Daily Papers

Efficient and accurate feed-forward multi-view reconstruction has long been an important task in computer vision. Recent transformer-based models like VGGT and pi^3 have achieved impressive results with simple architectures, yet they face an inherent runtime bottleneck, due to the quadratic complexity of the global attention layers, that limits the scalability to large image sets. In this paper, we empirically analyze the global attention matrix of these models and observe that probability mass concentrates on a small subset of patch-patch interactions that correspond to cross-view geometric matches. Motivated by the structured attention and inspired by recent advancement in large language models, we propose a replacement for the dense global attention operation based on highly optimized block-sparse kernels, yielding up to 4times faster inference with comparable task performance. Our retrofit requires no retraining of the backbone, extends to both VGGT and pi^3, and supports large image collections. Evaluations on a comprehensive suite of multi-view benchmarks demonstrate the effectiveness of our approach.

Open-vocabulary semantic segmentation aims to assign semantic labels to each pixel without being constrained by a predefined set of categories. While Contrastive Language-Image Pre-training (CLIP) excels in zero-shot classification, it struggles to align image patches with category embeddings because of its incoherent patch correlations. This study reveals that inter-class correlations are the main reason for impairing CLIP's segmentation performance. Accordingly, we propose CorrCLIP, which reconstructs the scope and value of patch correlations. Specifically, CorrCLIP leverages the Segment Anything Model (SAM) to define the scope of patch interactions, reducing inter-class correlations. To mitigate the problem that SAM-generated masks may contain patches belonging to different classes, CorrCLIP incorporates self-supervised models to compute coherent similarity values, suppressing the weight of inter-class correlations. Additionally, we introduce two additional branches to strengthen patch features' spatial details and semantic representation. Finally, we update segmentation maps with SAM-generated masks to improve spatial consistency. Based on the improvement across patch correlations, feature representations, and segmentation maps, CorrCLIP achieves superior performance across eight benchmarks. Codes are available at: https://github.com/zdk258/CorrCLIP.

Masked Image Modeling (MIM) achieves outstanding success in self-supervised representation learning. Unfortunately, MIM models typically have huge computational burden and slow learning process, which is an inevitable obstacle for their industrial applications. Although the lower layers play the key role in MIM, existing MIM models conduct reconstruction task only at the top layer of encoder. The lower layers are not explicitly guided and the interaction among their patches is only used for calculating new activations. Considering the reconstruction task requires non-trivial inter-patch interactions to reason target signals, we apply it to multiple local layers including lower and upper layers. Further, since the multiple layers expect to learn the information of different scales, we design local multi-scale reconstruction, where the lower and upper layers reconstruct fine-scale and coarse-scale supervision signals respectively. This design not only accelerates the representation learning process by explicitly guiding multiple layers, but also facilitates multi-scale semantical understanding to the input. Extensive experiments show that with significantly less pre-training burden, our model achieves comparable or better performance on classification, detection and segmentation tasks than existing MIM models.

Mimicking realistic dynamics in 3D garment animations is a challenging task due to the complex nature of multi-layered garments and the variety of outer forces involved. Existing approaches mostly focus on single-layered garments driven by only human bodies and struggle to handle general scenarios. In this paper, we propose a novel data-driven method, called LayersNet, to model garment-level animations as particle-wise interactions in a micro physics system. We improve simulation efficiency by representing garments as patch-level particles in a two-level structural hierarchy. Moreover, we introduce a novel Rotation Equivalent Transformation that leverages the rotation invariance and additivity of physics systems to better model outer forces. To verify the effectiveness of our approach and bridge the gap between experimental environments and real-world scenarios, we introduce a new challenging dataset, D-LAYERS, containing 700K frames of dynamics of 4,900 different combinations of multi-layered garments driven by both human bodies and randomly sampled wind. Our experiments show that LayersNet achieves superior performance both quantitatively and qualitatively. We will make the dataset and code publicly available at https://mmlab-ntu.github.io/project/layersnet/index.html .

Large Language Models (LLMs) have emerged as a new paradigm for recommendation by converting interacted item history into language modeling. However, constrained by the limited context length of LLMs, existing approaches have to truncate item history in the prompt, focusing only on recent interactions and sacrificing the ability to model long-term history. To enable LLMs to model long histories, we pursue a concise embedding representation for items and sessions. In the LLM embedding space, we construct an item's embedding by aggregating its textual token embeddings; similarly, we construct a session's embedding by aggregating its item embeddings. While efficient, this way poses two challenges since it ignores the temporal significance of user interactions and LLMs do not natively interpret our custom embeddings. To overcome these, we propose PatchRec, a multi-grained patch training method consisting of two stages: (1) Patch Pre-training, which familiarizes LLMs with aggregated embeddings -- patches, and (2) Patch Fine-tuning, which enables LLMs to capture time-aware significance in interaction history. Extensive experiments show that PatchRec effectively models longer behavior histories with improved efficiency. This work facilitates the practical use of LLMs for modeling long behavior histories. Codes are available at https://github.com/ljy0ustc/PatchRec.

Multi-label image classification is a prediction task that aims to identify more than one label from a given image. This paper considers the semantic consistency of the latent space between the visual patch and linguistic label domains and introduces the conditional transport (CT) theory to bridge the acknowledged gap. While recent cross-modal attention-based studies have attempted to align such two representations and achieved impressive performance, they required carefully-designed alignment modules and extra complex operations in the attention computation. We find that by formulating the multi-label classification as a CT problem, we can exploit the interactions between the image and label efficiently by minimizing the bidirectional CT cost. Specifically, after feeding the images and textual labels into the modality-specific encoders, we view each image as a mixture of patch embeddings and a mixture of label embeddings, which capture the local region features and the class prototypes, respectively. CT is then employed to learn and align those two semantic sets by defining the forward and backward navigators. Importantly, the defined navigators in CT distance model the similarities between patches and labels, which provides an interpretable tool to visualize the learned prototypes. Extensive experiments on three public image benchmarks show that the proposed model consistently outperforms the previous methods.

Holistic 3D modeling of molecularly defined brain structures is crucial for understanding complex brain functions. Emerging tissue profiling technologies enable the construction of a comprehensive atlas of the mammalian brain with sub-cellular resolution and spatially resolved gene expression data. However, such tera-scale volumetric datasets present significant computational challenges in understanding complex brain functions within their native 3D spatial context. Here, we propose the novel generative approach Tera-MIND, which can simulate Tera-scale Mouse braINs in 3D using a patch-based and boundary-aware Diffusion model. Taking spatial transcriptomic data as the conditional input, we generate virtual mouse brains with comprehensive cellular morphological detail at teravoxel scale. Through the lens of 3D gene-gene self-attention, we identify spatial molecular interactions for key transcriptomic pathways in the murine brain, exemplified by glutamatergic and dopaminergic neuronal systems. Importantly, these in-silico biological findings are consistent and reproducible across three tera-scale virtual mouse brains. Therefore, Tera-MIND showcases a promising path toward efficient and generative simulations of whole organ systems for biomedical research. Project website: http://musikisomorphie.github.io/Tera-MIND.html{https}

Weakly supervised semantic segmentation (WSSS) typically utilizes limited semantic annotations to obtain initial Class Activation Maps (CAMs). However, due to the inadequate coupling between class activation responses and semantic information in high-dimensional space, the CAM is prone to object co-occurrence or under-activation, resulting in inferior recognition accuracy. To tackle this issue, we propose DOEI, Dual Optimization of Embedding Information, a novel approach that reconstructs embedding representations through semantic-aware attention weight matrices to optimize the expression capability of embedding information. Specifically, DOEI amplifies tokens with high confidence and suppresses those with low confidence during the class-to-patch interaction. This alignment of activation responses with semantic information strengthens the propagation and decoupling of target features, enabling the generated embeddings to more accurately represent target features in high-level semantic space. In addition, we propose a hybrid-feature alignment module in DOEI that combines RGB values, embedding-guided features, and self-attention weights to increase the reliability of candidate tokens. Comprehensive experiments show that DOEI is an effective plug-and-play module that empowers state-of-the-art visual transformer-based WSSS models to significantly improve the quality of CAMs and segmentation performance on popular benchmarks, including PASCAL VOC (+3.6%, +1.5%, +1.2% mIoU) and MS COCO (+1.2%, +1.6% mIoU). Code will be available at https://github.com/AIGeeksGroup/DOEI.

Although Vision Transformer (ViT) has achieved significant success in computer vision, it does not perform well in dense prediction tasks due to the lack of inner-patch information interaction and the limited diversity of feature scale. Most existing studies are devoted to designing vision-specific transformers to solve the above problems, which introduce additional pre-training costs. Therefore, we present a plain, pre-training-free, and feature-enhanced ViT backbone with Convolutional Multi-scale feature interaction, named ViT-CoMer, which facilitates bidirectional interaction between CNN and transformer. Compared to the state-of-the-art, ViT-CoMer has the following advantages: (1) We inject spatial pyramid multi-receptive field convolutional features into the ViT architecture, which effectively alleviates the problems of limited local information interaction and single-feature representation in ViT. (2) We propose a simple and efficient CNN-Transformer bidirectional fusion interaction module that performs multi-scale fusion across hierarchical features, which is beneficial for handling dense prediction tasks. (3) We evaluate the performance of ViT-CoMer across various dense prediction tasks, different frameworks, and multiple advanced pre-training. Notably, our ViT-CoMer-L achieves 64.3% AP on COCO val2017 without extra training data, and 62.1% mIoU on ADE20K val, both of which are comparable to state-of-the-art methods. We hope ViT-CoMer can serve as a new backbone for dense prediction tasks to facilitate future research. The code will be released at https://github.com/Traffic-X/ViT-CoMer.

Token interaction operation is one of the core modules in MLP-based models to exchange and aggregate information between different spatial locations. However, the power of token interaction on the spatial dimension is highly dependent on the spatial resolution of the feature maps, which limits the model's expressive ability, especially in deep layers where the feature are down-sampled to a small spatial size. To address this issue, we present a novel method called Strip-MLP to enrich the token interaction power in three ways. Firstly, we introduce a new MLP paradigm called Strip MLP layer that allows the token to interact with other tokens in a cross-strip manner, enabling the tokens in a row (or column) to contribute to the information aggregations in adjacent but different strips of rows (or columns). Secondly, a Cascade Group Strip Mixing Module (CGSMM) is proposed to overcome the performance degradation caused by small spatial feature size. The module allows tokens to interact more effectively in the manners of within-patch and cross-patch, which is independent to the feature spatial size. Finally, based on the Strip MLP layer, we propose a novel Local Strip Mixing Module (LSMM) to boost the token interaction power in the local region. Extensive experiments demonstrate that Strip-MLP significantly improves the performance of MLP-based models on small datasets and obtains comparable or even better results on ImageNet. In particular, Strip-MLP models achieve higher average Top-1 accuracy than existing MLP-based models by +2.44\% on Caltech-101 and +2.16\% on CIFAR-100. The source codes will be available at~https://github.com/Med-Process/Strip_MLP{https://github.com/Med-Process/Strip\_MLP.

During Automated Program Repair (APR), it can be challenging to synthesize correct patches for real-world systems in general-purpose programming languages. Recent Large Language Models (LLMs) have been shown to be helpful "copilots" in assisting developers with various coding tasks, and have also been directly applied for patch synthesis. However, most LLMs treat programs as sequences of tokens, meaning that they are ignorant of the underlying semantics constraints of the target programming language. This results in plenty of statically invalid generated patches, impeding the practicality of the technique. Therefore, we propose Repilot, a framework to further copilot the AI "copilots" (i.e., LLMs) by synthesizing more valid patches during the repair process. Our key insight is that many LLMs produce outputs autoregressively (i.e., token by token), resembling human writing programs, which can be significantly boosted and guided through a Completion Engine. Repilot synergistically synthesizes a candidate patch through the interaction between an LLM and a Completion Engine, which 1) prunes away infeasible tokens suggested by the LLM and 2) proactively completes the token based on the suggestions provided by the Completion Engine. Our evaluation on a subset of the widely-used Defects4j 1.2 and 2.0 datasets shows that Repilot fixes 66 and 50 bugs, respectively, surpassing the best-performing baseline by 14 and 16 bugs fixed. More importantly, Repilot is capable of producing more valid and correct patches than the base LLM when given the same generation budget.

Multi-vector document retrieval systems, such as ColPali, excel in fine-grained matching for complex queries but incur significant storage and computational costs due to their reliance on high-dimensional patch embeddings and late-interaction scoring. To address these challenges, we propose HPC-ColPali, a Hierarchical Patch Compression framework that enhances the efficiency of ColPali while preserving its retrieval accuracy. Our approach integrates three innovative techniques: (1) K-Means quantization, which compresses patch embeddings into 1-byte centroid indices, achieving up to 32times storage reduction; (2) attention-guided dynamic pruning, utilizing Vision-Language Model attention weights to retain only the top-p% most salient patches, reducing late-interaction computation by up to 60\% with less than 2\% nDCG@10 loss; and (3) optional binary encoding of centroid indices into b-bit strings (b=lceillog_2 Krceil), enabling rapid Hamming distance-based similarity search for resource-constrained environments. Evaluated on the ViDoRe and SEC-Filings datasets, HPC-ColPali achieves 30--50\% lower query latency under HNSW indexing while maintaining high retrieval precision. When integrated into a Retrieval-Augmented Generation pipeline for legal summarization, it reduces hallucination rates by 30\% and halves end-to-end latency. These advancements establish HPC-ColPali as a scalable and efficient solution for multi-vector document retrieval across diverse applications. Code is available at https://github.com/DngBack/HPC-ColPali.

We propose an agglomerative Transformer (AGER) that enables Transformer-based human-object interaction (HOI) detectors to flexibly exploit extra instance-level cues in a single-stage and end-to-end manner for the first time. AGER acquires instance tokens by dynamically clustering patch tokens and aligning cluster centers to instances with textual guidance, thus enjoying two benefits: 1) Integrality: each instance token is encouraged to contain all discriminative feature regions of an instance, which demonstrates a significant improvement in the extraction of different instance-level cues and subsequently leads to a new state-of-the-art performance of HOI detection with 36.75 mAP on HICO-Det. 2) Efficiency: the dynamical clustering mechanism allows AGER to generate instance tokens jointly with the feature learning of the Transformer encoder, eliminating the need of an additional object detector or instance decoder in prior methods, thus allowing the extraction of desirable extra cues for HOI detection in a single-stage and end-to-end pipeline. Concretely, AGER reduces GFLOPs by 8.5% and improves FPS by 36%, even compared to a vanilla DETR-like pipeline without extra cue extraction.

Image quality assessment (IQA) aims to assess the perceptual quality of images. The outputs of the IQA algorithms are expected to be consistent with human subjective perception. In image restoration and enhancement tasks, images generated by generative adversarial networks (GAN) can achieve better visual performance than traditional CNN-generated images, although they have spatial shift and texture noise. Unfortunately, the existing IQA methods have unsatisfactory performance on the GAN-based distortion partially because of their low tolerance to spatial misalignment. To this end, we propose the reference-oriented deformable convolution, which can improve the performance of an IQA network on GAN-based distortion by adaptively considering this misalignment. We further propose a patch-level attention module to enhance the interaction among different patch regions, which are processed independently in previous patch-based methods. The modified residual block is also proposed by applying modifications to the classic residual block to construct a patch-region-based baseline called WResNet. Equipping this baseline with the two proposed modules, we further propose Region-Adaptive Deformable Network (RADN). The experiment results on the NTIRE 2021 Perceptual Image Quality Assessment Challenge dataset show the superior performance of RADN, and the ensemble approach won fourth place in the final testing phase of the challenge. Code is available at https://github.com/IIGROUP/RADN.

This paper attempts to address the object repetition issue in patch-wise higher-resolution image generation. We propose AccDiffusion, an accurate method for patch-wise higher-resolution image generation without training. An in-depth analysis in this paper reveals an identical text prompt for different patches causes repeated object generation, while no prompt compromises the image details. Therefore, our AccDiffusion, for the first time, proposes to decouple the vanilla image-content-aware prompt into a set of patch-content-aware prompts, each of which serves as a more precise description of an image patch. Besides, AccDiffusion also introduces dilated sampling with window interaction for better global consistency in higher-resolution image generation. Experimental comparison with existing methods demonstrates that our AccDiffusion effectively addresses the issue of repeated object generation and leads to better performance in higher-resolution image generation.

Diffusion models suffer severe object repetition and local distortion when the inference resolution differs from its pre-trained resolution. We propose AccDiffusion v2, an accurate method for patch-wise higher-resolution diffusion extrapolation without training. Our in-depth analysis in this paper shows that using an identical text prompt for different patches leads to repetitive generation, while the absence of a prompt undermines image details. In response, our AccDiffusion v2 novelly decouples the vanilla image-content-aware prompt into a set of patch-content-aware prompts, each of which serves as a more precise description of a patch. Further analysis reveals that local distortion arises from inaccurate descriptions in prompts about the local structure of higher-resolution images. To address this issue, AccDiffusion v2, for the first time, introduces an auxiliary local structural information through ControlNet during higher-resolution diffusion extrapolation aiming to mitigate the local distortions. Finally, our analysis indicates that global semantic information is conducive to suppressing both repetitive generation and local distortion. Hence, our AccDiffusion v2 further proposes dilated sampling with window interaction for better global semantic information during higher-resolution diffusion extrapolation. We conduct extensive experiments, including both quantitative and qualitative comparisons, to demonstrate the efficacy of our AccDiffusion v2. The quantitative comparison shows that AccDiffusion v2 achieves state-of-the-art performance in image generation extrapolation without training. The qualitative comparison intuitively illustrates that AccDiffusion v2 effectively suppresses the issues of repetitive generation and local distortion in image generation extrapolation. Our code is available at https://github.com/lzhxmu/AccDiffusion_v2.

Recent years have witnessed great progress in image restoration thanks to the advancements in modern deep neural networks e.g. Convolutional Neural Network and Transformer. However, existing restoration backbones are usually limited due to the inherent local reductive bias or quadratic computational complexity. Recently, Selective Structured State Space Model e.g., Mamba, has shown great potential for long-range dependencies modeling with linear complexity, but it is still under-explored in low-level computer vision. In this work, we introduce a simple but strong benchmark model, named MambaIR, for image restoration. In detail, we propose the Residual State Space Block as the core component, which employs convolution and channel attention to enhance the capabilities of the vanilla Mamba. In this way, our MambaIR takes advantage of local patch recurrence prior as well as channel interaction to produce restoration-specific feature representation. Extensive experiments demonstrate the superiority of our method, for example, MambaIR outperforms Transformer-based baseline SwinIR by up to 0.36dB, using similar computational cost but with a global receptive field. Code is available at https://github.com/csguoh/MambaIR.

Mechanistic interpretability seeks to understand the internal mechanisms of machine learning models, where localization -- identifying the important model components -- is a key step. Activation patching, also known as causal tracing or interchange intervention, is a standard technique for this task (Vig et al., 2020), but the literature contains many variants with little consensus on the choice of hyperparameters or methodology. In this work, we systematically examine the impact of methodological details in activation patching, including evaluation metrics and corruption methods. In several settings of localization and circuit discovery in language models, we find that varying these hyperparameters could lead to disparate interpretability results. Backed by empirical observations, we give conceptual arguments for why certain metrics or methods may be preferred. Finally, we provide recommendations for the best practices of activation patching going forwards.

Interactions among features are central to understanding the behavior of machine learning models. Recent research has made significant strides in detecting and quantifying feature interactions in single predictive models. However, we argue that the feature interactions extracted from a single pre-specified model may not be trustworthy since: a well-trained predictive model may not preserve the true feature interactions and there exist multiple well-performing predictive models that differ in feature interaction strengths. Thus, we recommend exploring feature interaction strengths in a model class of approximately equally accurate predictive models. In this work, we introduce the feature interaction score (FIS) in the context of a Rashomon set, representing a collection of models that achieve similar accuracy on a given task. We propose a general and practical algorithm to calculate the FIS in the model class. We demonstrate the properties of the FIS via synthetic data and draw connections to other areas of statistics. Additionally, we introduce a Halo plot for visualizing the feature interaction variance in high-dimensional space and a swarm plot for analyzing FIS in a Rashomon set. Experiments with recidivism prediction and image classification illustrate how feature interactions can vary dramatically in importance for similarly accurate predictive models. Our results suggest that the proposed FIS can provide valuable insights into the nature of feature interactions in machine learning models.

Activation patching is a popular mechanistic interpretability technique, but has many subtleties regarding how it is applied and how one may interpret the results. We provide a summary of advice and best practices, based on our experience using this technique in practice. We include an overview of the different ways to apply activation patching and a discussion on how to interpret the results. We focus on what evidence patching experiments provide about circuits, and on the choice of metric and associated pitfalls.

Networks provide a powerful formalism for modeling complex systems by using a model of pairwise interactions. But much of the structure within these systems involves interactions that take place among more than two nodes at once; for example, communication within a group rather than person-to person, collaboration among a team rather than a pair of coauthors, or biological interaction between a set of molecules rather than just two. Such higher-order interactions are ubiquitous, but their empirical study has received limited attention, and little is known about possible organizational principles of such structures. Here we study the temporal evolution of 19 datasets with explicit accounting for higher-order interactions. We show that there is a rich variety of structure in our datasets but datasets from the same system types have consistent patterns of higher-order structure. Furthermore, we find that tie strength and edge density are competing positive indicators of higher-order organization, and these trends are consistent across interactions involving differing numbers of nodes. To systematically further the study of theories for such higher-order structures, we propose higher-order link prediction as a benchmark problem to assess models and algorithms that predict higher-order structure. We find a fundamental differences from traditional pairwise link prediction, with a greater role for local rather than long-range information in predicting the appearance of new interactions.

Systems of interacting objects often evolve under the influence of field effects that govern their dynamics, yet previous works have abstracted away from such effects, and assume that systems evolve in a vacuum. In this work, we focus on discovering these fields, and infer them from the observed dynamics alone, without directly observing them. We theorize the presence of latent force fields, and propose neural fields to learn them. Since the observed dynamics constitute the net effect of local object interactions and global field effects, recently popularized equivariant networks are inapplicable, as they fail to capture global information. To address this, we propose to disentangle local object interactions -- which are SE(n) equivariant and depend on relative states -- from external global field effects -- which depend on absolute states. We model interactions with equivariant graph networks, and combine them with neural fields in a novel graph network that integrates field forces. Our experiments show that we can accurately discover the underlying fields in charged particles settings, traffic scenes, and gravitational n-body problems, and effectively use them to learn the system and forecast future trajectories.

Exposing meaningful and interpretable neural interactions is critical to understanding neural circuits. Inferred neural interactions from neural signals primarily reflect functional interactions. In a long experiment, subject animals may experience different stages defined by the experiment, stimuli, or behavioral states, and hence functional interactions can change over time. To model dynamically changing functional interactions, prior work employs state-switching generalized linear models with hidden Markov models (i.e., HMM-GLMs). However, we argue they lack biological plausibility, as functional interactions are shaped and confined by the underlying anatomical connectome. Here, we propose a novel prior-informed state-switching GLM. We introduce both a Gaussian prior and a one-hot prior over the GLM in each state. The priors are learnable. We will show that the learned prior should capture the state-constant interaction, shedding light on the underlying anatomical connectome and revealing more likely physical neuron interactions. The state-dependent interaction modeled by each GLM offers traceability to capture functional variations across multiple brain states. Our methods effectively recover true interaction structures in simulated data, achieve the highest predictive likelihood with real neural datasets, and render interaction structures and hidden states more interpretable when applied to real neural data.

Recently, self-supervised learning (SSL) was shown to be vulnerable to patch-based data poisoning backdoor attacks. It was shown that an adversary can poison a small part of the unlabeled data so that when a victim trains an SSL model on it, the final model will have a backdoor that the adversary can exploit. This work aims to defend self-supervised learning against such attacks. We use a three-step defense pipeline, where we first train a model on the poisoned data. In the second step, our proposed defense algorithm (PatchSearch) uses the trained model to search the training data for poisoned samples and removes them from the training set. In the third step, a final model is trained on the cleaned-up training set. Our results show that PatchSearch is an effective defense. As an example, it improves a model's accuracy on images containing the trigger from 38.2% to 63.7% which is very close to the clean model's accuracy, 64.6%. Moreover, we show that PatchSearch outperforms baselines and state-of-the-art defense approaches including those using additional clean, trusted data. Our code is available at https://github.com/UCDvision/PatchSearch

The impact of person-job fit on job satisfaction and performance is widely acknowledged, which highlights the importance of providing workers with next steps at the right time in their career. This task of predicting the next step in a career is known as career path prediction, and has diverse applications such as turnover prevention and internal job mobility. Existing methods to career path prediction rely on large amounts of private career history data to model the interactions between job titles and companies. We propose leveraging the unexplored textual descriptions that are part of work experience sections in resumes. We introduce a structured dataset of 2,164 anonymized career histories, annotated with ESCO occupation labels. Based on this dataset, we present a novel representation learning approach, CareerBERT, specifically designed for work history data. We develop a skill-based model and a text-based model for career path prediction, which achieve 35.24% and 39.61% recall@10 respectively on our dataset. Finally, we show that both approaches are complementary as a hybrid approach achieves the strongest result with 43.01% recall@10.

Complex Logical Query Answering (CLQA) over incomplete knowledge graphs is a challenging task. Recently, Query Embedding (QE) methods are proposed to solve CLQA by performing multi-hop logical reasoning. However, most of them only consider historical query context information while ignoring future information, which leads to their failure to capture the complex dependencies behind the elements of a query. In recent years, the transformer architecture has shown a strong ability to model long-range dependencies between words. The bidirectional attention mechanism proposed by the transformer can solve the limitation of these QE methods regarding query context. Still, as a sequence model, it is difficult for the transformer to model complex logical queries with branch structure computation graphs directly. To this end, we propose a neural one-point embedding method called Pathformer based on the tree-like computation graph, i.e., query computation tree. Specifically, Pathformer decomposes the query computation tree into path query sequences by branches and then uses the transformer encoder to recursively encode these path query sequences to obtain the final query embedding. This allows Pathformer to fully utilize future context information to explicitly model the complex interactions between various parts of the path query. Experimental results show that Pathformer outperforms existing competitive neural QE methods, and we found that Pathformer has the potential to be applied to non-one-point embedding space.

Diffusion models have exhibited exciting capabilities in generating images and are also very promising for video creation. However, the inference speed of diffusion models is limited by the slow sampling process, restricting its use cases. The sequential denoising steps required for generating a single sample could take tens or hundreds of iterations and thus have become a significant bottleneck. This limitation is more salient for applications that are interactive in nature or require small latency. To address this challenge, we propose Partially Conditioned Patch Parallelism (PCPP) to accelerate the inference of high-resolution diffusion models. Using the fact that the difference between the images in adjacent diffusion steps is nearly zero, Patch Parallelism (PP) leverages multiple GPUs communicating asynchronously to compute patches of an image in multiple computing devices based on the entire image (all patches) in the previous diffusion step. PCPP develops PP to reduce computation in inference by conditioning only on parts of the neighboring patches in each diffusion step, which also decreases communication among computing devices. As a result, PCPP decreases the communication cost by around 70% compared to DistriFusion (the state of the art implementation of PP) and achieves 2.36sim 8.02times inference speed-up using 4sim 8 GPUs compared to 2.32sim 6.71times achieved by DistriFusion depending on the computing device configuration and resolution of generation at the cost of a possible decrease in image quality. PCPP demonstrates the potential to strike a favorable trade-off, enabling high-quality image generation with substantially reduced latency.

Large Language Models (LLMs) have demonstrated strong capabilities but remain fundamentally static, unable to adapt their internal parameters to novel tasks, evolving knowledge domains, or dynamic interaction contexts. As LLMs are increasingly deployed in open-ended, interactive environments, this static nature has become a critical bottleneck, necessitating agents that can adaptively reason, act, and evolve in real time. This paradigm shift -- from scaling static models to developing self-evolving agents -- has sparked growing interest in architectures and methods enabling continual learning and adaptation from data, interactions, and experiences. This survey provides the first systematic and comprehensive review of self-evolving agents, organized around three foundational dimensions -- what to evolve, when to evolve, and how to evolve. We examine evolutionary mechanisms across agent components (e.g., models, memory, tools, architecture), categorize adaptation methods by stages (e.g., intra-test-time, inter-test-time), and analyze the algorithmic and architectural designs that guide evolutionary adaptation (e.g., scalar rewards, textual feedback, single-agent and multi-agent systems). Additionally, we analyze evaluation metrics and benchmarks tailored for self-evolving agents, highlight applications in domains such as coding, education, and healthcare, and identify critical challenges and research directions in safety, scalability, and co-evolutionary dynamics. By providing a structured framework for understanding and designing self-evolving agents, this survey establishes a roadmap for advancing adaptive agentic systems in both research and real-world deployments, ultimately shedding lights to pave the way for the realization of Artificial Super Intelligence (ASI), where agents evolve autonomously, performing at or beyond human-level intelligence across a wide array of tasks.

Deep sparse networks are widely investigated as a neural network architecture for prediction tasks with high-dimensional sparse features, with which feature interaction selection is a critical component. While previous methods primarily focus on how to search feature interaction in a coarse-grained space, less attention has been given to a finer granularity. In this work, we introduce a hybrid-grained feature interaction selection approach that targets both feature field and feature value for deep sparse networks. To explore such expansive space, we propose a decomposed space which is calculated on the fly. We then develop a selection algorithm called OptFeature, which efficiently selects the feature interaction from both the feature field and the feature value simultaneously. Results from experiments on three large real-world benchmark datasets demonstrate that OptFeature performs well in terms of accuracy and efficiency. Additional studies support the feasibility of our method.

Context: Bugs in code are inevitable and can lead to severe consequences, ranging from security vulnerabilities to operational failures. Debugging software remains challenging despite advances in testing and verification, often requiring extensive manual effort. Learning-based automated program repair (APR) has shown promise in reducing the time, effort, and cost of manually fixing bugs. However, existing techniques face several challenges, including language-dependent strategies, limited bug context utilization, and difficulties in handling bugs that span multiple locations in the code. Objective: This paper introduces MultiMend, a learning-based APR approach designed to improve repair performance on multiple programming languages with language-independent context augmentation and multi-hunk patch generation. Method: MultiMend fine-tunes a pre-trained encoder-decoder transformer model (CodeT5) to generate bug-fixing patches. It embeds source code lines and applies retrieval-augmented generation to augment the buggy context with relevant lines during patch generation. The approach systematically constructs patches for multi-hunk bugs to reduce the needed patch validations. We evaluate MultiMend on four benchmarks with four programming languages and compare it with state-of-the-art methods. Results: Experimental results show that MultiMend achieves competitive effectiveness and efficiency against compared tools. Across all benchmarks, MultiMend fixes 2,077 bugs, of which 1,455 are identical to the developer's patch, and 106 are for multi-hunk bugs. Both context augmentation and multi-hunk patch generation positively contribute to the results. Conclusion: MultiMend shows promising performance across benchmarks. The findings highlight its applicability to real-world software maintenance and its potential to reduce manual debugging efforts.

Automated Program Repair (APR) is a task to automatically generate patches for the buggy code. However, most research focuses on generating correct patches while ignoring the consistency between the fixed code and the original buggy code. How to conduct adaptive bug fixing and generate patches with minimal modifications have seldom been investigated. To bridge this gap, we first introduce a novel task, namely AdaPR (Adaptive Program Repair). We then propose a two-stage approach AdaPatcher (Adaptive Patch Generator) to enhance program repair while maintaining the consistency. In the first stage, we utilize a Bug Locator with self-debug learning to accurately pinpoint bug locations. In the second stage, we train a Program Modifier to ensure consistency between the post-modified fixed code and the pre-modified buggy code. The Program Modifier is enhanced with a location-aware repair learning strategy to generate patches based on identified buggy lines, a hybrid training strategy for selective reference and an adaptive preference learning to prioritize fewer changes. The experimental results show that our approach outperforms a set of baselines by a large margin, validating the effectiveness of our two-stage framework for the newly proposed AdaPR task.

We present a method to create universal, robust, targeted adversarial image patches in the real world. The patches are universal because they can be used to attack any scene, robust because they work under a wide variety of transformations, and targeted because they can cause a classifier to output any target class. These adversarial patches can be printed, added to any scene, photographed, and presented to image classifiers; even when the patches are small, they cause the classifiers to ignore the other items in the scene and report a chosen target class. To reproduce the results from the paper, our code is available at https://github.com/tensorflow/cleverhans/tree/master/examples/adversarial_patch

Machine learning models are vulnerable to adversarial perturbations, and a thought-provoking paper by Bubeck and Sellke has analyzed this phenomenon through the lens of over-parameterization: interpolating smoothly the data requires significantly more parameters than simply memorizing it. However, this "universal" law provides only a necessary condition for robustness, and it is unable to discriminate between models. In this paper, we address these gaps by focusing on empirical risk minimization in two prototypical settings, namely, random features and the neural tangent kernel (NTK). We prove that, for random features, the model is not robust for any degree of over-parameterization, even when the necessary condition coming from the universal law of robustness is satisfied. In contrast, for even activations, the NTK model meets the universal lower bound, and it is robust as soon as the necessary condition on over-parameterization is fulfilled. This also addresses a conjecture in prior work by Bubeck, Li and Nagaraj. Our analysis decouples the effect of the kernel of the model from an "interaction matrix", which describes the interaction with the test data and captures the effect of the activation. Our theoretical results are corroborated by numerical evidence on both synthetic and standard datasets (MNIST, CIFAR-10).

Automated issue solving aims to resolve real-world issues in software repositories. The most popular benchmarks for automated issue solving are SWE-bench and its human-filtered subset SWE-bench Verified. These benchmarks leverage testing to validate generated patches. However, because testing is rarely exhaustive, a patch may pass the tests but nevertheless fail to match the developers' expectations. Unfortunately, it is currently unclear to what extent evaluations performed with SWE-bench suffer from such plausible but incorrect patches. This paper presents an in-depth empirical study of the correctness of plausible patches generated by three state-of-the-art issue-solving tools evaluated on SWE-bench Verified. We extensively test and inspect generated patches, and compare them against human-written ground truth patches. The core of our methodology is a novel technique PatchDiff for differential patch testing, which automatically exposes behavioral discrepancies between two patches. Our findings reveal critical weaknesses in SWE-bench's patch validation mechanism, which causes 7.8% of all patches to count as correct while failing the developer-written test suite. Moreover, our novel automated technique reveals that even more (29.6%) plausible patches induce different behavior than the ground truth patches. These behavioral differences are often due to similar, but divergent implementations (46.8%) and due to generated patches that adapt more behavior than the ground truth patches (27.3%). Our manual inspection shows that 28.6% of behaviorally divergent patches are certainly incorrect. Combined, the different weaknesses lead to an inflation of reported resolution rates by 6.2 absolute percent points. Our findings are a call to arms for more robust and reliable evaluation of issue-solving tools. We envision our automated differential patch testing technique to be useful for this purpose.

We model and study the processes of excitation, absorption, and transfer in various networks. The model consists of a harmonic oscillator representing a single-mode radiation field, a qubit acting as an antenna, a network through which the excitation propagates, and a qubit at the end serving as a sink. We investigate how off-resonant excitations can be optimally absorbed and transmitted through the network. Three strategies are considered: optimising network energies, adjusting the couplings between the radiation field, the antenna, and the network, or introducing and optimising driving fields at the start and end of the network. These strategies are tested on three different types of network with increasing complexity: nearest-neighbour and star configurations, and one associated with the Fenna-Matthews-Olson complex. The results show that, among the various strategies, the introduction of driving fields is the most effective, leading to a significant increase in the probability of reaching the sink in a given time. This result remains stable across networks of varying dimensionalities and types, and the driving process requires only a few parameters to be effective.

Noise is a ubiquitous feature of the physical world. As a result, the first prerequisite of life is fault tolerance: maintaining integrity of state despite external bombardment. Recent experimental advances have revealed that biological systems achieve fault tolerance by implementing mathematically intricate error-correcting codes and by organizing in a modular fashion that physically separates functionally distinct subsystems. These elaborate structures represent a vanishing volume in the massive genetic configuration space. How is it possible that the primitive process of evolution, by which all biological systems evolved, achieved such unusual results? In this work, through experiments in Boolean networks, we show that the simultaneous presence of error correction and modularity in biological systems is no coincidence. Rather, it is a typical co-occurrence in noisy dynamic systems undergoing evolution. From this, we deduce the principle of error correction enhanced evolvability: systems possessing error-correcting codes are more effectively improved by evolution than those without.

Large-scale, diverse robot datasets have emerged as a promising path toward enabling dexterous manipulation policies to generalize to novel environments, but acquiring such datasets presents many challenges. While teleoperation provides high-fidelity datasets, its high cost limits its scalability. Instead, what if people could use their own hands, just as they do in everyday life, to collect data? In DexWild, a diverse team of data collectors uses their hands to collect hours of interactions across a multitude of environments and objects. To record this data, we create DexWild-System, a low-cost, mobile, and easy-to-use device. The DexWild learning framework co-trains on both human and robot demonstrations, leading to improved performance compared to training on each dataset individually. This combination results in robust robot policies capable of generalizing to novel environments, tasks, and embodiments with minimal additional robot-specific data. Experimental results demonstrate that DexWild significantly improves performance, achieving a 68.5% success rate in unseen environments-nearly four times higher than policies trained with robot data only-and offering 5.8x better cross-embodiment generalization. Video results, codebases, and instructions at https://dexwild.github.io

We present CIFLEX (Contextual Instruction Flow for Sub-task Execution), which is a novel execution system for efficient sub-task handling in multi-turn interactions with a single on-device large language model (LLM). As LLMs become increasingly capable, a single model is expected to handle diverse sub-tasks that more effectively and comprehensively support answering user requests. Naive approach reprocesses the entire conversation context when switching between main and sub-tasks (e.g., query rewriting, summarization), incurring significant computational overhead. CIFLEX mitigates this overhead by reusing the key-value (KV) cache from the main task and injecting only task-specific instructions into isolated side paths. After sub-task execution, the model rolls back to the main path via cached context, thereby avoiding redundant prefill computation. To support sub-task selection, we also develop a hierarchical classification strategy tailored for small-scale models, decomposing multi-choice decisions into binary ones. Experiments show that CIFLEX significantly reduces computational costs without degrading task performance, enabling scalable and efficient multi-task dialogue on-device.

Social interactions form the foundation of human societies. Artificial intelligence has made significant progress in certain areas, but enabling machines to seamlessly understand social interactions remains an open challenge. It is important to address this gap by endowing machines with social capabilities. We identify three key capabilities needed for effective social understanding: 1) understanding multimodal social cues, 2) understanding multi-party dynamics, and 3) understanding beliefs. Building upon these foundations, we classify and review existing machine learning works on social understanding from the perspectives of verbal, non-verbal, and multimodal social cues. The verbal branch focuses on understanding linguistic signals such as speaker intent, dialogue sentiment, and commonsense reasoning. The non-verbal branch addresses techniques for perceiving social meaning from visual behaviors such as body gestures, gaze patterns, and facial expressions. The multimodal branch covers approaches that integrate verbal and non-verbal multimodal cues to holistically interpret social interactions such as recognizing emotions, conversational dynamics, and social situations. By reviewing the scope and limitations of current approaches and benchmarks, we aim to clarify the development trajectory and illuminate the path towards more comprehensive intelligence for social understanding. We hope this survey will spur further research interest and insights into this area.

In recent years, more vulnerabilities have been discovered every day, while manual vulnerability repair requires specialized knowledge and is time-consuming. As a result, many detected or even published vulnerabilities remain unpatched, thereby increasing the exposure of software systems to attacks. Recent advancements in agents based on Large Language Models have demonstrated their increasing capabilities in code understanding and generation, which can be promising to achieve automated vulnerability repair. However, the effectiveness of agents based on static information retrieval is still not sufficient for patch generation. To address the challenge, we propose a program repair agent called VulDebugger that fully utilizes both static and dynamic context, and it debugs programs in a manner akin to humans. The agent inspects the actual state of the program via the debugger and infers expected states via constraints that need to be satisfied. By continuously comparing the actual state with the expected state, it deeply understands the root causes of the vulnerabilities and ultimately accomplishes repairs. We experimentally evaluated VulDebugger on 50 real-life projects. With 60.00% successfully fixed, VulDebugger significantly outperforms state-of-the-art approaches for vulnerability repair.

We introduce EQ-Bench, a novel benchmark designed to evaluate aspects of emotional intelligence in Large Language Models (LLMs). We assess the ability of LLMs to understand complex emotions and social interactions by asking them to predict the intensity of emotional states of characters in a dialogue. The benchmark is able to discriminate effectively between a wide range of models. We find that EQ-Bench correlates strongly with comprehensive multi-domain benchmarks like MMLU (Hendrycks et al., 2020) (r=0.97), indicating that we may be capturing similar aspects of broad intelligence. Our benchmark produces highly repeatable results using a set of 60 English-language questions. We also provide open-source code for an automated benchmarking pipeline at https://github.com/EQ-bench/EQ-Bench and a leaderboard at https://eqbench.com

In rapid release development processes, patches that fix critical issues, or implement high-value features are often promoted directly from the development channel to a stabilization channel, potentially skipping one or more stabilization channels. This practice is called patch uplift. Patch uplift is risky, because patches that are rushed through the stabilization phase can end up introducing regressions in the code. This paper examines patch uplift operations at Mozilla, with the aim to identify the characteristics of uplifted patches that introduce regressions. Through statistical and manual analyses, we quantitatively and qualitatively investigate the reasons behind patch uplift decisions and the characteristics of uplifted patches that introduced regressions. Additionally, we interviewed three Mozilla release managers to understand organizational factors that affect patch uplift decisions and outcomes. Results show that most patches are uplifted because of a wrong functionality or a crash. Uplifted patches that lead to faults tend to have larger patch size, and most of the faults are due to semantic or memory errors in the patches. Also, release managers are more inclined to accept patch uplift requests that concern certain specific components, and-or that are submitted by certain specific developers.

Chain of Thought (CoT) of multi-step benefits from the logical structure of the reasoning steps and task-specific actions, significantly enhancing the mathematical reasoning capabilities of large language models. As the prevalence of long CoT, the number of reasoning steps exceeds manageable token limits and leads to higher computational demands. Inspired by the fundamental logic of human cognition, ``derive, then reduce'', we conceptualize the standard multi-step CoT as a novel Markov Chain of Thought (MCoT). In this study, we consider the mathematical reasoning task, defining each reasoning step as text accompanied by a Python code snippet. To facilitate a longer reasoning path, self-correction is enabled through interactions with the code interpreter. Our MCoT aims to compress previous reasoning steps into a simplified question, enabling efficient next-step inference without relying on a lengthy KV cache. In our experiments, we curate the MCoTInstruct dataset, and the empirical results indicate that MCoT not only significantly enhances efficiency but also maintains comparable accuracy. While much remains to be explored, this work paves the way for exploring the long CoT reasoning abilities of LLMs.

Structured state-space models (SSMs) such as S4, stemming from the seminal work of Gu et al., are gaining popularity as effective approaches for modeling sequential data. Deep SSMs demonstrate outstanding performance across a diverse set of domains, at a reduced training and inference cost compared to attention-based transformers. Recent developments show that if the linear recurrence powering SSMs allows for multiplicative interactions between inputs and hidden states (e.g. GateLoop, Mamba, GLA), then the resulting architecture can surpass in both in accuracy and efficiency attention-powered foundation models trained on text, at scales of billion parameters. In this paper, we give theoretical grounding to this recent finding using tools from Rough Path Theory: we show that when random linear recurrences are equipped with simple input-controlled transitions (selectivity mechanism), then the hidden state is provably a low-dimensional projection of a powerful mathematical object called the signature of the input -- capturing non-linear interactions between tokens at distinct timescales. Our theory not only motivates the success of modern selective state-space models such as Mamba but also provides a solid framework to understand the expressive power of future SSM variants.

Despite the recent successes of vanilla Graph Neural Networks (GNNs) on many tasks, their foundation on pairwise interaction networks inherently limits their capacity to discern latent higher-order interactions in complex systems. To bridge this capability gap, we propose a novel approach exploiting the rich mathematical theory of simplicial complexes (SCs) - a robust tool for modeling higher-order interactions. Current SC-based GNNs are burdened by high complexity and rigidity, and quantifying higher-order interaction strengths remains challenging. Innovatively, we present a higher-order Flower-Petals (FP) model, incorporating FP Laplacians into SCs. Further, we introduce a Higher-order Graph Convolutional Network (HiGCN) grounded in FP Laplacians, capable of discerning intrinsic features across varying topological scales. By employing learnable graph filters, a parameter group within each FP Laplacian domain, we can identify diverse patterns where the filters' weights serve as a quantifiable measure of higher-order interaction strengths. The theoretical underpinnings of HiGCN's advanced expressiveness are rigorously demonstrated. Additionally, our empirical investigations reveal that the proposed model accomplishes state-of-the-art (SOTA) performance on a range of graph tasks and provides a scalable and flexible solution to explore higher-order interactions in graphs.

Efficient exploration is essential for intelligent systems interacting with their environment, but existing language models often fall short in scenarios that require strategic information gathering. In this paper, we present PAPRIKA, a fine-tuning approach that enables language models to develop general decision-making capabilities that are not confined to particular environments. By training on synthetic interaction data from different tasks that require diverse strategies, PAPRIKA teaches models to explore and adapt their behavior on a new task based on environment feedback in-context without more gradient updates. Experimental results show that models fine-tuned with PAPRIKA can effectively transfer their learned decision-making capabilities to entirely unseen tasks without additional training. Unlike traditional training, our approach's primary bottleneck lies in sampling useful interaction data instead of model updates. To improve sample efficiency, we propose a curriculum learning strategy that prioritizes sampling trajectories from tasks with high learning potential. These results suggest a promising path towards AI systems that can autonomously solve novel sequential decision-making problems that require interactions with the external world.

Transformer based models have provided significant performance improvements in monaural speech separation. However, there is still a performance gap compared to a recent proposed upper bound. The major limitation of the current dual-path Transformer models is the inefficient modelling of long-range elemental interactions and local feature patterns. In this work, we achieve the upper bound by proposing a gated single-head transformer architecture with convolution-augmented joint self-attentions, named MossFormer (Monaural speech separation TransFormer). To effectively solve the indirect elemental interactions across chunks in the dual-path architecture, MossFormer employs a joint local and global self-attention architecture that simultaneously performs a full-computation self-attention on local chunks and a linearised low-cost self-attention over the full sequence. The joint attention enables MossFormer model full-sequence elemental interaction directly. In addition, we employ a powerful attentive gating mechanism with simplified single-head self-attentions. Besides the attentive long-range modelling, we also augment MossFormer with convolutions for the position-wise local pattern modelling. As a consequence, MossFormer significantly outperforms the previous models and achieves the state-of-the-art results on WSJ0-2/3mix and WHAM!/WHAMR! benchmarks. Our model achieves the SI-SDRi upper bound of 21.2 dB on WSJ0-3mix and only 0.3 dB below the upper bound of 23.1 dB on WSJ0-2mix.

Large language models (LLMs) have demonstrated excellent capabilities in the field of biomedical question answering, but their application in real-world clinical consultations still faces core challenges. Existing systems rely on a one-way information transmission mode where patients must fully describe their symptoms in a single round, leading to nonspecific diagnostic recommendations when complaints are vague. Traditional multi-turn dialogue methods based on supervised learning are constrained by static data-driven paradigms, lacking generalizability and struggling to intelligently extract key clinical information. To address these limitations, we propose DoctorAgent-RL, a reinforcement learning (RL)-based multi-agent collaborative framework that models medical consultations as a dynamic decision-making process under uncertainty. The doctor agent continuously optimizes its questioning strategy within the RL framework through multi-turn interactions with the patient agent, dynamically adjusting its information-gathering path based on comprehensive rewards from the Consultation Evaluator. This RL fine-tuning mechanism enables LLMs to autonomously develop interaction strategies aligned with clinical reasoning logic, rather than superficially imitating patterns in existing dialogue data. Notably, we constructed MTMedDialog, the first English multi-turn medical consultation dataset capable of simulating patient interactions. Experiments demonstrate that DoctorAgent-RL outperforms existing models in both multi-turn reasoning capability and final diagnostic performance, demonstrating practical value in assisting clinical consultations. https://github.com/JarvisUSTC/DoctorAgent-RL

In this study, we establish a baseline for a new task named multimodal multi-round referring and grounding (MRG), opening up a promising direction for instance-level multimodal dialogues. We present a new benchmark and an efficient vision-language model for this purpose. The new benchmark, named CB-300K, spans challenges including multi-round dialogue, complex spatial relationships among multiple instances, and consistent reasoning, which are beyond those shown in existing benchmarks. The proposed model, named ChatterBox, utilizes a two-branch architecture to collaboratively handle vision and language tasks. By tokenizing instance regions, the language branch acquires the ability to perceive referential information. Meanwhile, ChatterBox feeds a query embedding in the vision branch to a token receiver for visual grounding. A two-stage optimization strategy is devised, making use of both CB-300K and auxiliary external data to improve the model's stability and capacity for instance-level understanding. Experiments show that ChatterBox outperforms existing models in MRG both quantitatively and qualitatively, paving a new path towards multimodal dialogue scenarios with complicated and precise interactions. Code, data, and model are available at: https://github.com/sunsmarterjie/ChatterBox.

Large language models augmented with task-relevant documents have demonstrated impressive performance on knowledge-intensive tasks. However, regarding how to obtain effective documents, the existing methods are mainly divided into two categories. One is to retrieve from an external knowledge base, and the other is to utilize large language models to generate documents. We propose an iterative retrieval-generation collaborative framework. It is not only able to leverage both parametric and non-parametric knowledge, but also helps to find the correct reasoning path through retrieval-generation interactions, which is very important for tasks that require multi-step reasoning. We conduct experiments on four question answering datasets, including single-hop QA and multi-hop QA tasks. Empirical results show that our method significantly improves the reasoning ability of large language models and outperforms previous baselines.

Large Language Models (LLMs) have shown strong inductive reasoning ability across various domains, but their reliability is hindered by the outdated knowledge and hallucinations. Retrieval-Augmented Generation mitigates these issues by grounding LLMs with external knowledge; however, most existing RAG pipelines rely on unstructured text, limiting interpretability and structured reasoning. Knowledge graphs, which represent facts as relational triples, offer a more structured and compact alternative. Recent studies have explored integrating knowledge graphs with LLMs for knowledge graph question answering (KGQA), with a significant proportion adopting the retrieve-then-reasoning paradigm. In this framework, graph-based retrievers have demonstrated strong empirical performance, yet they still face challenges in generalization ability. In this work, we propose RAPL, a novel framework for efficient and effective graph retrieval in KGQA. RAPL addresses these limitations through three aspects: (1) a two-stage labeling strategy that combines heuristic signals with parametric models to provide causally grounded supervision; (2) a model-agnostic graph transformation approach to capture both intra- and inter-triple interactions, thereby enhancing representational capacity; and (3) a path-based reasoning strategy that facilitates learning from the injected rational knowledge, and supports downstream reasoner through structured inputs. Empirically, RAPL outperforms state-of-the-art methods by 2.66%-20.34%, and significantly reduces the performance gap between smaller and more powerful LLM-based reasoners, as well as the gap under cross-dataset settings, highlighting its superior retrieval capability and generalizability. Codes are available at: https://github.com/tianyao-aka/RAPL.

Recurrent neural networks (RNNs) are widely used throughout neuroscience as models of local neural activity. Many properties of single RNNs are well characterized theoretically, but experimental neuroscience has moved in the direction of studying multiple interacting areas, and RNN theory needs to be likewise extended. We take a constructive approach towards this problem, leveraging tools from nonlinear control theory and machine learning to characterize when combinations of stable RNNs will themselves be stable. Importantly, we derive conditions which allow for massive feedback connections between interacting RNNs. We parameterize these conditions for easy optimization using gradient-based techniques, and show that stability-constrained "networks of networks" can perform well on challenging sequential-processing benchmark tasks. Altogether, our results provide a principled approach towards understanding distributed, modular function in the brain.

Numerous biological and physical processes can be modeled as systems of interacting entities evolving continuously over time, e.g. the dynamics of communicating cells or physical particles. Learning the dynamics of such systems is essential for predicting the temporal evolution of populations across novel samples and unseen environments. Flow-based models allow for learning these dynamics at the population level - they model the evolution of the entire distribution of samples. However, current flow-based models are limited to a single initial population and a set of predefined conditions which describe different dynamics. We argue that multiple processes in natural sciences have to be represented as vector fields on the Wasserstein manifold of probability densities. That is, the change of the population at any moment in time depends on the population itself due to the interactions between samples. In particular, this is crucial for personalized medicine where the development of diseases and their respective treatment response depends on the microenvironment of cells specific to each patient. We propose Meta Flow Matching (MFM), a practical approach to integrating along these vector fields on the Wasserstein manifold by amortizing the flow model over the initial populations. Namely, we embed the population of samples using a Graph Neural Network (GNN) and use these embeddings to train a Flow Matching model. This gives MFM the ability to generalize over the initial distributions unlike previously proposed methods. We demonstrate the ability of MFM to improve prediction of individual treatment responses on a large scale multi-patient single-cell drug screen dataset.

Click-through prediction (CTR) models transform features into latent vectors and enumerate possible feature interactions to improve performance based on the input feature set. Therefore, when selecting an optimal feature set, we should consider the influence of both feature and its interaction. However, most previous works focus on either feature field selection or only select feature interaction based on the fixed feature set to produce the feature set. The former restricts search space to the feature field, which is too coarse to determine subtle features. They also do not filter useless feature interactions, leading to higher computation costs and degraded model performance. The latter identifies useful feature interaction from all available features, resulting in many redundant features in the feature set. In this paper, we propose a novel method named OptFS to address these problems. To unify the selection of feature and its interaction, we decompose the selection of each feature interaction into the selection of two correlated features. Such a decomposition makes the model end-to-end trainable given various feature interaction operations. By adopting feature-level search space, we set a learnable gate to determine whether each feature should be within the feature set. Because of the large-scale search space, we develop a learning-by-continuation training scheme to learn such gates. Hence, OptFS generates the feature set only containing features which improve the final prediction results. Experimentally, we evaluate OptFS on three public datasets, demonstrating OptFS can optimize feature sets which enhance the model performance and further reduce both the storage and computational cost.

We study neural network loss landscapes through the lens of mode connectivity, the observation that minimizers of neural networks retrieved via training on a dataset are connected via simple paths of low loss. Specifically, we ask the following question: are minimizers that rely on different mechanisms for making their predictions connected via simple paths of low loss? We provide a definition of mechanistic similarity as shared invariances to input transformations and demonstrate that lack of linear connectivity between two models implies they use dissimilar mechanisms for making their predictions. Relevant to practice, this result helps us demonstrate that naive fine-tuning on a downstream dataset can fail to alter a model's mechanisms, e.g., fine-tuning can fail to eliminate a model's reliance on spurious attributes. Our analysis also motivates a method for targeted alteration of a model's mechanisms, named connectivity-based fine-tuning (CBFT), which we analyze using several synthetic datasets for the task of reducing a model's reliance on spurious attributes.

Interference is ubiquitous when conducting causal experiments over networks. Except for certain network structures, causal inference on the network in the presence of interference is difficult due to the entanglement between the treatment assignments and the interference levels. In this article, we conduct causal inference under interference on an observed, sparse but connected network, and we propose a novel design of experiments based on an independent set. Compared to conventional designs, the independent-set design focuses on an independent subset of data and controls their interference exposures through the assignments to the rest (auxiliary set). We provide a lower bound on the size of the independent set from a greedy algorithm , and justify the theoretical performance of estimators under the proposed design. Our approach is capable of estimating both spillover effects and treatment effects. We justify its superiority over conventional methods and illustrate the empirical performance through simulations.

Automated Program Repair (APR) improves software reliability by generating patches for a buggy program automatically. Recent APR techniques leverage deep learning (DL) to build models to learn to generate patches from existing patches and code corpora. While promising, DL-based APR techniques suffer from the abundant syntactically or semantically incorrect patches in the patch space. These patches often disobey the syntactic and semantic domain knowledge of source code and thus cannot be the correct patches to fix a bug. We propose a DL-based APR approach KNOD, which incorporates domain knowledge to guide patch generation in a direct and comprehensive way. KNOD has two major novelties, including (1) a novel three-stage tree decoder, which directly generates Abstract Syntax Trees of patched code according to the inherent tree structure, and (2) a novel domain-rule distillation, which leverages syntactic and semantic rules and teacher-student distributions to explicitly inject the domain knowledge into the decoding procedure during both the training and inference phases. We evaluate KNOD on three widely-used benchmarks. KNOD fixes 72 bugs on the Defects4J v1.2, 25 bugs on the QuixBugs, and 50 bugs on the additional Defects4J v2.0 benchmarks, outperforming all existing APR tools.

The static synaptic connectivity of neuronal circuits stands in direct contrast to the dynamics of their function. As in changing community interactions, different neurons can participate actively in various combinations to effect behaviors at different times. We introduce an unsupervised approach to learn the dynamic affinities between neurons in live, behaving animals, and to reveal which communities form among neurons at different times. The inference occurs in two major steps. First, pairwise non-linear affinities between neuronal traces from brain-wide calcium activity are organized by non-negative tensor factorization (NTF). Each factor specifies which groups of neurons are most likely interacting for an inferred interval in time, and for which animals. Finally, a generative model that allows for weighted community detection is applied to the functional motifs produced by NTF to reveal a dynamic functional connectome. Since time codes the different experimental variables (e.g., application of chemical stimuli), this provides an atlas of neural motifs active during separate stages of an experiment (e.g., stimulus application or spontaneous behaviors). Results from our analysis are experimentally validated, confirming that our method is able to robustly predict causal interactions between neurons to generate behavior. Code is available at https://github.com/dyballa/dynamic-connectomes.

Graphs have often been used to answer questions about the interaction between real-world entities by taking advantage of their capacity to represent complex topologies. Complex networks are known to be graphs that capture such non-trivial topologies; they are able to represent human phenomena such as epidemic processes, the dynamics of populations, and the urbanization of cities. The investigation of complex networks has been extrapolated to many fields of science, with particular emphasis on computing techniques, including artificial intelligence. In such a case, the analysis of the interaction between entities of interest is transposed to the internal learning of algorithms, a paradigm whose investigation is able to expand the state of the art in Computer Science. By exploring this paradigm, this thesis puts together complex networks and machine learning techniques to improve the understanding of the human phenomena observed in pandemics, pendular migration, and street networks. Accordingly, we contribute with: (i) a new neural network architecture capable of modeling dynamic processes observed in spatial and temporal data with applications in epidemics propagation, weather forecasting, and patient monitoring in intensive care units; (ii) a machine-learning methodology for analyzing and predicting links in the scope of human mobility between all the cities of Brazil; and, (iii) techniques for identifying inconsistencies in the urban planning of cities while tracking the most influential vertices, with applications over Brazilian and worldwide cities. We obtained results sustained by sound evidence of advances to the state of the art in artificial intelligence, rigorous formalisms, and ample experimentation. Our findings rely upon real-world applications in a range of domains, demonstrating the applicability of our methodologies.

Many have observed that the development and deployment of generative machine learning (ML) and artificial intelligence (AI) models follow a distinctive pattern in which pre-trained models are adapted and fine-tuned for specific downstream tasks. However, there is limited empirical work that examines the structure of these interactions. This paper analyzes 1.86 million models on Hugging Face, a leading peer production platform for model development. Our study of model family trees -- networks that connect fine-tuned models to their base or parent -- reveals sprawling fine-tuning lineages that vary widely in size and structure. Using an evolutionary biology lens to study ML models, we use model metadata and model cards to measure the genetic similarity and mutation of traits over model families. We find that models tend to exhibit a family resemblance, meaning their genetic markers and traits exhibit more overlap when they belong to the same model family. However, these similarities depart in certain ways from standard models of asexual reproduction, because mutations are fast and directed, such that two `sibling' models tend to exhibit more similarity than parent/child pairs. Further analysis of the directional drifts of these mutations reveals qualitative insights about the open machine learning ecosystem: Licenses counter-intuitively drift from restrictive, commercial licenses towards permissive or copyleft licenses, often in violation of upstream license's terms; models evolve from multi-lingual compatibility towards english-only compatibility; and model cards reduce in length and standardize by turning, more often, to templates and automatically generated text. Overall, this work takes a step toward an empirically grounded understanding of model fine-tuning and suggests that ecological models and methods can yield novel scientific insights.

A complex system with cluttered observations may be a coupled mixture of multiple simple sub-systems corresponding to latent entities. Such sub-systems may hold distinct dynamics in the continuous-time domain; therein, complicated interactions between sub-systems also evolve over time. This setting is fairly common in the real world but has been less considered. In this paper, we propose a sequential learning approach under this setting by decoupling a complex system for handling irregularly sampled and cluttered sequential observations. Such decoupling brings about not only subsystems describing the dynamics of each latent entity but also a meta-system capturing the interaction between entities over time. Specifically, we argue that the meta-system evolving within a simplex is governed by projected differential equations (ProjDEs). We further analyze and provide neural-friendly projection operators in the context of Bregman divergence. Experimental results on synthetic and real-world datasets show the advantages of our approach when facing complex and cluttered sequential data compared to the state-of-the-art.

Mechanistic interpretability aims to understand model behaviors in terms of specific, interpretable features, often hypothesized to manifest as low-dimensional subspaces of activations. Specifically, recent studies have explored subspace interventions (such as activation patching) as a way to simultaneously manipulate model behavior and attribute the features behind it to given subspaces. In this work, we demonstrate that these two aims diverge, potentially leading to an illusory sense of interpretability. Counterintuitively, even if a subspace intervention makes the model's output behave as if the value of a feature was changed, this effect may be achieved by activating a dormant parallel pathway leveraging another subspace that is causally disconnected from model outputs. We demonstrate this phenomenon in a distilled mathematical example, in two real-world domains (the indirect object identification task and factual recall), and present evidence for its prevalence in practice. In the context of factual recall, we further show a link to rank-1 fact editing, providing a mechanistic explanation for previous work observing an inconsistency between fact editing performance and fact localization. However, this does not imply that activation patching of subspaces is intrinsically unfit for interpretability. To contextualize our findings, we also show what a success case looks like in a task (indirect object identification) where prior manual circuit analysis informs an understanding of the location of a feature. We explore the additional evidence needed to argue that a patched subspace is faithful.

The structure of biological neural circuits-modular, hierarchical, and sparsely interconnected-reflects an efficient trade-off between wiring cost, functional specialization, and robustness. These principles offer valuable insights for artificial neural network (ANN) design, especially as networks grow in depth and scale. Sparsity, in particular, has been widely explored for reducing memory and computation, improving speed, and enhancing generalization. Motivated by systems neuroscience findings, we explore how patterns of functional connectivity in the mouse visual cortex-specifically, ensemble-to-ensemble communication, can inform ANN design. We introduce G2GNet, a novel architecture that imposes sparse, modular connectivity across feedforward layers. Despite having significantly fewer parameters than fully connected models, G2GNet achieves superior accuracy on standard vision benchmarks. To our knowledge, this is the first architecture to incorporate biologically observed functional connectivity patterns as a structural bias in ANN design. We complement this static bias with a dynamic sparse training (DST) mechanism that prunes and regrows edges during training. We also propose a Hebbian-inspired rewiring rule based on activation correlations, drawing on principles of biological plasticity. G2GNet achieves up to 75% sparsity while improving accuracy by up to 4.3% on benchmarks, including Fashion-MNIST, CIFAR-10, and CIFAR-100, outperforming dense baselines with far fewer computations.

Deep neural networks have been shown to be susceptible to adversarial examples -- small, imperceptible changes constructed to cause mis-classification in otherwise highly accurate image classifiers. As a practical alternative, recent work proposed so-called adversarial patches: clearly visible, but adversarially crafted rectangular patches in images. These patches can easily be printed and applied in the physical world. While defenses against imperceptible adversarial examples have been studied extensively, robustness against adversarial patches is poorly understood. In this work, we first devise a practical approach to obtain adversarial patches while actively optimizing their location within the image. Then, we apply adversarial training on these location-optimized adversarial patches and demonstrate significantly improved robustness on CIFAR10 and GTSRB. Additionally, in contrast to adversarial training on imperceptible adversarial examples, our adversarial patch training does not reduce accuracy.

Evolvability is an important feature that impacts the ability of evolutionary processes to find interesting novel solutions and to deal with changing conditions of the problem to solve. The estimation of evolvability is not straightforward and is generally too expensive to be directly used as selective pressure in the evolutionary process. Indirectly promoting evolvability as a side effect of other easier and faster to compute selection pressures would thus be advantageous. In an unbounded behavior space, it has already been shown that evolvable individuals naturally appear and tend to be selected as they are more likely to invade empty behavior niches. Evolvability is thus a natural byproduct of the search in this context. However, practical agents and environments often impose limits on the reach-able behavior space. How do these boundaries impact evolvability? In this context, can evolvability still be promoted without explicitly rewarding it? We show that Novelty Search implicitly creates a pressure for high evolvability even in bounded behavior spaces, and explore the reasons for such a behavior. More precisely we show that, throughout the search, the dynamic evaluation of novelty rewards individuals which are very mobile in the behavior space, which in turn promotes evolvability.

We investigate Josephson arrays consisting of a dice-lattice network of superconducting weak links surrounding rhombic plaquettes of proximitized semiconductor. Josephson coupling of the weak links and electron density in the plaquettes are independently controlled by separate electrostatic gates. Applied magnetic flux results in an intricate pattern of switching currents associated with frustration, f. For depleted plaquettes, the switching current is nearly periodic in f, expected for a phase-only description, while occupied plaquettes yield a decreasing envelope of switching currents with increasing f. A model of flux dependence based on ballistic small-area junctions and diffusive large-area plaquettes yields excellent agreement with experiment.

Visual environments are structured, consisting of distinct objects or entities. These entities have properties -- both visible and latent -- that determine the manner in which they interact with one another. To partition images into entities, deep-learning researchers have proposed structural inductive biases such as slot-based architectures. To model interactions among entities, equivariant graph neural nets (GNNs) are used, but these are not particularly well suited to the task for two reasons. First, GNNs do not predispose interactions to be sparse, as relationships among independent entities are likely to be. Second, GNNs do not factorize knowledge about interactions in an entity-conditional manner. As an alternative, we take inspiration from cognitive science and resurrect a classic approach, production systems, which consist of a set of rule templates that are applied by binding placeholder variables in the rules to specific entities. Rules are scored on their match to entities, and the best fitting rules are applied to update entity properties. In a series of experiments, we demonstrate that this architecture achieves a flexible, dynamic flow of control and serves to factorize entity-specific and rule-based information. This disentangling of knowledge achieves robust future-state prediction in rich visual environments, outperforming state-of-the-art methods using GNNs, and allows for the extrapolation from simple (few object) environments to more complex environments.

Neural networks often suffer from catastrophic interference (CI): performance on previously learned tasks drops off significantly when learning a new task. This contrasts strongly with humans, who can sequentially learn new tasks without appreciably forgetting previous tasks. Prior work has explored various techniques for mitigating CI such as regularization, rehearsal, generative replay, and distillation methods. The current work takes a different approach, one guided by cognitive science research showing that in naturalistic environments, the probability of encountering a task decreases as a power-law of the time since it was last performed. We argue that a realistic evaluation of techniques for the mitigation of CI should be performed in simulated naturalistic learning environments. Thus, we evaluate the extent of mitigation of CI when training simple rehearsal-based methods in power-law environments similar to the ones humans face. Our work explores this novel rehearsal-based approach for a domain-incremental task: learning permutations in the MNIST task. We compare our rehearsal environment with other baselines to show its efficacy in promoting continual learning. Additionally, we investigate whether this environment shows forward facilitation, i.e., faster learning of later tasks. Next, we explore the robustness of our learning environment to the number of tasks, model size, and amount of data rehearsed after each task. Notably, our results show that the performance is comparable or superior to that of models trained using popular regularization methods and also to rehearsals in non-power-law environments. The benefits of this training paradigm include simplicity and the lack of a need for extra neural circuitry. In addition, because our method is orthogonal to other methods, future research can combine training in power-law environments with other continual learning mechanisms.

Large language models of code (Code-LLMs) have recently brought tremendous advances to code completion, a fundamental feature of programming assistance and code intelligence. However, most existing works ignore the possible presence of bugs in the code context for generation, which are inevitable in software development. Therefore, we introduce and study the buggy-code completion problem, inspired by the realistic scenario of real-time code suggestion where the code context contains potential bugs -- anti-patterns that can become bugs in the completed program. To systematically study the task, we introduce two datasets: one with synthetic bugs derived from semantics-altering operator changes (buggy-HumanEval) and one with realistic bugs derived from user submissions to coding problems (buggy-FixEval). We find that the presence of potential bugs significantly degrades the generation performance of the high-performing Code-LLMs. For instance, the passing rates of CodeGen-2B-mono on test cases of buggy-HumanEval drop more than 50% given a single potential bug in the context. Finally, we investigate several post-hoc methods for mitigating the adverse effect of potential bugs and find that there remains a large gap in post-mitigation performance.

When individuals encounter observations that violate their expectations, when will they adjust their expectations and when will they maintain them despite these observations? For example, when individuals expect objects of type A to be smaller than objects B, but observe the opposite, when will they adjust their expectation about the relationship between the two objects (to A being larger than B)? Naively, one would predict that the larger the violation, the greater the adaptation. However, experiments reveal that when violations are extreme, individuals are more likely to hold on to their prior expectations rather than adjust them. To address this puzzle, we tested the adaptation of artificial neural networks (ANNs) capable of relational learning and found a similar phenomenon: Standard learning dynamics dictates that small violations would lead to adjustments of expected relations while larger ones would be resolved using a different mechanism -- a change in object representation that bypasses the need for adaptation of the relational expectations. These results suggest that the experimentally-observed stability of prior expectations when facing large expectation violations is a natural consequence of learning dynamics and does not require any additional mechanisms. We conclude by discussing the effect of intermediate adaptation steps on this stability.

We introduce rd-spiral, an open-source Python library for simulating 2D reaction-diffusion systems using pseudo-spectral methods. The framework combines FFT-based spatial discretization with adaptive Dormand-Prince time integration, achieving exponential convergence while maintaining pedagogical clarity. We analyze three dynamical regimes: stable spirals, spatiotemporal chaos, and pattern decay, revealing extreme non-Gaussian statistics (kurtosis >96) in stable states. Information-theoretic metrics show 10.7% reduction in activator-inhibitor coupling during turbulence versus 6.5% in stable regimes. The solver handles stiffness ratios >6:1 with features including automated equilibrium classification and checkpointing. Effect sizes (delta=0.37--0.78) distinguish regimes, with asymmetric field sensitivities to perturbations. By balancing computational rigor with educational transparency, rd-spiral bridges theoretical and practical nonlinear dynamics.

Automated Program Repair (APR) can help developers automatically generate patches for bugs. Due to the impressive performance obtained using Large Pre-Trained Language Models (LLMs) on many code related tasks, researchers have started to directly use LLMs for APR. However, prior approaches simply repeatedly sample the LLM given the same constructed input/prompt created from the original buggy code, which not only leads to generating the same incorrect patches repeatedly but also miss the critical information in testcases. To address these limitations, we propose conversational APR, a new paradigm for program repair that alternates between patch generation and validation in a conversational manner. In conversational APR, we iteratively build the input to the model by combining previously generated patches with validation feedback. As such, we leverage the long-term context window of LLMs to not only avoid generating previously incorrect patches but also incorporate validation feedback to help the model understand the semantic meaning of the program under test. We evaluate 10 different LLM including the newly developed ChatGPT model to demonstrate the improvement of conversational APR over the prior LLM for APR approach.

Many complex tasks can be decomposed into simpler, independent parts. Discovering such underlying compositional structure has the potential to enable compositional generalization. Despite progress, our most powerful systems struggle to compose flexibly. It therefore seems natural to make models more modular to help capture the compositional nature of many tasks. However, it is unclear under which circumstances modular systems can discover hidden compositional structure. To shed light on this question, we study a teacher-student setting with a modular teacher where we have full control over the composition of ground truth modules. This allows us to relate the problem of compositional generalization to that of identification of the underlying modules. In particular we study modularity in hypernetworks representing a general class of multiplicative interactions. We show theoretically that identification up to linear transformation purely from demonstrations is possible without having to learn an exponential number of module combinations. We further demonstrate empirically that under the theoretically identified conditions, meta-learning from finite data can discover modular policies that generalize compositionally in a number of complex environments.

Learning features from data is one of the defining characteristics of deep learning, but our theoretical understanding of the role features play in deep learning is still rudimentary. To address this gap, we introduce a new tool, the interaction tensor, for empirically analyzing the interaction between data and model through features. With the interaction tensor, we make several key observations about how features are distributed in data and how models with different random seeds learn different features. Based on these observations, we propose a conceptual framework for feature learning. Under this framework, the expected accuracy for a single hypothesis and agreement for a pair of hypotheses can both be derived in closed-form. We demonstrate that the proposed framework can explain empirically observed phenomena, including the recently discovered Generalization Disagreement Equality (GDE) that allows for estimating the generalization error with only unlabeled data. Further, our theory also provides explicit construction of natural data distributions that break the GDE. Thus, we believe this work provides valuable new insight into our understanding of feature learning.

Antibodies are Y-shaped proteins that neutralize pathogens and constitute the core of our adaptive immune system. De novo generation of new antibodies that target specific antigens holds the key to accelerating vaccine discovery. However, this co-design of the amino acid sequence and the 3D structure subsumes and accentuates some central challenges from multiple tasks, including protein folding (sequence to structure), inverse folding (structure to sequence), and docking (binding). We strive to surmount these challenges with a new generative model AbODE that extends graph PDEs to accommodate both contextual information and external interactions. Unlike existing approaches, AbODE uses a single round of full-shot decoding and elicits continuous differential attention that encapsulates and evolves with latent interactions within the antibody as well as those involving the antigen. We unravel fundamental connections between AbODE and temporal networks as well as graph-matching networks. The proposed model significantly outperforms existing methods on standard metrics across benchmarks.

Accurate prediction of drug-target interactions is critical for advancing drug discovery. By reducing time and cost, machine learning and deep learning can accelerate this discovery process. Our approach utilises the powerful Barlow Twins architecture for feature-extraction while considering the structure of the target protein, achieving state-of-the-art predictive performance against multiple established benchmarks. The use of gradient boosting machine as the underlying predictor ensures fast and efficient predictions without the need for large computational resources. In addition, we further benchmarked new baselines against existing methods. Together, these innovations improve the efficiency and effectiveness of drug-target interaction predictions, providing robust tools for accelerating drug development and deepening the understanding of molecular interactions.

Dynamical systems with complex behaviours, e.g. immune system cells interacting with a pathogen, are commonly modelled by splitting the behaviour into different regimes, or modes, each with simpler dynamics, and then learning the switching behaviour from one mode to another. Switching Dynamical Systems (SDS) are a powerful tool that automatically discovers these modes and mode-switching behaviour from time series data. While effective, these methods focus on independent objects, where the modes of one object are independent of the modes of the other objects. In this paper, we focus on the more general interacting object setting for switching dynamical systems, where the per-object dynamics also depends on an unknown and dynamically changing subset of other objects and their modes. To this end, we propose a novel graph-based approach for switching dynamical systems, GRAph Switching dynamical Systems (GRASS), in which we use a dynamic graph to characterize interactions between objects and learn both intra-object and inter-object mode-switching behaviour. We introduce two new datasets for this setting, a synthesized ODE-driven particles dataset and a real-world Salsa Couple Dancing dataset. Experiments show that GRASS can consistently outperforms previous state-of-the-art methods.

Many recent language model (LM) interpretability studies have adopted the circuits framework, which aims to find the minimal computational subgraph, or circuit, that explains LM behavior on a given task. Most studies determine which edges belong in a LM's circuit by performing causal interventions on each edge independently, but this scales poorly with model size. Edge attribution patching (EAP), gradient-based approximation to interventions, has emerged as a scalable but imperfect solution to this problem. In this paper, we introduce a new method - EAP with integrated gradients (EAP-IG) - that aims to better maintain a core property of circuits: faithfulness. A circuit is faithful if all model edges outside the circuit can be ablated without changing the model's performance on the task; faithfulness is what justifies studying circuits, rather than the full model. Our experiments demonstrate that circuits found using EAP are less faithful than those found using EAP-IG, even though both have high node overlap with circuits found previously using causal interventions. We conclude more generally that when using circuits to compare the mechanisms models use to solve tasks, faithfulness, not overlap, is what should be measured.

The objective of this study is to evaluate the potential for History Matching (HM) to tune a climate system with multi-scale dynamics. By considering a toy climate model, namely, the two-scale Lorenz96 model and producing experiments in perfect-model setting, we explore in detail how several built-in choices need to be carefully tested. We also demonstrate the importance of introducing physical expertise in the range of parameters, a priori to running HM. Finally we revisit a classical procedure in climate model tuning, that consists of tuning the slow and fast components separately. By doing so in the Lorenz96 model, we illustrate the non-uniqueness of plausible parameters and highlight the specificity of metrics emerging from the coupling. This paper contributes also to bridging the communities of uncertainty quantification, machine learning and climate modeling, by making connections between the terms used by each community for the same concept and presenting promising collaboration avenues that would benefit climate modeling research.

Machine learning models are known to be susceptible to adversarial perturbation. One famous attack is the adversarial patch, a sticker with a particularly crafted pattern that makes the model incorrectly predict the object it is placed on. This attack presents a critical threat to cyber-physical systems that rely on cameras such as autonomous cars. Despite the significance of the problem, conducting research in this setting has been difficult; evaluating attacks and defenses in the real world is exceptionally costly while synthetic data are unrealistic. In this work, we propose the REAP (REalistic Adversarial Patch) benchmark, a digital benchmark that allows the user to evaluate patch attacks on real images, and under real-world conditions. Built on top of the Mapillary Vistas dataset, our benchmark contains over 14,000 traffic signs. Each sign is augmented with a pair of geometric and lighting transformations, which can be used to apply a digitally generated patch realistically onto the sign. Using our benchmark, we perform the first large-scale assessments of adversarial patch attacks under realistic conditions. Our experiments suggest that adversarial patch attacks may present a smaller threat than previously believed and that the success rate of an attack on simpler digital simulations is not predictive of its actual effectiveness in practice. We release our benchmark publicly at https://github.com/wagner-group/reap-benchmark.

Network Architecture Search and specifically Regularized Evolution is a common way to refine the structure of a deep learning model.However, little is known about how models empirically evolve over time which has design implications for designing caching policies, refining the search algorithm for particular applications, and other important use cases.In this work, we algorithmically analyze and quantitatively characterize the patterns of model evolution for a set of models from the Candle project and the Nasbench-201 search space.We show how the evolution of the model structure is influenced by the regularized evolution algorithm. We describe how evolutionary patterns appear in distributed settings and opportunities for caching and improved scheduling. Lastly, we describe the conditions that affect when particular model architectures rise and fall in popularity based on their frequency of acting as a donor in a sliding window.

Chaotic systems are intrinsically sensitive to small errors, challenging efforts to construct predictive data-driven models of real-world dynamical systems such as fluid flows or neuronal activity. Prior efforts comprise either specialized models trained separately on individual time series, or foundation models trained on vast time series databases with little underlying dynamical structure. Motivated by dynamical systems theory, we present Panda, Patched Attention for Nonlinear DynAmics. We train Panda on a novel synthetic, extensible dataset of 2 times 10^4 chaotic dynamical systems that we discover using an evolutionary algorithm. Trained purely on simulated data, Panda exhibits emergent properties: zero-shot forecasting of unseen real world chaotic systems, and nonlinear resonance patterns in cross-channel attention heads. Despite having been trained only on low-dimensional ordinary differential equations, Panda spontaneously develops the ability to predict partial differential equations without retraining. We demonstrate a neural scaling law for differential equations, underscoring the potential of pretrained models for probing abstract mathematical domains like nonlinear dynamics.

Modeling the interaction between proteins and ligands and accurately predicting their binding structures is a critical yet challenging task in drug discovery. Recent advancements in deep learning have shown promise in addressing this challenge, with sampling-based and regression-based methods emerging as two prominent approaches. However, these methods have notable limitations. Sampling-based methods often suffer from low efficiency due to the need for generating multiple candidate structures for selection. On the other hand, regression-based methods offer fast predictions but may experience decreased accuracy. Additionally, the variation in protein sizes often requires external modules for selecting suitable binding pockets, further impacting efficiency. In this work, we propose FABind, an end-to-end model that combines pocket prediction and docking to achieve accurate and fast protein-ligand binding. FABind incorporates a unique ligand-informed pocket prediction module, which is also leveraged for docking pose estimation. The model further enhances the docking process by incrementally integrating the predicted pocket to optimize protein-ligand binding, reducing discrepancies between training and inference. Through extensive experiments on benchmark datasets, our proposed FABind demonstrates strong advantages in terms of effectiveness and efficiency compared to existing methods. Our code is available at https://github.com/QizhiPei/FABind

Finetuning-free personalized image generation can synthesize customized images without test-time finetuning, attracting wide research interest owing to its high efficiency. Current finetuning-free methods simply adopt a single training stage with a simple image reconstruction task, and they typically generate low-quality images inconsistent with the reference images during test-time. To mitigate this problem, inspired by the recent DPO (i.e., direct preference optimization) technique, this work proposes an additional training stage to improve the pre-trained personalized generation models. However, traditional DPO only determines the overall superiority or inferiority of two samples, which is not suitable for personalized image generation because the generated images are commonly inconsistent with the reference images only in some local image patches. To tackle this problem, this work proposes PatchDPO that estimates the quality of image patches within each generated image and accordingly trains the model. To this end, PatchDPO first leverages the pre-trained vision model with a proposed self-supervised training method to estimate the patch quality. Next, PatchDPO adopts a weighted training approach to train the model with the estimated patch quality, which rewards the image patches with high quality while penalizing the image patches with low quality. Experiment results demonstrate that PatchDPO significantly improves the performance of multiple pre-trained personalized generation models, and achieves state-of-the-art performance on both single-object and multi-object personalized image generation. Our code is available at https://github.com/hqhQAQ/PatchDPO.

We bound the time it takes for a group of birds to reach steady state in a standard flocking model. We prove that (i) within single exponential time fragmentation ceases and each bird settles on a fixed flying direction; (ii) the flocking network converges only after a number of steps that is an iterated exponential of height logarithmic in the number of birds. We also prove the highly surprising result that this bound is optimal. The model directs the birds to adjust their velocities repeatedly by averaging them with their neighbors within a fixed radius. The model is deterministic, but we show that it can tolerate a reasonable amount of stochastic or even adversarial noise. Our methods are highly general and we speculate that the results extend to a wider class of models based on undirected flocking networks, whether defined metrically or topologically. This work introduces new techniques of broader interest, including the "flight net," the "iterated spectral shift," and a certain "residue-clearing" argument in circuit complexity.