional structure, geometric properties of the loss landscape, learning dynamics, and emergent computational structures in neural networks.

Applications · Language, Speech and Dialog

Renxi Wang, Xudong Han, Lei Ji, Shu Wang, Timothy Baldwin, Haonan Li

As large language models (LLMs) advance, their inability to autonomously execute tasks by directly interacting with external tools remains a critical limitation. Traditional methods rely on inputting tool descriptions as context, which is constrained by context length and requires separate, often inefficient, retrieval mechanisms. We introduce ToolGen, a paradigm shift that integrates tool knowledge directly into the LLM’s parameters by representing each tool as a unique token. This enables the LLM to generate tool calls and arguments as part of its next token prediction capabilities, seamlessly blending tool invocation with language generation. Our framework allows the LLM to access and utilize a vast amount of tools with no additional retrieval step, significantly enhancing both performance and scalability. Experimental results with over 47,000 tools show that ToolGen not only achieves superior results in both tool retrieval and autonomous task completion but also sets the stage for a new era of AI agents that can adapt to tools across diverse domains. By fundamentally transforming tool retrieval into a generative process, ToolGen paves the way for more versatile, efficient, and autonomous AI systems. ToolGen enables end-to-end tool learning and opens opportunities for integration with other advanced techniques such as chain-of-thought and reinforcement learning, thereby expanding the practical capabilities of LLMs