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Jun 1

From Activation to Causality: Discovery of Causal Visual Representations in the Human Brain

Identifying which brain regions represent a visual concept in the human brain is a central challenge in neuroscience. Existing approaches have localized coarse functional regions (e.g., faces, places) through activation maximization, identifying regions that activate strongly for a target concept relative to other concepts. Yet strong activation alone does not establish that a region represents the concept itself, as responses may instead be driven by correlated visual or semantic cues. We introduce BrainCause, an automated framework that combines generative and brain models to synthesize controlled stimuli and validate neural representations through targeted causal testing. Given a query specifying a concept of interest, our framework constructs targeted stimulus sets comprising concept images, counterfactual edits that remove the target concept while preserving other image content, and images with candidate correlated distractors. It then uses an image-to-fMRI encoding model to predict brain responses and searches for representations that respond specifically to the target concept over correlated alternatives. BrainCause returns validated candidate representations and proposes follow-up fMRI experiments to further test or extend its discoveries. Our approach successfully recovers known functional localizations and identifies new candidate representations across dozens of concepts, validated on both predicted and measured fMRI data. Critically, we show that without causal validation, a large fraction of localizations would be false positives, confirming that activation alone is insufficient evidence of representation.

  • 8 authors
·
May 21

DiffuMatch: Category-Agnostic Spectral Diffusion Priors for Robust Non-rigid Shape Matching

Deep functional maps have recently emerged as a powerful tool for solving non-rigid shape correspondence tasks. Methods that use this approach combine the power and flexibility of the functional map framework, with data-driven learning for improved accuracy and generality. However, most existing methods in this area restrict the learning aspect only to the feature functions and still rely on axiomatic modeling for formulating the training loss or for functional map regularization inside the networks. This limits both the accuracy and the applicability of the resulting approaches only to scenarios where assumptions of the axiomatic models hold. In this work, we show, for the first time, that both in-network regularization and functional map training can be replaced with data-driven methods. For this, we first train a generative model of functional maps in the spectral domain using score-based generative modeling, built from a large collection of high-quality maps. We then exploit the resulting model to promote the structural properties of ground truth functional maps on new shape collections. Remarkably, we demonstrate that the learned models are category-agnostic, and can fully replace commonly used strategies such as enforcing Laplacian commutativity or orthogonality of functional maps. Our key technical contribution is a novel distillation strategy from diffusion models in the spectral domain. Experiments demonstrate that our learned regularization leads to better results than axiomatic approaches for zero-shot non-rigid shape matching. Our code is available at: https://github.com/daidedou/diffumatch/

  • 4 authors
·
Jul 31, 2025

Geographic Location Encoding with Spherical Harmonics and Sinusoidal Representation Networks

Learning feature representations of geographical space is vital for any machine learning model that integrates geolocated data, spanning application domains such as remote sensing, ecology, or epidemiology. Recent work mostly embeds coordinates using sine and cosine projections based on Double Fourier Sphere (DFS) features -- these embeddings assume a rectangular data domain even on global data, which can lead to artifacts, especially at the poles. At the same time, relatively little attention has been paid to the exact design of the neural network architectures these functional embeddings are combined with. This work proposes a novel location encoder for globally distributed geographic data that combines spherical harmonic basis functions, natively defined on spherical surfaces, with sinusoidal representation networks (SirenNets) that can be interpreted as learned Double Fourier Sphere embedding. We systematically evaluate the cross-product of positional embeddings and neural network architectures across various classification and regression benchmarks and synthetic evaluation datasets. In contrast to previous approaches that require the combination of both positional encoding and neural networks to learn meaningful representations, we show that both spherical harmonics and sinusoidal representation networks are competitive on their own but set state-of-the-art performances across tasks when combined. We provide source code at www.github.com/marccoru/locationencoder

  • 5 authors
·
Oct 10, 2023

Are formal and functional linguistic mechanisms dissociated in language models?

Although large language models (LLMs) are increasingly capable, these capabilities are unevenly distributed: they excel at formal linguistic tasks, such as producing fluent, grammatical text, but struggle more with functional linguistic tasks like reasoning and consistent fact retrieval. Inspired by neuroscience, recent work suggests that to succeed on both formal and functional linguistic tasks, LLMs should use different mechanisms for each; such localization could either be built-in or emerge spontaneously through training. In this paper, we ask: do current models, with fast-improving functional linguistic abilities, exhibit distinct localization of formal and functional linguistic mechanisms? We answer this by finding and comparing the "circuits", or minimal computational subgraphs, responsible for various formal and functional tasks. Comparing 5 LLMs across 10 distinct tasks, we find that while there is indeed little overlap between circuits for formal and functional tasks, there is also little overlap between formal linguistic tasks, as exists in the human brain. Thus, a single formal linguistic network, unified and distinct from functional task circuits, remains elusive. However, in terms of cross-task faithfulness - the ability of one circuit to solve another's task - we observe a separation between formal and functional mechanisms, suggesting that shared mechanisms between formal tasks may exist.

  • 3 authors
·
Mar 14, 2025

FunGrasp: Functional Grasping for Diverse Dexterous Hands

Functional grasping is essential for humans to perform specific tasks, such as grasping scissors by the finger holes to cut materials or by the blade to safely hand them over. Enabling dexterous robot hands with functional grasping capabilities is crucial for their deployment to accomplish diverse real-world tasks. Recent research in dexterous grasping, however, often focuses on power grasps while overlooking task- and object-specific functional grasping poses. In this paper, we introduce FunGrasp, a system that enables functional dexterous grasping across various robot hands and performs one-shot transfer to unseen objects. Given a single RGBD image of functional human grasping, our system estimates the hand pose and transfers it to different robotic hands via a human-to-robot (H2R) grasp retargeting module. Guided by the retargeted grasping poses, a policy is trained through reinforcement learning in simulation for dynamic grasping control. To achieve robust sim-to-real transfer, we employ several techniques including privileged learning, system identification, domain randomization, and gravity compensation. In our experiments, we demonstrate that our system enables diverse functional grasping of unseen objects using single RGBD images, and can be successfully deployed across various dexterous robot hands. The significance of the components is validated through comprehensive ablation studies. Project page: https://hly-123.github.io/FunGrasp/ .

  • 5 authors
·
Nov 24, 2024 1

EP2P-Loc: End-to-End 3D Point to 2D Pixel Localization for Large-Scale Visual Localization

Visual localization is the task of estimating a 6-DoF camera pose of a query image within a provided 3D reference map. Thanks to recent advances in various 3D sensors, 3D point clouds are becoming a more accurate and affordable option for building the reference map, but research to match the points of 3D point clouds with pixels in 2D images for visual localization remains challenging. Existing approaches that jointly learn 2D-3D feature matching suffer from low inliers due to representational differences between the two modalities, and the methods that bypass this problem into classification have an issue of poor refinement. In this work, we propose EP2P-Loc, a novel large-scale visual localization method that mitigates such appearance discrepancy and enables end-to-end training for pose estimation. To increase the number of inliers, we propose a simple algorithm to remove invisible 3D points in the image, and find all 2D-3D correspondences without keypoint detection. To reduce memory usage and search complexity, we take a coarse-to-fine approach where we extract patch-level features from 2D images, then perform 2D patch classification on each 3D point, and obtain the exact corresponding 2D pixel coordinates through positional encoding. Finally, for the first time in this task, we employ a differentiable PnP for end-to-end training. In the experiments on newly curated large-scale indoor and outdoor benchmarks based on 2D-3D-S and KITTI, we show that our method achieves the state-of-the-art performance compared to existing visual localization and image-to-point cloud registration methods.

  • 3 authors
·
Sep 14, 2023

Yes, we CANN: Constrained Approximate Nearest Neighbors for local feature-based visual localization

Large-scale visual localization systems continue to rely on 3D point clouds built from image collections using structure-from-motion. While the 3D points in these models are represented using local image features, directly matching a query image's local features against the point cloud is challenging due to the scale of the nearest-neighbor search problem. Many recent approaches to visual localization have thus proposed a hybrid method, where first a global (per image) embedding is used to retrieve a small subset of database images, and local features of the query are matched only against those. It seems to have become common belief that global embeddings are critical for said image-retrieval in visual localization, despite the significant downside of having to compute two feature types for each query image. In this paper, we take a step back from this assumption and propose Constrained Approximate Nearest Neighbors (CANN), a joint solution of k-nearest-neighbors across both the geometry and appearance space using only local features. We first derive the theoretical foundation for k-nearest-neighbor retrieval across multiple metrics and then showcase how CANN improves visual localization. Our experiments on public localization benchmarks demonstrate that our method significantly outperforms both state-of-the-art global feature-based retrieval and approaches using local feature aggregation schemes. Moreover, it is an order of magnitude faster in both index and query time than feature aggregation schemes for these datasets. Code will be released.

  • 3 authors
·
Jun 15, 2023

Brain Diffusion for Visual Exploration: Cortical Discovery using Large Scale Generative Models

A long standing goal in neuroscience has been to elucidate the functional organization of the brain. Within higher visual cortex, functional accounts have remained relatively coarse, focusing on regions of interest (ROIs) and taking the form of selectivity for broad categories such as faces, places, bodies, food, or words. Because the identification of such ROIs has typically relied on manually assembled stimulus sets consisting of isolated objects in non-ecological contexts, exploring functional organization without robust a priori hypotheses has been challenging. To overcome these limitations, we introduce a data-driven approach in which we synthesize images predicted to activate a given brain region using paired natural images and fMRI recordings, bypassing the need for category-specific stimuli. Our approach -- Brain Diffusion for Visual Exploration ("BrainDiVE") -- builds on recent generative methods by combining large-scale diffusion models with brain-guided image synthesis. Validating our method, we demonstrate the ability to synthesize preferred images with appropriate semantic specificity for well-characterized category-selective ROIs. We then show that BrainDiVE can characterize differences between ROIs selective for the same high-level category. Finally we identify novel functional subdivisions within these ROIs, validated with behavioral data. These results advance our understanding of the fine-grained functional organization of human visual cortex, and provide well-specified constraints for further examination of cortical organization using hypothesis-driven methods.

  • 4 authors
·
Jun 5, 2023

Functional Bayesian Tucker Decomposition for Continuous-indexed Tensor Data

Tucker decomposition is a powerful tensor model to handle multi-aspect data. It demonstrates the low-rank property by decomposing the grid-structured data as interactions between a core tensor and a set of object representations (factors). A fundamental assumption of such decomposition is that there are finite objects in each aspect or mode, corresponding to discrete indexes of data entries. However, real-world data is often not naturally posed in this setting. For example, geographic data is represented as continuous indexes of latitude and longitude coordinates, and cannot fit tensor models directly. To generalize Tucker decomposition to such scenarios, we propose Functional Bayesian Tucker Decomposition (FunBaT). We treat the continuous-indexed data as the interaction between the Tucker core and a group of latent functions. We use Gaussian processes (GP) as functional priors to model the latent functions. Then, we convert each GP into a state-space prior by constructing an equivalent stochastic differential equation (SDE) to reduce computational cost. An efficient inference algorithm is developed for scalable posterior approximation based on advanced message-passing techniques. The advantage of our method is shown in both synthetic data and several real-world applications. We release the code of FunBaT at https://github.com/xuangu-fang/Functional-Bayesian-Tucker-Decomposition.

  • 6 authors
·
Nov 8, 2023

Functionality understanding and segmentation in 3D scenes

Understanding functionalities in 3D scenes involves interpreting natural language descriptions to locate functional interactive objects, such as handles and buttons, in a 3D environment. Functionality understanding is highly challenging, as it requires both world knowledge to interpret language and spatial perception to identify fine-grained objects. For example, given a task like 'turn on the ceiling light', an embodied AI agent must infer that it needs to locate the light switch, even though the switch is not explicitly mentioned in the task description. To date, no dedicated methods have been developed for this problem. In this paper, we introduce Fun3DU, the first approach designed for functionality understanding in 3D scenes. Fun3DU uses a language model to parse the task description through Chain-of-Thought reasoning in order to identify the object of interest. The identified object is segmented across multiple views of the captured scene by using a vision and language model. The segmentation results from each view are lifted in 3D and aggregated into the point cloud using geometric information. Fun3DU is training-free, relying entirely on pre-trained models. We evaluate Fun3DU on SceneFun3D, the most recent and only dataset to benchmark this task, which comprises over 3000 task descriptions on 230 scenes. Our method significantly outperforms state-of-the-art open-vocabulary 3D segmentation approaches. Project page: https://jcorsetti.github.io/fun3du

  • 5 authors
·
Nov 25, 2024

Task-Specific Skill Localization in Fine-tuned Language Models

Pre-trained language models can be fine-tuned to solve diverse NLP tasks, including in few-shot settings. Thus fine-tuning allows the model to quickly pick up task-specific ``skills,'' but there has been limited study of where these newly-learnt skills reside inside the massive model. This paper introduces the term skill localization for this problem and proposes a solution. Given the downstream task and a model fine-tuned on that task, a simple optimization is used to identify a very small subset of parameters (sim0.01% of model parameters) responsible for (>95%) of the model's performance, in the sense that grafting the fine-tuned values for just this tiny subset onto the pre-trained model gives performance almost as well as the fine-tuned model. While reminiscent of recent works on parameter-efficient fine-tuning, the novel aspects here are that: (i) No further re-training is needed on the subset (unlike, say, with lottery tickets). (ii) Notable improvements are seen over vanilla fine-tuning with respect to calibration of predictions in-distribution (40-90% error reduction) as well as the quality of predictions out-of-distribution (OOD). In models trained on multiple tasks, a stronger notion of skill localization is observed, where the sparse regions corresponding to different tasks are almost disjoint, and their overlap (when it happens) is a proxy for task similarity. Experiments suggest that localization via grafting can assist certain forms of continual learning.

  • 4 authors
·
Feb 13, 2023

Weighted least-squares approximation with determinantal point processes and generalized volume sampling

We consider the problem of approximating a function from L^2 by an element of a given m-dimensional space V_m, associated with some feature map varphi, using evaluations of the function at random points x_1,dots,x_n. After recalling some results on optimal weighted least-squares using independent and identically distributed points, we consider weighted least-squares using projection determinantal point processes (DPP) or volume sampling. These distributions introduce dependence between the points that promotes diversity in the selected features varphi(x_i). We first provide a generalized version of volume-rescaled sampling yielding quasi-optimality results in expectation with a number of samples n = O(mlog(m)), that means that the expected L^2 error is bounded by a constant times the best approximation error in L^2. Also, further assuming that the function is in some normed vector space H continuously embedded in L^2, we further prove that the approximation is almost surely bounded by the best approximation error measured in the H-norm. This includes the cases of functions from L^infty or reproducing kernel Hilbert spaces. Finally, we present an alternative strategy consisting in using independent repetitions of projection DPP (or volume sampling), yielding similar error bounds as with i.i.d. or volume sampling, but in practice with a much lower number of samples. Numerical experiments illustrate the performance of the different strategies.

  • 2 authors
·
Dec 21, 2023

Continuum Attention for Neural Operators

Transformers, and the attention mechanism in particular, have become ubiquitous in machine learning. Their success in modeling nonlocal, long-range correlations has led to their widespread adoption in natural language processing, computer vision, and time series problems. Neural operators, which map spaces of functions into spaces of functions, are necessarily both nonlinear and nonlocal if they are universal; it is thus natural to ask whether the attention mechanism can be used in the design of neural operators. Motivated by this, we study transformers in the function space setting. We formulate attention as a map between infinite dimensional function spaces and prove that the attention mechanism as implemented in practice is a Monte Carlo or finite difference approximation of this operator. The function space formulation allows for the design of transformer neural operators, a class of architectures designed to learn mappings between function spaces. In this paper, we state and prove the first universal approximation result for transformer neural operators, using only a slight modification of the architecture implemented in practice. The prohibitive cost of applying the attention operator to functions defined on multi-dimensional domains leads to the need for more efficient attention-based architectures. For this reason we also introduce a function space generalization of the patching strategy from computer vision, and introduce a class of associated neural operators. Numerical results, on an array of operator learning problems, demonstrate the promise of our approaches to function space formulations of attention and their use in neural operators.

  • 4 authors
·
Dec 19, 2025

ProteinRPN: Towards Accurate Protein Function Prediction with Graph-Based Region Proposals

Protein function prediction is a crucial task in bioinformatics, with significant implications for understanding biological processes and disease mechanisms. While the relationship between sequence and function has been extensively explored, translating protein structure to function continues to present substantial challenges. Various models, particularly, CNN and graph-based deep learning approaches that integrate structural and functional data, have been proposed to address these challenges. However, these methods often fall short in elucidating the functional significance of key residues essential for protein functionality, as they predominantly adopt a retrospective perspective, leading to suboptimal performance. Inspired by region proposal networks in computer vision, we introduce the Protein Region Proposal Network (ProteinRPN) for accurate protein function prediction. Specifically, the region proposal module component of ProteinRPN identifies potential functional regions (anchors) which are refined through the hierarchy-aware node drop pooling layer favoring nodes with defined secondary structures and spatial proximity. The representations of the predicted functional nodes are enriched using attention mechanisms and subsequently fed into a Graph Multiset Transformer, which is trained with supervised contrastive (SupCon) and InfoNCE losses on perturbed protein structures. Our model demonstrates significant improvements in predicting Gene Ontology (GO) terms, effectively localizing functional residues within protein structures. The proposed framework provides a robust, scalable solution for protein function annotation, advancing the understanding of protein structure-function relationships in computational biology.

  • 3 authors
·
Sep 1, 2024

SceneHGN: Hierarchical Graph Networks for 3D Indoor Scene Generation with Fine-Grained Geometry

3D indoor scenes are widely used in computer graphics, with applications ranging from interior design to gaming to virtual and augmented reality. They also contain rich information, including room layout, as well as furniture type, geometry, and placement. High-quality 3D indoor scenes are highly demanded while it requires expertise and is time-consuming to design high-quality 3D indoor scenes manually. Existing research only addresses partial problems: some works learn to generate room layout, and other works focus on generating detailed structure and geometry of individual furniture objects. However, these partial steps are related and should be addressed together for optimal synthesis. We propose SCENEHGN, a hierarchical graph network for 3D indoor scenes that takes into account the full hierarchy from the room level to the object level, then finally to the object part level. Therefore for the first time, our method is able to directly generate plausible 3D room content, including furniture objects with fine-grained geometry, and their layout. To address the challenge, we introduce functional regions as intermediate proxies between the room and object levels to make learning more manageable. To ensure plausibility, our graph-based representation incorporates both vertical edges connecting child nodes with parent nodes from different levels, and horizontal edges encoding relationships between nodes at the same level. Extensive experiments demonstrate that our method produces superior generation results, even when comparing results of partial steps with alternative methods that can only achieve these. We also demonstrate that our method is effective for various applications such as part-level room editing, room interpolation, and room generation by arbitrary room boundaries.

  • 6 authors
·
Feb 16, 2023

Function2Scene: 3D Indoor Scene Layout from Functional Specifications

Most text-driven 3D indoor scene synthesis methods generate rooms from object-centric prompts, asking what furniture should be placed rather than how the space is used. Yet in real interior design, a layout is judged by how well it supports its occupants, e.g., their activities and physical needs. We introduce Function2Scene, a framework for generating 3D indoor layouts from functional specifications, i.e., natural-language design briefs describing who will use a room and what they need to do there. Given such a specification, our system parses occupant personas and activities, derives a customized set of functional design constraints from a taxonomy of 17 criteria spanning spatial, ergonomic, activity, and environmental considerations, and uses these constraints to guide layout generation. Rather than relying on an LLM to directly produce a final scene, Function2Scene performs iterative evaluation and refinement through a tool-augmented check-and-repair loop, combining geometric measurements, LLM-based contextual reasoning, and VLM-based visual assessment. Experiments on 30 professionally written interior-design cases show that Function2Scene produces layouts that better satisfy functional requirements than recent LLM-based scene synthesis baselines, with our results preferred in 94.3% of pairwise comparisons. Our work reframes text-driven indoor scene synthesis from placing plausible objects to designing spaces that support human use.

  • 7 authors
·
May 28 1

Localize-and-Stitch: Efficient Model Merging via Sparse Task Arithmetic

Model merging offers an effective strategy to combine the strengths of multiple finetuned models into a unified model that preserves the specialized capabilities of each. Existing methods merge models in a global manner, performing arithmetic operations across all model parameters. However, such global merging often leads to task interference, degrading the performance of the merged model. In this work, we introduce Localize-and-Stitch, a novel approach that merges models in a localized way. Our algorithm works in two steps: i) Localization: identify tiny (1% of the total parameters) localized regions in the finetuned models containing essential skills for the downstream tasks, and ii) Stitching: reintegrate only these essential regions back into the pretrained model for task synergy. We demonstrate that our approach effectively locates sparse regions responsible for finetuned performance, and the localized regions could be treated as compact and interpretable representations of the finetuned models (tasks). Empirically, we evaluate our method on various vision and language benchmarks, showing that it outperforms existing model merging methods under different data availability scenarios. Beyond strong empirical performance, our algorithm also facilitates model compression and preserves pretrained knowledge, enabling flexible and continual skill composition from multiple finetuned models with minimal storage and computational overhead. Our code is available at https://github.com/uiuctml/Localize-and-Stitch.

  • 5 authors
·
Aug 24, 2024

Does Localization Inform Editing? Surprising Differences in Causality-Based Localization vs. Knowledge Editing in Language Models

Language models learn a great quantity of factual information during pretraining, and recent work localizes this information to specific model weights like mid-layer MLP weights. In this paper, we find that we can change how a fact is stored in a model by editing weights that are in a different location than where existing methods suggest that the fact is stored. This is surprising because we would expect that localizing facts to specific model parameters would tell us where to manipulate knowledge in models, and this assumption has motivated past work on model editing methods. Specifically, we show that localization conclusions from representation denoising (also known as Causal Tracing) do not provide any insight into which model MLP layer would be best to edit in order to override an existing stored fact with a new one. This finding raises questions about how past work relies on Causal Tracing to select which model layers to edit. Next, we consider several variants of the editing problem, including erasing and amplifying facts. For one of our editing problems, editing performance does relate to localization results from representation denoising, but we find that which layer we edit is a far better predictor of performance. Our results suggest, counterintuitively, that better mechanistic understanding of how pretrained language models work may not always translate to insights about how to best change their behavior. Our code is available at https://github.com/google/belief-localization

  • 4 authors
·
Jan 10, 2023

VLM-Loc: Localization in Point Cloud Maps via Vision-Language Models

Text-to-point-cloud (T2P) localization aims to infer precise spatial positions within 3D point cloud maps from natural language descriptions, reflecting how humans perceive and communicate spatial layouts through language. However, existing methods largely rely on shallow text-point cloud correspondence without effective spatial reasoning, limiting their accuracy in complex environments. To address this limitation, we propose VLM-Loc, a framework that leverages the spatial reasoning capability of large vision-language models (VLMs) for T2P localization. Specifically, we transform point clouds into bird's-eye-view (BEV) images and scene graphs that jointly encode geometric and semantic context, providing structured inputs for the VLM to learn cross-modal representations bridging linguistic and spatial semantics. On top of these representations, we introduce a partial node assignment mechanism that explicitly associates textual cues with scene graph nodes, enabling interpretable spatial reasoning for accurate localization. To facilitate systematic evaluation across diverse scenes, we present CityLoc, a benchmark built from multi-source point clouds for fine-grained T2P localization. Experiments on CityLoc demonstrate VLM-Loc achieves superior accuracy and robustness compared to state-of-the-art methods. Our code, model, and dataset are available at https://github.com/MCG-NKU/nku-3d-vision{repository}.

  • 8 authors
·
Mar 10

LIDL: LLM Integration Defect Localization via Knowledge Graph-Enhanced Multi-Agent Analysis

LLM-integrated software, which embeds or interacts with large language models (LLMs) as functional components, exhibits probabilistic and context-dependent behaviors that fundamentally differ from those of traditional software. This shift introduces a new category of integration defects that arise not only from code errors but also from misaligned interactions among LLM-specific artifacts, including prompts, API calls, configurations, and model outputs. However, existing defect localization techniques are ineffective at identifying these LLM-specific integration defects because they fail to capture cross-layer dependencies across heterogeneous artifacts, cannot exploit incomplete or misleading error traces, and lack semantic reasoning capabilities for identifying root causes. To address these challenges, we propose LIDL, a multi-agent framework for defect localization in LLM-integrated software. LIDL (1) constructs a code knowledge graph enriched with LLM-aware annotations that represent interaction boundaries across source code, prompts, and configuration files, (2) fuses three complementary sources of error evidence inferred by LLMs to surface candidate defect locations, and (3) applies context-aware validation that uses counterfactual reasoning to distinguish true root causes from propagated symptoms. We evaluate LIDL on 146 real-world defect instances collected from 105 GitHub repositories and 16 agent-based systems. The results show that LIDL significantly outperforms five state-of-the-art baselines across all metrics, achieving a Top-3 accuracy of 0.64 and a MAP of 0.48, which represents a 64.1% improvement over the best-performing baseline. Notably, LIDL achieves these gains while reducing cost by 92.5%, demonstrating both high accuracy and cost efficiency.

  • 11 authors
·
Jan 8

Denotational validation of higher-order Bayesian inference

We present a modular semantic account of Bayesian inference algorithms for probabilistic programming languages, as used in data science and machine learning. Sophisticated inference algorithms are often explained in terms of composition of smaller parts. However, neither their theoretical justification nor their implementation reflects this modularity. We show how to conceptualise and analyse such inference algorithms as manipulating intermediate representations of probabilistic programs using higher-order functions and inductive types, and their denotational semantics. Semantic accounts of continuous distributions use measurable spaces. However, our use of higher-order functions presents a substantial technical difficulty: it is impossible to define a measurable space structure over the collection of measurable functions between arbitrary measurable spaces that is compatible with standard operations on those functions, such as function application. We overcome this difficulty using quasi-Borel spaces, a recently proposed mathematical structure that supports both function spaces and continuous distributions. We define a class of semantic structures for representing probabilistic programs, and semantic validity criteria for transformations of these representations in terms of distribution preservation. We develop a collection of building blocks for composing representations. We use these building blocks to validate common inference algorithms such as Sequential Monte Carlo and Markov Chain Monte Carlo. To emphasize the connection between the semantic manipulation and its traditional measure theoretic origins, we use Kock's synthetic measure theory. We demonstrate its usefulness by proving a quasi-Borel counterpart to the Metropolis-Hastings-Green theorem.

  • 10 authors
·
Nov 8, 2017

RF-ULM: Deep Learning for Radio-Frequency Ultrasound Localization Microscopy

In Ultrasound Localization Microscopy (ULM),achieving high-resolution images relies on the precise localization of contrast agent particles across consecutive beam-formed frames. However, our study uncovers an enormous potential: The process of delay-and-sum beamforming leads to an irreversible reduction of Radio-Frequency (RF) data, while its implications for localization remain largely unexplored. The rich contextual information embedded within RF wavefronts, including their hyperbolic shape and phase, offers great promise for guiding Deep Neural Networks (DNNs) in challenging localization scenarios. To fully exploit this data, we propose to directly localize scatterers in RF signals. Our approach involves a custom super-resolution DNN using learned feature channel shuffling and a novel semi-global convolutional sampling block tailored for reliable and accurate wavefront localization. Additionally, we introduce a geometric point transformation that facilitates seamless mapping between RF and B-mode coordinate space. To understand the impact of beamforming on ULM, we validate the effectiveness of our method by conducting an extensive comparison with State-Of-The-Art (SOTA) techniques. We present the inaugural in vivo results from an RF-trained DNN, highlighting its real-world practicality. Our findings show that RF-ULM bridges the domain gap between synthetic and real datasets, offering a considerable advantage in terms of precision and complexity. To enable the broader research community to benefit from our findings, our code and the associated SOTA methods are made available at https://github.com/hahnec/rf-ulm.

  • 5 authors
·
Oct 2, 2023

CAPSUL: A Comprehensive Human Protein Benchmark for Subcellular Localization

Subcellular localization is a crucial biological task for drug target identification and function annotation. Although it has been biologically realized that subcellular localization is closely associated with protein structure, no existing dataset offers comprehensive 3D structural information with detailed subcellular localization annotations, thus severely hindering the application of promising structure-based models on this task. To address this gap, we introduce a new benchmark called CAPSUL, a Comprehensive humAn Protein benchmark for SUbcellular Localization. It features a dataset that integrates diverse 3D structural representations with fine-grained subcellular localization annotations carefully curated by domain experts. We evaluate this benchmark using a variety of state-of-the-art sequence-based and structure-based models, showcasing the importance of involving structural features in this task. Furthermore, we explore reweighting and single-label classification strategies to facilitate future investigation on structure-based methods for this task. Lastly, we showcase the powerful interpretability of structure-based methods through a case study on the Golgi apparatus, where we discover a decisive localization pattern α-helix from attention mechanisms, demonstrating the potential for bridging the gap with intuitive biological interpretability and paving the way for data-driven discoveries in cell biology.

  • 6 authors
·
Mar 19

The Blueprints of Intelligence: A Functional-Topological Foundation for Perception and Representation

Real-world phenomena do not generate arbitrary variability: their signals concentrate on compact, low-variability subsets of functional space, enabling rapid generalization from few examples. A small child can recognize a dog after extremely limited exposure because the perceptual manifold of "dog" is compact, structured, and low-dimensional. We formalize this principle through a deterministic functional-topological framework in which the set of valid realizations produced by a physical process forms a compact subset of a Banach space, endowed with stable invariants, a finite Hausdorff radius, and an induced continuous perceptual functional. This geometry provides explicit limits on knowledge, conditions for identifiability, and guarantees for generalization from sparse evidence -- properties fundamental to both natural and artificial intelligence. Across electromechanical, electrochemical, and physiological domains, we show that real-world processes consistently generate compact perceptual manifolds with the same geometric characteristics. Their boundaries can be discovered in a fully self-supervised manner as the empirical radius saturates with increasing sampling, even when the governing equations are unknown. These results demonstrate that deterministic functional topology offers a unified mathematical foundation for perception, representation, and world-model construction. It provides a geometric explanation for why biological learners and self-supervised AI systems can generalize from few observations, and establishes compact perceptual manifolds as a fundamental building block for future AI architectures. Finally, this work unifies biological perception and modern self-supervised models under a single geometric principle: both derive their generalization ability from the compactness and invariants of real-world perceptual manifolds.

  • 1 authors
·
Dec 4, 2025

Integrating Efficient Optimal Transport and Functional Maps For Unsupervised Shape Correspondence Learning

In the realm of computer vision and graphics, accurately establishing correspondences between geometric 3D shapes is pivotal for applications like object tracking, registration, texture transfer, and statistical shape analysis. Moving beyond traditional hand-crafted and data-driven feature learning methods, we incorporate spectral methods with deep learning, focusing on functional maps (FMs) and optimal transport (OT). Traditional OT-based approaches, often reliant on entropy regularization OT in learning-based framework, face computational challenges due to their quadratic cost. Our key contribution is to employ the sliced Wasserstein distance (SWD) for OT, which is a valid fast optimal transport metric in an unsupervised shape matching framework. This unsupervised framework integrates functional map regularizers with a novel OT-based loss derived from SWD, enhancing feature alignment between shapes treated as discrete probability measures. We also introduce an adaptive refinement process utilizing entropy regularized OT, further refining feature alignments for accurate point-to-point correspondences. Our method demonstrates superior performance in non-rigid shape matching, including near-isometric and non-isometric scenarios, and excels in downstream tasks like segmentation transfer. The empirical results on diverse datasets highlight our framework's effectiveness and generalization capabilities, setting new standards in non-rigid shape matching with efficient OT metrics and an adaptive refinement module.

  • 5 authors
·
Mar 4, 2024

Precise Parameter Localization for Textual Generation in Diffusion Models

Novel diffusion models can synthesize photo-realistic images with integrated high-quality text. Surprisingly, we demonstrate through attention activation patching that only less than 1% of diffusion models' parameters, all contained in attention layers, influence the generation of textual content within the images. Building on this observation, we improve textual generation efficiency and performance by targeting cross and joint attention layers of diffusion models. We introduce several applications that benefit from localizing the layers responsible for textual content generation. We first show that a LoRA-based fine-tuning solely of the localized layers enhances, even more, the general text-generation capabilities of large diffusion models while preserving the quality and diversity of the diffusion models' generations. Then, we demonstrate how we can use the localized layers to edit textual content in generated images. Finally, we extend this idea to the practical use case of preventing the generation of toxic text in a cost-free manner. In contrast to prior work, our localization approach is broadly applicable across various diffusion model architectures, including U-Net (e.g., LDM and SDXL) and transformer-based (e.g., DeepFloyd IF and Stable Diffusion 3), utilizing diverse text encoders (e.g., from CLIP to the large language models like T5). Project page available at https://t2i-text-loc.github.io/.

  • 5 authors
·
Feb 14, 2025 2

HaLo-NeRF: Learning Geometry-Guided Semantics for Exploring Unconstrained Photo Collections

Internet image collections containing photos captured by crowds of photographers show promise for enabling digital exploration of large-scale tourist landmarks. However, prior works focus primarily on geometric reconstruction and visualization, neglecting the key role of language in providing a semantic interface for navigation and fine-grained understanding. In constrained 3D domains, recent methods have leveraged vision-and-language models as a strong prior of 2D visual semantics. While these models display an excellent understanding of broad visual semantics, they struggle with unconstrained photo collections depicting such tourist landmarks, as they lack expert knowledge of the architectural domain. In this work, we present a localization system that connects neural representations of scenes depicting large-scale landmarks with text describing a semantic region within the scene, by harnessing the power of SOTA vision-and-language models with adaptations for understanding landmark scene semantics. To bolster such models with fine-grained knowledge, we leverage large-scale Internet data containing images of similar landmarks along with weakly-related textual information. Our approach is built upon the premise that images physically grounded in space can provide a powerful supervision signal for localizing new concepts, whose semantics may be unlocked from Internet textual metadata with large language models. We use correspondences between views of scenes to bootstrap spatial understanding of these semantics, providing guidance for 3D-compatible segmentation that ultimately lifts to a volumetric scene representation. Our results show that HaLo-NeRF can accurately localize a variety of semantic concepts related to architectural landmarks, surpassing the results of other 3D models as well as strong 2D segmentation baselines. Our project page is at https://tau-vailab.github.io/HaLo-NeRF/.

  • 6 authors
·
Feb 14, 2024 1

FOCUS: Forcing In-Context Object Localization through Visual Support Constraints and Policy Optimization

In-context localization (ICL) seeks to localize a target object specified by a small set of support examples in a query image, operating on the fly without training or parameter updates. Despite rapid advances in vision-language models (VLMs), achieving category-agnostic and visually grounded ICL remains an open problem, even though it is essential for applications such as image editing, personalized visual search, and retrieval. Existing methods are fragile and rely on explicit category supervision, which not only limits applicability in realistic settings with unnamed or instance-specific objects but also introduces category bias that steers predictions toward semantic priors rather than visual evidence. We introduce a two-stage training framework that explicitly optimizes in-context attention between support bounding boxes and query images without category supervision. We further refine localization via reinforcement learning using Group Relative Policy Optimization (GRPO) to directly minimize localization error. This formulation enforces visual correspondence over semantic priors, yielding robust instance-level localization. Empirically, a 7B-parameter model trained with our objectives outperforms models up to 72B parameters, demonstrating that context-aware localization objectives can surpass scaling alone. Comprehensive ablations validate the contribution of each component.

  • 2 authors
·
May 28

Principled Approaches for Extending Neural Architectures to Function Spaces for Operator Learning

A wide range of scientific problems, such as those described by continuous-time dynamical systems and partial differential equations (PDEs), are naturally formulated on function spaces. While function spaces are typically infinite-dimensional, deep learning has predominantly advanced through applications in computer vision and natural language processing that focus on mappings between finite-dimensional spaces. Such fundamental disparities in the nature of the data have limited neural networks from achieving a comparable level of success in scientific applications as seen in other fields. Neural operators are a principled way to generalize neural networks to mappings between function spaces, offering a pathway to replicate deep learning's transformative impact on scientific problems. For instance, neural operators can learn solution operators for entire classes of PDEs, e.g., physical systems with different boundary conditions, coefficient functions, and geometries. A key factor in deep learning's success has been the careful engineering of neural architectures through extensive empirical testing. Translating these neural architectures into neural operators allows operator learning to enjoy these same empirical optimizations. However, prior neural operator architectures have often been introduced as standalone models, not directly derived as extensions of existing neural network architectures. In this paper, we identify and distill the key principles for constructing practical implementations of mappings between infinite-dimensional function spaces. Using these principles, we propose a recipe for converting several popular neural architectures into neural operators with minimal modifications. This paper aims to guide practitioners through this process and details the steps to make neural operators work in practice. Our code can be found at https://github.com/neuraloperator/NNs-to-NOs

  • 7 authors
·
Jun 12, 2025

Steerable but Not Decodable: Function Vectors Operate Beyond the Logit Lens

Activation steering presupposes that task-relevant behaviors correspond to linear directions in activation space -- directions that should both steer the model and be readable along the unembedding. Function vectors (FVs), extracted as mean differences across ICL demonstrations, are the canonical test case; the prediction: steering and decoding succeed or fail together. Across 12 tasks, 6 models from 3 families, and 4,032 directed cross-template pairs, we find the opposite. FV steering routinely succeeds where the logit lens cannot decode the correct answer at any intermediate layer, while the converse -- decodable without steerable -- is nearly empty (3 of 72). The gap is not representational dialect. A diagonal tuned lens closes 1 of 14 steerable-not-decodable cases; a 2-layer MLP probe with a Hewitt \& Liang control closes 5 of 10 via nonlinearly encoded structure but leaves 5 invisible to every decoder tested. Even at > 0.90 steering accuracy, projecting the FV through the unembedding yields incoherent token distributions: FVs encode computational instructions, not answer directions. A model-family asymmetry sharpens the picture. Mistral FVs rewrite intermediate representations, while Llama and Gemma FVs steer the final output without leaving a logit-lens-visible trace, corroborated by three signals (post-steering deltas, activation-patching recovery, FV norm-transfer correlations). A previously reported negative cosine-transfer correlation dissolves at scale, adding at most ΔR^2 = 0.011 beyond task identity. These results decompose the linear representation hypothesis into linear decodability and linear steerability and show they come apart opposite to intuition, with implications for safety monitoring: vocabulary-projection tools are blind to FV-style interventions on widely deployed model families.

  • 1 authors
·
May 7

ThinkFL: Self-Refining Failure Localization for Microservice Systems via Reinforcement Fine-Tuning

As modern microservice systems grow increasingly popular and complex-often consisting of hundreds or even thousands of fine-grained, interdependent components-they are becoming more susceptible to frequent and subtle failures. Ensuring system reliability therefore hinges on accurate and efficient failure localization. Traditional failure localization approaches based on small models lack the flexibility to adapt to diverse failure scenarios, while recent LLM-based methods suffer from two major limitations: they often rely on rigid invocation workflows that constrain the model's ability to dynamically explore optimal localization paths, and they require resource-intensive inference, making them cost-prohibitive for real-world deployment. To address these challenges, we explore the use of reinforcement fine-tuning to equip lightweight LLMs with reasoning and self-refinement capabilities, significantly improving the cost-effectiveness and adaptability of LLM-based failure localization. We begin with an empirical study to identify three key capabilities essential for accurate localization. Building on these insights, we propose a progressive multi-stage GRPO fine-tuning framework, which integrates a multi-factor failure localization grader and a recursion-of-thought actor module. The resulting model, ThinkFL, not only outperforms existing state-of-the-art LLMs and baseline methods in localization accuracy but also reduces end-to-end localization latency from minutes to seconds, demonstrating strong potential for real-world applications.

  • 9 authors
·
Apr 25, 2025

Unveiling and Bridging the Functional Perception Gap in MLLMs: Atomic Visual Alignment and Hierarchical Evaluation via PET-Bench

While Multimodal Large Language Models (MLLMs) have demonstrated remarkable proficiency in tasks such as abnormality detection and report generation for anatomical modalities, their capability in functional imaging remains largely unexplored. In this work, we identify and quantify a fundamental functional perception gap: the inability of current vision encoders to decode functional tracer biodistribution independent of morphological priors. Identifying Positron Emission Tomography (PET) as the quintessential modality to investigate this disconnect, we introduce PET-Bench, the first large-scale functional imaging benchmark comprising 52,308 hierarchical QA pairs from 9,732 multi-site, multi-tracer PET studies. Extensive evaluation of 19 state-of-the-art MLLMs reveals a critical safety hazard termed the Chain-of-Thought (CoT) hallucination trap. We observe that standard CoT prompting, widely considered to enhance reasoning, paradoxically decouples linguistic generation from visual evidence in PET, producing clinically fluent but factually ungrounded diagnoses. To resolve this, we propose Atomic Visual Alignment (AVA), a simple fine-tuning strategy that enforces the mastery of low-level functional perception prior to high-level diagnostic reasoning. Our results demonstrate that AVA effectively bridges the perception gap, transforming CoT from a source of hallucination into a robust inference tool and improving diagnostic accuracy by up to 14.83%. Code and data are available at https://github.com/yezanting/PET-Bench.

  • 17 authors
·
Jan 6

GridPE: Unifying Positional Encoding in Transformers with a Grid Cell-Inspired Framework

Understanding spatial location and relationships is a fundamental capability for modern artificial intelligence systems. Insights from human spatial cognition provide valuable guidance in this domain. Neuroscientific discoveries have highlighted the role of grid cells as a fundamental neural component for spatial representation, including distance computation, path integration, and scale discernment. In this paper, we introduce a novel positional encoding scheme inspired by Fourier analysis and the latest findings in computational neuroscience regarding grid cells. Assuming that grid cells encode spatial position through a summation of Fourier basis functions, we demonstrate the translational invariance of the grid representation during inner product calculations. Additionally, we derive an optimal grid scale ratio for multi-dimensional Euclidean spaces based on principles of biological efficiency. Utilizing these computational principles, we have developed a Grid-cell inspired Positional Encoding technique, termed GridPE, for encoding locations within high-dimensional spaces. We integrated GridPE into the Pyramid Vision Transformer architecture. Our theoretical analysis shows that GridPE provides a unifying framework for positional encoding in arbitrary high-dimensional spaces. Experimental results demonstrate that GridPE significantly enhances the performance of transformers, underscoring the importance of incorporating neuroscientific insights into the design of artificial intelligence systems.

  • 4 authors
·
Sep 13, 2024

UAL-Bench: The First Comprehensive Unusual Activity Localization Benchmark

Localizing unusual activities, such as human errors or surveillance incidents, in videos holds practical significance. However, current video understanding models struggle with localizing these unusual events likely because of their insufficient representation in models' pretraining datasets. To explore foundation models' capability in localizing unusual activity, we introduce UAL-Bench, a comprehensive benchmark for unusual activity localization, featuring three video datasets: UAG-OOPS, UAG-SSBD, UAG-FunQA, and an instruction-tune dataset: OOPS-UAG-Instruct, to improve model capabilities. UAL-Bench evaluates three approaches: Video-Language Models (Vid-LLMs), instruction-tuned Vid-LLMs, and a novel integration of Vision-Language Models and Large Language Models (VLM-LLM). Our results show the VLM-LLM approach excels in localizing short-span unusual events and predicting their onset (start time) more accurately than Vid-LLMs. We also propose a new metric, R@1, TD <= p, to address limitations in existing evaluation methods. Our findings highlight the challenges posed by long-duration videos, particularly in autism diagnosis scenarios, and the need for further advancements in localization techniques. Our work not only provides a benchmark for unusual activity localization but also outlines the key challenges for existing foundation models, suggesting future research directions on this important task.

  • 5 authors
·
Oct 1, 2024

PEEKABOO: Hiding parts of an image for unsupervised object localization

Localizing objects in an unsupervised manner poses significant challenges due to the absence of key visual information such as the appearance, type and number of objects, as well as the lack of labeled object classes typically available in supervised settings. While recent approaches to unsupervised object localization have demonstrated significant progress by leveraging self-supervised visual representations, they often require computationally intensive training processes, resulting in high resource demands in terms of computation, learnable parameters, and data. They also lack explicit modeling of visual context, potentially limiting their accuracy in object localization. To tackle these challenges, we propose a single-stage learning framework, dubbed PEEKABOO, for unsupervised object localization by learning context-based representations at both the pixel- and shape-level of the localized objects through image masking. The key idea is to selectively hide parts of an image and leverage the remaining image information to infer the location of objects without explicit supervision. The experimental results, both quantitative and qualitative, across various benchmark datasets, demonstrate the simplicity, effectiveness and competitive performance of our approach compared to state-of-the-art methods in both single object discovery and unsupervised salient object detection tasks. Code and pre-trained models are available at: https://github.com/hasibzunair/peekaboo

  • 2 authors
·
Jul 24, 2024

ARISE: A Repository-level Graph Representation and Toolset for Agentic Fault Localization and Program Repair

Repository-level fault localization (FL) and automated program repair (APR) require an agent to identify the relevant code units across files, follow call and data dependencies, and generate a valid patch. Existing graph-based systems provide structural representations of repositories (files, classes, functions and their relationships) but do not model how variable values flow within procedures, leaving agents without the semantic precision needed for function- and line-level localization. We present ARISE (Agentic Repository-level Issue Solving Engine), which augments an LLM-based agent with a multi-granularity program graph that extends structural relationships down to statement-level nodes connected by intra-procedural definition-use edges. ARISE exposes this graph through a three-tier tool API, which brings data-flow slicing as a first-class, queryable agent primitive that allows the model to trace, in a single call, which statements define or consume a variable of interest. We evaluate on SWE-bench Lite (300 real GitHub issues, 11 Python repositories) using Qwen2.5-Coder-32B-Instruct as the backbone. Compared to the unmodified SWE-agent baseline, ARISE improves Function Recall@1 by 17.0 points and Line Recall@1 by 15.0 points. These localization gains translate directly into repair success, with ARISE achieving 22.0% Pass@1 (66/300), a 4.7 percentage-point improvement over SWE-agent. Controlled ablations confirm that the improvement is driven by the data-flow graph rather than the tool schema, and that large code models consume structured slice output directly without requiring a natural-language summarization layer. The graph builder and slicing API are designed as a framework-agnostic, drop-in toolset for future APR research.

  • 2 authors
·
May 3

FMB: a Functional Manipulation Benchmark for Generalizable Robotic Learning

In this paper, we propose a real-world benchmark for studying robotic learning in the context of functional manipulation: a robot needs to accomplish complex long-horizon behaviors by composing individual manipulation skills in functionally relevant ways. The core design principles of our Functional Manipulation Benchmark (FMB) emphasize a harmonious balance between complexity and accessibility. Tasks are deliberately scoped to be narrow, ensuring that models and datasets of manageable scale can be utilized effectively to track progress. Simultaneously, they are diverse enough to pose a significant generalization challenge. Furthermore, the benchmark is designed to be easily replicable, encompassing all essential hardware and software components. To achieve this goal, FMB consists of a variety of 3D-printed objects designed for easy and accurate replication by other researchers. The objects are procedurally generated, providing a principled framework to study generalization in a controlled fashion. We focus on fundamental manipulation skills, including grasping, repositioning, and a range of assembly behaviors. The FMB can be used to evaluate methods for acquiring individual skills, as well as methods for combining and ordering such skills to solve complex, multi-stage manipulation tasks. We also offer an imitation learning framework that includes a suite of policies trained to solve the proposed tasks. This enables researchers to utilize our tasks as a versatile toolkit for examining various parts of the pipeline. For example, researchers could propose a better design for a grasping controller and evaluate it in combination with our baseline reorientation and assembly policies as part of a pipeline for solving multi-stage tasks. Our dataset, object CAD files, code, and evaluation videos can be found on our project website: https://functional-manipulation-benchmark.github.io

  • 8 authors
·
Jan 16, 2024

LoFiT: Localized Fine-tuning on LLM Representations

Recent work in interpretability shows that large language models (LLMs) can be adapted for new tasks in a learning-free way: it is possible to intervene on LLM representations to elicit desired behaviors for alignment. For instance, adding certain bias vectors to the outputs of certain attention heads is reported to boost the truthfulness of models. In this work, we show that localized fine-tuning serves as an effective alternative to such representation intervention methods. We introduce a framework called Localized Fine-Tuning on LLM Representations (LoFiT), which identifies a subset of attention heads that are most important for learning a specific task, then trains offset vectors to add to the model's hidden representations at those selected heads. LoFiT localizes to a sparse set of heads (3%) and learns the offset vectors from limited training data, comparable to the settings used for representation intervention. For truthfulness and reasoning tasks, we find that LoFiT's intervention vectors are more effective for LLM adaptation than vectors from representation intervention methods such as Inference-time Intervention. We also find that the localization step is important: selecting a task-specific set of attention heads can lead to higher performance than intervening on heads selected for a different task. Finally, for the tasks we study, LoFiT achieves comparable performance to other parameter-efficient fine-tuning methods such as LoRA, despite modifying 20x-200x fewer parameters than these methods.

  • 3 authors
·
Jun 3, 2024

A Unified Hierarchical Framework for Fine-grained Cross-view Geo-localization over Large-scale Scenarios

Cross-view geo-localization is a promising solution for large-scale localization problems, requiring the sequential execution of retrieval and metric localization tasks to achieve fine-grained predictions. However, existing methods typically focus on designing standalone models for these two tasks, resulting in inefficient collaboration and increased training overhead. In this paper, we propose UnifyGeo, a novel unified hierarchical geo-localization framework that integrates retrieval and metric localization tasks into a single network. Specifically, we first employ a unified learning strategy with shared parameters to jointly learn multi-granularity representation, facilitating mutual reinforcement between these two tasks. Subsequently, we design a re-ranking mechanism guided by a dedicated loss function, which enhances geo-localization performance by improving both retrieval accuracy and metric localization references. Extensive experiments demonstrate that UnifyGeo significantly outperforms the state-of-the-arts in both task-isolated and task-associated settings. Remarkably, on the challenging VIGOR benchmark, which supports fine-grained localization evaluation, the 1-meter-level localization recall rate improves from 1.53\% to 39.64\% and from 0.43\% to 25.58\% under same-area and cross-area evaluations, respectively. Code will be made publicly available.

  • 5 authors
·
May 12, 2025

LocAgent: Graph-Guided LLM Agents for Code Localization

Code localization--identifying precisely where in a codebase changes need to be made--is a fundamental yet challenging task in software maintenance. Existing approaches struggle to efficiently navigate complex codebases when identifying relevant code sections. The challenge lies in bridging natural language problem descriptions with the appropriate code elements, often requiring reasoning across hierarchical structures and multiple dependencies. We introduce LocAgent, a framework that addresses code localization through graph-based representation. By parsing codebases into directed heterogeneous graphs, LocAgent creates a lightweight representation that captures code structures (files, classes, functions) and their dependencies (imports, invocations, inheritance), enabling LLM agents to effectively search and locate relevant entities through powerful multi-hop reasoning. Experimental results on real-world benchmarks demonstrate that our approach significantly enhances accuracy in code localization. Notably, our method with the fine-tuned Qwen-2.5-Coder-Instruct-32B model achieves comparable results to SOTA proprietary models at greatly reduced cost (approximately 86% reduction), reaching up to 92.7% accuracy on file-level localization while improving downstream GitHub issue resolution success rates by 12% for multiple attempts (Pass@10). Our code is available at https://github.com/gersteinlab/LocAgent.

  • 9 authors
·
Mar 12, 2025 2

Domain Elastic Transform: Bayesian Function Registration for High-Dimensional Scientific Data

Nonrigid registration is conventionally divided into point set registration, which aligns sparse geometries, and image registration, which aligns continuous intensity fields on regular grids. However, this dichotomy creates a critical bottleneck for emerging scientific data, such as spatial transcriptomics, where high-dimensional vector-valued functions, e.g., gene expression, are defined on irregular, sparse manifolds. Consequently, researchers currently face a forced choice: either sacrifice single-cell resolution via voxelization to utilize image-based tools, or ignore the critical functional signal to utilize geometric tools. To resolve this dilemma, we propose Domain Elastic Transform (DET), a grid-free probabilistic framework that unifies geometric and functional alignment. By treating data as functions on irregular domains, DET registers high-dimensional signals directly without binning. We formulate the problem within a rigorous Bayesian framework, modeling domain deformation as an elastic motion guided by a joint spatial-functional likelihood. The method is fully unsupervised and scalable, utilizing feature-sensitive downsampling to handle massive atlases. We demonstrate that DET achieves 92\% topological preservation on MERFISH data where state-of-the-art optimal transport methods struggle (<5\%), and successfully registers whole-embryo Stereo-seq atlases across developmental stages -- a task involving massive scale and complex nonrigid growth. The implementation of DET is available on {https://github.com/ohirose/bcpd} (since Mar, 2025).

  • 2 authors
·
Mar 21

Configurable Foundation Models: Building LLMs from a Modular Perspective

Advancements in LLMs have recently unveiled challenges tied to computational efficiency and continual scalability due to their requirements of huge parameters, making the applications and evolution of these models on devices with limited computation resources and scenarios requiring various abilities increasingly cumbersome. Inspired by modularity within the human brain, there is a growing tendency to decompose LLMs into numerous functional modules, allowing for inference with part of modules and dynamic assembly of modules to tackle complex tasks, such as mixture-of-experts. To highlight the inherent efficiency and composability of the modular approach, we coin the term brick to represent each functional module, designating the modularized structure as configurable foundation models. In this paper, we offer a comprehensive overview and investigation of the construction, utilization, and limitation of configurable foundation models. We first formalize modules into emergent bricks - functional neuron partitions that emerge during the pre-training phase, and customized bricks - bricks constructed via additional post-training to improve the capabilities and knowledge of LLMs. Based on diverse functional bricks, we further present four brick-oriented operations: retrieval and routing, merging, updating, and growing. These operations allow for dynamic configuration of LLMs based on instructions to handle complex tasks. To verify our perspective, we conduct an empirical analysis on widely-used LLMs. We find that the FFN layers follow modular patterns with functional specialization of neurons and functional neuron partitions. Finally, we highlight several open issues and directions for future research. Overall, this paper aims to offer a fresh modular perspective on existing LLM research and inspire the future creation of more efficient and scalable foundational models.

openbmb OpenBMB
·
Sep 4, 2024 2

Divide-and-Conquer Meets Consensus: Unleashing the Power of Functions in Code Generation

Despite recent progress made by large language models in code generation, they still struggle with programs that meet complex requirements. Recent work utilizes plan-and-solve decomposition to decrease the complexity and leverage self-tests to refine the generated program. Yet, planning deep-inside requirements in advance can be challenging, and the tests need to be accurate to accomplish self-improvement. To this end, we propose FunCoder, a code generation framework incorporating the divide-and-conquer strategy with functional consensus. Specifically, FunCoder recursively branches off sub-functions as smaller goals during code generation, represented by a tree hierarchy. These sub-functions are then composited to attain more complex objectives. Additionally, we designate functions via a consensus formed by identifying similarities in program behavior, mitigating error propagation. FunCoder outperforms state-of-the-art methods by +9.8% on average in HumanEval, MBPP, xCodeEval and MATH with GPT-3.5 and GPT-4. Moreover, our method demonstrates superiority on smaller models: With FunCoder, StableCode-3b surpasses GPT-3.5 by +18.6% and achieves 97.7% of GPT-4's performance on HumanEval. Further analysis reveals that our proposed dynamic function decomposition is capable of handling complex requirements, and the functional consensus prevails over self-testing in correctness evaluation.

  • 7 authors
·
May 30, 2024

Task Arithmetic in the Tangent Space: Improved Editing of Pre-Trained Models

Task arithmetic has recently emerged as a cost-effective and scalable approach to edit pre-trained models directly in weight space: By adding the fine-tuned weights of different tasks, the model's performance can be improved on these tasks, while negating them leads to task forgetting. Yet, our understanding of the effectiveness of task arithmetic and its underlying principles remains limited. We present a comprehensive study of task arithmetic in vision-language models and show that weight disentanglement is the crucial factor that makes it effective. This property arises during pre-training and manifests when distinct directions in weight space govern separate, localized regions in function space associated with the tasks. Notably, we show that fine-tuning models in their tangent space by linearizing them amplifies weight disentanglement. This leads to substantial performance improvements across multiple task arithmetic benchmarks and diverse models. Building on these findings, we provide theoretical and empirical analyses of the neural tangent kernel (NTK) of these models and establish a compelling link between task arithmetic and the spatial localization of the NTK eigenfunctions. Overall, our work uncovers novel insights into the fundamental mechanisms of task arithmetic and offers a more reliable and effective approach to edit pre-trained models through the NTK linearization.

  • 3 authors
·
May 22, 2023

Clustering of higher order connected correlations in C^* dynamical systems

In the context of C^* dynamical systems, we consider a locally compact group G acting by ^*-automorphisms on a C^* algebra U of observables, and assume a state of U that satisfies the clustering property with respect to a net of group elements of G. That is, the two-point connected correlation function vanishes in the limit on the net, when one observable is translated under the group action. Then we show that all higher order connected correlation functions (Ursell functions, or classical cumulants) and all free correlation functions (free cumulants, from free probability) vanish at the same rate in that limit. Additionally, we show that mean clustering, also called ergodicity, extends to higher order correlations. We then apply those results to equilibrium states of quantum spin lattice models. Under certain assumptions on the range of the interaction, high temperature Gibbs states are known to be exponentially clustering w.r.t. space translations. Combined with the Lieb-Robinson bound, one obtains exponential clustering for space-time translations outside the Lieb-Robinson light-cone. Therefore, by our present results, all the higher order connected and free correlation functions will vanish exponentially under space-time translations outside the Lieb-Robinson light cone, in high temperature Gibbs states. Another consequence is that their long-time averaging over a space-time ray vanishes for almost every ray velocity.

  • 2 authors
·
Aug 1, 2024

DEAL-300K: Diffusion-based Editing Area Localization with a 300K-Scale Dataset and Frequency-Prompted Baseline

Diffusion-based image editing has made semantic level image manipulation easy for general users, but it also enables realistic local forgeries that are hard to localize. Existing benchmarks mainly focus on the binary detection of generated images or the localization of manually edited regions and do not reflect the properties of diffusion-based edits, which often blend smoothly into the original content. We present Diffusion-Based Image Editing Area Localization Dataset (DEAL-300K), a large scale dataset for diffusion-based image manipulation localization (DIML) with more than 300,000 annotated images. We build DEAL-300K by using a multi-modal large language model to generate editing instructions, a mask-free diffusion editor to produce manipulated images, and an active-learning change detection pipeline to obtain pixel-level annotations. On top of this dataset, we propose a localization framework that uses a frozen Visual Foundation Model (VFM) together with Multi Frequency Prompt Tuning (MFPT) to capture both semantic and frequency-domain cues of edited regions. Trained on DEAL-300K, our method reaches a pixel-level F1 score of 82.56% on our test split and 80.97% on the external CoCoGlide benchmark, providing strong baselines and a practical foundation for future DIML research.The dataset can be accessed via https://github.com/ymhzyj/DEAL-300K.

  • 5 authors
·
Nov 28, 2025

Understanding and Enforcing Weight Disentanglement in Task Arithmetic

Task arithmetic provides an efficient, training-free way to edit pre-trained models, yet lacks a fundamental theoretical explanation for its success. The existing concept of ``weight disentanglement" describes the ideal outcome of non-interfering task composition but does not reveal its underlying cause. Crucially, what intrinsic properties of the pre-trained model (θ_0) or the task vectors (τ_t) enable this disentanglement remains underexplored. In this paper, we introduce Task-Feature Specialization (TFS), a model's ability to allocate distinct internal features to different tasks, as the fundamental principle. We first prove that TFS is a sufficient condition for weight disentanglement. More importantly, we find that TFS also gives rise to an observable geometric consequence: weight vector orthogonality. This positions TFS as the common cause for both the desired functional outcome (disentanglement) and a measurable geometric property (orthogonality). This relationship provides the key insight for our method: since the abstract TFS property is intractable to enforce directly, we can instead promote weight disentanglement by shaping its concrete geometric consequence, orthogonality. Therefore, we propose OrthoReg, a simple and effective regularization method that actively enforces an internal orthogonal structure on weight updates (ΔW) that constitute τ_t during fine-tuning. And we theoretically prove that OrthoReg promotes disentanglement. Extensive experiments demonstrate that OrthoReg consistently and significantly enhances the performance of various task arithmetic methods. Code is available at https://github.com/RL-MIND/OrthoReg{https://github.com/RL-MIND/OrthoReg}.

RL-MIND RL-MIND Group
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Apr 18 3