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Deep Learning · Generative Models and Autoencoders

Jiaxiang Tang, Ruijie Lu, Max Li, Zekun Hao, Xuan Li, Fangyin Wei, Shuran Song, Gang Zeng, Ming-Yu Liu, Tsung-Yi Lin

Recent progress in 3D object generation has greatly improved both the quality and efficiency. However, most existing methods generate a single mesh with all parts fused together, which limits the ability to edit or manipulate individual parts. A key challenge is that different objects may have a varying number of parts. To address this, we propose a new end-to-end framework for part-level 3D object generation. Given a single input image, our method generates high-quality 3D objects with an arbitrary number of complete and semantically meaningful parts. We introduce a dual volume packing strategy that organizes all parts into two complementary volumes, allowing for the creation of complete and interleaved parts that assemble into the final object. Experiments show that our model achieves better quality, diversity, and generalization than previous image-based part-level generation methods. Our project page is at \url{https://research.nvidia.com/labs/dir/partpacker/}.

Social Aspects · Trustworthy Machine Learning

Linda Zeng, Rithwik Gupta, Divij Motwani, Yi Zhang, Diji Yang

Retrieval-augmented generation (RAG) has shown impressive capabilities in mitigating hallucinations in large language models (LLMs). However, LLMs struggle to maintain consistent reasoning when exposed to misleading or conflicting evidence, especially in real-world domains such as politics, where information is polarized or selectively framed. Mainstream RAG benchmarks evaluate models under clean retrieval settings, where systems generate answers from gold-standard documents, or under synthetically perturbed settings, where documents are artificially injected with noise. These assumptions fail to reflect real-world conditions, often leading to an overestimation of RAG system performance. To address this gap, we introduce \textsc{RAGuard}, the first benchmark to evaluate the robustness of RAG systems against \textit{misleading} retrievals. Unlike prior benchmarks that rely on synthetic noise, our fact-checking dataset captures naturally occurring misinformation by constructing its retrieval corpus from Reddit discussions. It categorizes retrieved evidence into three types: \textit{supporting}, \textit{misleading}, and \textit{unrelated}, providing a realistic and challenging testbed for assessing how well RAG systems navigate different types of evidence. Our experiments reveal that, when exposed to potentially misleading retrievals, all tested LLM-powered RAG systems perform worse than their zero-shot baselines (i.e., no retrieval at all), while human annotators consistently perform better, highlighting LLMs' susceptibility to noisy environments. To our knowledge, \textsc{RAGuard} is the first benchmark to systematically assess the robustness of the RAG against misleading evidence.We expect this benchmark to drive future research toward improving RAG systems beyond idealized datasets, making them more reliable for real-world applications.

Deep Learning · Everything Else

Da Yu, Edith Cohen, Badih Ghazi, Yangsibo Huang, Pritish Kamath, Ravi Kumar, Daogao Liu, Chiyuan Zhang

We propose SCONE (**S**calable, **C**ontextualized, **O**ffloaded, **N**-gram **E**mbedding), a new method for extending input embedding layers to enhance language model performance. To avoid increased decoding costs, SCONE retains the original vocabulary while introducing embeddings for a set of frequent $n$-grams. These embeddings provide contextualized representation for each input token and are learned with a separate model during training. After training, embeddings are precomputed and stored in off-accelerator memory; during inference, querying them has minimal impact on latency due to the low complexity of embedding lookups. SCONE enables two new scaling strategies: increasing the number of $n$-gram embeddings and scaling the model used to learn them, both while maintaining fixed accelerator usage during inference (in terms of FLOPS and memory). We show that scaling both aspects enables a model with 1B accelerator-resident parameters to outperform a 1.9B-parameter baseline across diverse corpora, while using only about half the FLOPS and accelerator memory during inference.

Social Aspects · Trustworthy Machine Learning

Yedi Zhang, Sun Emma, Annabelle En, Jin Song Dong

Large language models (LLMs) have emerged as a dominant AI paradigm due to their exceptional text understanding and generation capabilities. However, their tendency to generate inconsistent or erroneous outputs challenges their reliability, especially in high-stakes domains requiring accuracy and trustworthiness. Existing research primarily focuses on detecting and mitigating model misbehavior in general-purpose scenarios, often overlooking the potential of integrating domain-specific knowledge. In this work, we advance misbehavior detection by incorporating domain knowledge. The core idea is to design a general specification language that enables domain experts to customize domain-specific constraints in a lightweight and intuitive manner, supporting later runtime monitoring of LLM outputs. To achieve this, we design a novel specification language ESL, and introduce a runtime verification framework RvLLM to validate LLM output against domain-specific constraints defined in ESL. RvLLM operates in two main stages: interpretation and reasoning. During interpretation, it derives interpretations of the specification based on the context, which then guide the reasoning process to identify inconsistencies. When new knowledge is derived, RvLLM issues a follow-up query to the LLM to further verify the consistency. We evaluate RvLLM on three representative tasks: violation detection against Singapore Rapid Transit Systems Act, numerical comparison, and inequality solving. Experimental results show that RvLLM effectively detects erroneous outputs across various LLMs in a lightweight and flexible manner. The results reveal that despite their impressive capabilities, LLMs remain prone to low-level errors due to a lack of formal guarantees during inference, and our framework offers a potential long-term solution by leveraging expert domain knowledge to rigorously and efficiently verify LLM outputs.

Deep Learning · Robustness

Myeongho Jeon, Jan Sobotka, Suhwan Choi, Maria Brbic

As future superhuman models become increasingly complex, accurately supervising their behavior may exceed human capabilities. Recent works have demonstrated that in such scenarios, weak models can effectively supervise strong models, a phenomenon known as weak-to-strong generalization. However, we find that naive weak-to-strong generalization fails under distribution shifts, often leading to worse performance of the strong model than its weak supervisors. To address this, we propose RAVEN, a robust weak-to-strong generalization framework that dynamically learns the optimal combinations of weak models in addition to parameters of the strong model. We demonstrate the effectiveness of RAVEN on image classification, text classification, and preference alignment tasks. RAVEN outperforms alternative baselines by over 30% on out-of-distribution tasks while matching or surpassing existing methods on in-distribution tasks. Moreover, our results show that RAVEN assigns higher weights to more accurate weak models, demonstrating its ability to automatically identify trustworthy supervision.

Applications · Genetics, Cell Biology, etc

Joel Dapello, Marcel Nassar, Ridvan Eksi, Ban Wang, Jules Gagnon-Marchand, Kenneth Gao, akram Baharlouei, Kyra Thrush, Nina Riehs, Amy Peterson 等

Understanding cellular responses to chemical interventions is critical to the discovery of effective therapeutics. Because individual biological techniques often measure only one axis of cellular response at a time, high-quality multimodal datasets are needed to unlock a holistic understanding of how cells respond to treatments and to advance computational methods that integrate modalities. However, many techniques destroy cells and thus preclude paired measurements, and attempts to match disparate unimodal datasets are often confounded by data being generated in incompatible experimental settings. Here we introduce scGeneScope, a multimodal single‑cell RNA sequencing (scRNA-seq) and Cell Painting microscopy image dataset conditionally paired by chemical treatment, designed to facilitate the development and benchmarking of unimodal, multimodal, and multiple profile machine learning methods for cellular profiling. 28 chemicals, each acting on distinct biological pathways or mechanisms of action (MoAs), were applied to U2-OS cells in two experimental data generation rounds, creating paired sets of replicates that were then profiled independently by scRNA‑seq or Cell Painting. Using scGeneScope, we derive a replicate- and experiment-split treatment identification benchmark simulating MoA discovery under realistic laboratory variability conditions and evaluate unimodal, multimodal, and multiprofile models ranging in complexity from linear approaches to recent foundation models. Multiprofile integration improved performance in both the unimodal and multimodal settings, with gains more consistent in the former. Evaluation of unimodal models for MoA identification demonstrated that recent scRNA-seq foundation models deployed zero-shot were consistently outperformed by classic fit-to-data methods, underscoring the need for careful, realistic benchmarking in machine learning for biology. We release the scGeneScope dataset and benchmarking code to support further research.

Applications · Language, Speech and Dialog

Jingbo Yang, Bairu Hou, Wei Wei, Yujia Bao, Shiyu Chang

We describe KVLink, an approach for efficient key-value (KV) cache reuse in large language models (LLMs). In many LLM applications, different inputs can share overlapping context, such as the same retrieved document appearing in multiple queries. However, the LLMs still need to encode the entire context for each query, leading to redundant computation. In this paper, we investigate a new strategy to eliminate such inefficiency, where the KV cache of each document is precomputed independently. During inference, the KV caches of retrieved documents are concatenated, allowing the model to reuse cached representations instead of recomputing them. To mitigate the performance degradation when using KV caches computed independently for each document, KVLink introduces two key techniques: adjusting positional embeddings of the KV cache at inference to match the global position after concatenation, and using trainable special tokens to restore self-attention across independently encoded documents. Experiments across 7 datasets demonstrate that KVLink improves question answering accuracy by an average of 4% over state-of-the-art methods. Furthermore, by leveraging precomputed KV caches, our approach reduces time-to-first-token by up to 96% compared to standard LLM inference, making it a scalable and efficient solution for context reuse. Additionally, KVLink can be combined with KV cache compression to further save cache loading and storage overhead while outperforming the baselines.

Deep Learning · Algorithms

Arian Raje, Baris Askin, Divyansh Jhunjhunwala, Gauri Joshi

Large Language Models (LLMs) have yet to effectively leverage the vast amounts of edge-device data, and Federated Learning (FL) offers a promising paradigm to collaboratively fine-tune LLMs without transferring private edge data to the cloud. To operate within the computational and communication constraints of edge devices, recent literature on federated fine-tuning of LLMs proposes the use of low-rank adaptation (LoRA) and similar parameter-efficient methods. However, LoRA-based methods suffer from accuracy degradation in FL settings, primarily because of data and computational heterogeneity across clients. We propose Ravan, an adaptive multi-head LoRA method that balances parameter efficiency and model expressivity by reparameterizing the weight updates as the sum of multiple LoRA heads, $s_i\textbf{B}_i\textbf{H}_i\textbf{A}_i$, in which only the $\textbf{H}_i$ parameters and their lightweight scaling factors $s_i$ are trained. These trainable scaling factors let the optimization focus on the most useful heads, recovering a higher-rank approximation of the full update without increasing the number of communicated parameters since clients upload $s_i\textbf{H}_i$ directly. Experiments on vision and language benchmarks show that Ravan improves test accuracy by 2–8\% over prior parameter-efficient baselines, making it a robust and scalable solution for federated fine-tuning of LLMs.

Social Aspects · Trustworthy Machine Learning

Buyun Liang, Liangzu Peng, Jinqi Luo, Darshan Thaker, Kwan Ho Ryan Chan, Rene Vidal

Large Language Models (LLMs) are increasingly deployed in high-risk domains. However, state-of-the-art LLMs often produce hallucinations, raising serious concerns about their reliability. Prior work has explored adversarial attacks for hallucination elicitation in LLMs, but it often produces unrealistic prompts, either by inserting gibberish tokens or by altering the original meaning. As a result, these approaches offer limited insight into how hallucinations may occur in practice. While adversarial attacks in computer vision often involve realistic modifications to input images, the problem of finding realistic adversarial prompts for eliciting LLM hallucinations has remained largely underexplored. To address this gap, we propose Semantically Equivalent and Coherent Attacks (SECA) to elicit hallucinations via realistic modifications to the prompt that preserve its meaning while maintaining semantic coherence. Our contributions are threefold: (i) we formulate finding realistic attacks for hallucination elicitation as a constrained optimization problem over the input prompt space under semantic equivalence and coherence constraints; (ii) we introduce a constraint-preserving zeroth-order method to effectively search for adversarial yet feasible prompts; and (iii) we demonstrate through experiments on open-ended multiple-choice question answering tasks that SECA achieves higher attack success rates while incurring almost no constraint violations compared to existing methods. SECA highlights the sensitivity of both open-source and commercial gradient-inaccessible LLMs to realistic and plausible prompt variations. Code is available at https://github.com/Buyun-Liang/SECA.

Optimization

Lachlan MacDonald, Hancheng Min, Leandro Palma, Salma Tarmoun, Ziqing Xu, Rene Vidal

Classical optimisation theory guarantees monotonic objective decrease for gradient descent (GD) when employed in a small step size, or "stable", regime. In contrast, gradient descent on neural networks is frequently performed in a large step size regime called the "edge of stability", in which the objective decreases non-monotonically with an observed implicit bias towards flat minima. In this paper, we take a step toward quantifying this phenomenon by providing convergence rates for gradient descent with large learning rates in an overparametrised least squares setting. The key insight behind our analysis is that, as a consequence of overparametrisation, the set of global minimisers forms a Riemannian manifold $M$, which enables the decomposition of the GD dynamics into components parallel and orthogonal to $M$. The parallel component corresponds to Riemannian gradient descent on the objective sharpness, while the orthogonal component corresponds to a quadratic dynamical system. This insight allows us to derive convergence rates in three regimes characterised by the learning rate size: the subcritical regime, in which transient instability is overcome in finite time before linear convergence to a suboptimally flat global minimum; the critical regime, in which instability persists for all time with a power-law convergence toward the optimally flat global minimum; the supercritical regime, in which instability persists for all time with linear convergence to an oscillation of period two centred on the optimally flat global minimum.

General Machine Learning · Everything Else

Kwan Ho Ryan Chan, Yuyan Ge, Edgar Dobriban, Hamed Hassani, Rene Vidal

A significant use case of instruction-finetuned Large Language Models (LLMs) is to solve question-answering tasks interactively. In this setting, an LLM agent is tasked with making a prediction by sequentially querying relevant information from the user, as opposed to a single-turn conversation. This paper explores sequential querying strategies that aim to minimize the expected number of queries. One such strategy is Information Pursuit (IP), a greedy algorithm that at each iteration selects the query that maximizes information gain or equivalently minimizes uncertainty. However, obtaining accurate estimates of mutual information or conditional entropy for LLMs is very difficult in practice due to over- or under-confident LLM probabilities, which leads to suboptimal query selection and predictive performance. To better estimate the uncertainty at each iteration, we propose *Conformal Information Pursuit (C-IP)*, an alternative approach to sequential information gain based on conformal prediction sets. More specifically, C-IP leverages a relationship between prediction sets and conditional entropy at each iteration to estimate uncertainty based on the average size of conformal prediction sets. In contrast to conditional entropy, we find that conformal prediction sets are a distribution-free and robust method of measuring uncertainty. Experiments with 20 Questions show that C-IP obtains better predictive performance and shorter query-answer chains compared to previous approaches to IP and uncertainty-based chain-of-thought methods. Furthermore, extending to an interactive medical setting between a doctor and a patient on the MediQ dataset, C-IP achieves competitive performance with direct single-turn prediction while offering greater interpretability.

Theory · Everything Else

Hancheng Min, Zhihui Zhu, Rene Vidal

Among many mysteries behind the success of deep networks lies the exceptional discriminative power of their learned representations as manifested by the intriguing Neural Collapse (NC) phenomenon, where simple feature structures emerge at the last layer of a trained neural network. Prior works on the theoretical understandings of NC have focused on analyzing the optimization landscape of matrix-factorization-like problems by considering the last-layer features as unconstrained free optimization variables and showing that their global minima exhibit NC. In this paper, we show that gradient flow on a two-layer ReLU network for classifying orthogonally separable data provably exhibits NC, thereby advancing prior results in two ways: First, we relax the assumption of unconstrained features, showing the effect of data structure and nonlinear activations on NC characterizations. Second, we reveal the role of the implicit bias of the training dynamics in facilitating the emergence of NC.

Computer Vision · Vision Models & Multimodal

Kaleab Kinfu, Rene Vidal

Recent advances in multi-modal representation learning have led to unified embedding spaces that align modalities such as images, text, audio, and vision. However, human motion sequences, a modality that is fundamental for understanding dynamic human activities, remains largely unrepresented in these frameworks. Semantic understanding of actions requires multi-modal grounding: text conveys descriptive semantics, vision provides visual context, and audio provides environmental cues. To bridge this gap, we propose MotionBind, a novel architecture that extends the LanguageBind embedding space to incorporate human motion. MotionBind has two major components. The first one is a Multi-Scale Temporal Motion Transformer (MuTMoT) that maps motion sequences to semantically meaningful embeddings. Multimodal alignment is achieved via diverse cross-modal supervision, including motion-text pairs from HumanML3D and KIT-ML, motion-video pairs rendered from AMASS, and motion-video-audio triplets from AIST++. The second component is a Retrieval-Augmented Latent diffusion Model (REALM) that can generate motion sequences conditioned on many modalities. MotionBind achieves state-of-the-art or competitive performance across motion reconstruction, cross-modal retrieval, zero-shot action recognition, and text-to-motion generation benchmarks.

Applications · Neuroscience, Cognitive Science

Federico D'Agostino, Lisa Schwetlick, Matthias Bethge, Matthias Kümmerer

Understanding how humans move their eyes to gather visual information is a central question in neuroscience, cognitive science, and vision research. While recent deep learning (DL) models achieve state-of-the-art performance in predicting human scanpaths, their underlying decision processes remain opaque. At an opposite end of the modeling spectrum, cognitively inspired mechanistic models aim to explain scanpath behavior through interpretable cognitive mechanisms but lag far behind in predictive accuracy. In this work, we bridge this gap by using a high-performing deep model—DeepGaze III—to discover and test mechanisms that improve a leading mechanistic model, SceneWalk. By identifying individual fixations where DeepGaze III succeeds and SceneWalk fails, we isolate behaviorally meaningful discrepancies and use them to motivate targeted extensions of the mechanistic framework. These include time-dependent temperature scaling, saccadic momentum and an adaptive cardinal attention bias: Simple, interpretable additions that substantially boost predictive performance. With these extensions, SceneWalk’s explained variance on the MIT1003 dataset doubles from 35% to 70%, setting a new state of the art in mechanistic scanpath prediction. Our findings show how performance-optimized neural networks can serve as tools for cognitive model discovery, offering a new path toward interpretable and high-performing models of visual behavior. Our code is available at https://github.com/bethgelab/what-moves-the-eyes

Optimization · Large Scale, Parallel and Distributed

Gyudong Kim, Hyukju Na, Jin Kim, Hyunsung Jang, Jaemin Park, Jaegi Hwang, NAMKOO HA, Seungryong Kim, Young Geun Kim

As training billion-scale transformers becomes increasingly common, employing multiple distributed GPUs along with parallel training methods has become a standard practice. However, existing transformer designs suffer from significant communication overhead, especially in Tensor Parallelism (TP), where each block’s MHA–MLP connection requires an all-reduce communication. Through our investigation, we show that the MHA-MLP connections can be bypassed for efficiency, while the attention output of the first layer can serve as an alternative signal for the bypassed connection. Motivated by the observations, we propose FAL (First Attentions Last), an efficient transformer architecture that redirects the first MHA output to the MLP inputs of the following layers, eliminating the per-block MHA-MLP connections. This removes the all-reduce communication and enables parallel execution of MHA and MLP on a single GPU. We also introduce FAL+, which adds the normalized first attention output to the MHA outputs of the following layers to augment the MLP input for the model quality. Our evaluation shows that FAL reduces multi-GPU training time by up to 44%, improves single-GPU throughput by up to 1.18×, and achieves better perplexity compared to the baseline GPT. FAL+ achieves even lower perplexity without increasing the training time than the baseline.

Applications · Neuroscience, Cognitive Science

Alicia Zeng, Jack Gallant

Encoding models based on word embeddings or artificial neural network (ANN) features reliably predict brain responses to naturalistic stimuli but remain difficult to interpret. A central limitation is superposition—the entanglement of distinct semantic features along correlated directions in dense embeddings, which arises when latent features outnumber the embedding dimensions. This entanglement renders regression weights non-identifiable: different combinations of semantic directions can produce identical predicted brain activity, preventing principled interpretation of voxel selectivity. To overcome this, we introduce the Sparse Concept Encoding Model, which transforms dense embeddings into a higher-dimensional, sparse, and non-negative space of learned concept atoms. This transformation yields an axis-aligned semantic basis where each dimension corresponds to an interpretable concept, enabling direct readout of conceptual selectivity from voxel weights. When applied to fMRI data collected during story listening, our model matches the prediction performance of conventional dense models while substantially enhancing interpretability. It enables novel neuroscientific analyses such as disentangling overlapping cortical representations of time, space, and number, and revealing structured similarity among distributed conceptual maps. This framework offers a scalable and interpretable bridge between ANN-derived features and human conceptual representations in the brain.

Applications · Health

Hao Zhang, Zhan Zhuang, Xuehao Wang, Xiaodong Yang, Yu Zhang

Human Activity Recognition (HAR) with wearable sensors is challenged by limited interpretability, which significantly impacts cross-dataset generalization. To address this challenge, we propose Motion-Primitive Transformer (MoPFormer), a novel self-supervised framework that enhances interpretability by tokenizing inertial measurement unit signals into semantically meaningful motion primitives and leverages a Transformer architecture to learn rich temporal representations. MoPFormer comprises two stages. The first stage is to partition multi-channel sensor streams into short segments and quantize them into discrete ``motion primitive'' codewords, while the second stage enriches those tokenized sequences through a context-aware embedding module and then processes them with a Transformer encoder. The proposed MoPFormer can be pre-trained using a masked motion-modeling objective that reconstructs missing primitives, enabling it to develop robust representations across diverse sensor configurations. Experiments on six HAR benchmarks demonstrate that MoPFormer not only outperforms state-of-the-art methods but also successfully generalizes across multiple datasets. More importantly, the learned motion primitives significantly enhance both interpretability and cross-dataset performance by capturing fundamental movement patterns that remain consistent across similar activities, regardless of dataset origin.

Deep Learning · Theory

Jingfeng Wu, Pierre Marion, Peter Bartlett

We study *gradient descent* (GD) with a constant stepsize for $\ell_2$-regularized logistic regression with linearly separable data. Classical theory suggests small stepsizes to ensure monotonic reduction of the optimization objective, achieving exponential convergence in $\widetilde{\mathcal{O}}(\kappa)$ steps with $\kappa$ being the condition number. Surprisingly, we show that this can be *accelerated* to $\widetilde{\mathcal{O}}(\sqrt{\kappa})$ by simply using a large stepsize---for which the objective evolves *nonmonotonically*. The acceleration brought by large stepsizes extends to minimizing the population risk for separable distributions, improving on the best-known upper bounds on the number of steps to reach a near-optimum. Finally, we characterize the largest stepsize for the local convergence of GD, which also determines the global convergence in special scenarios. Our results extend the analysis of Wu et al. (2024) from convex settings with minimizers at infinity to strongly convex cases with finite minimizers.

Probabilistic Methods · Gaussian Processes

Amon Lahr, Johannes Köhler, Anna Scampicchio, Melanie Zeilinger

Non-conservative uncertainty bounds are key for both assessing an estimation algorithm’s accuracy and in view of downstream tasks, such as its deployment in safety-critical contexts. In this paper, we derive a tight, non-asymptotic uncertainty bound for kernel-based estimation, which can also handle correlated noise sequences. Its computation relies on a mild norm-boundedness assumption on the unknown function and the noise, returning the worst-case function realization within the hypothesis class at an arbitrary query input location. The value of this function is shown to be given in terms of the posterior mean and covariance of a Gaussian process for an optimal choice of the measurement noise covariance. By rigorously analyzing the proposed approach and comparing it with other results in the literature, we show its effectiveness in returning tight and easy-to-compute bounds for kernel-based estimates.

Applications

Yifeng He, Luning Yang, Christopher Gonzalo, Hao Chen

Large Language Models (LLMs) are increasingly integrated into the software engineering ecosystem.Their test-time compute reasoning capabilities promise significant potential in understanding program logic and semantics beyond mere token recognition. However, current benchmarks evaluating reasoning LLMs for code lack a formal, program-centric deductive framework for the soundness of evaluation, incompetent in assessing of whether models genuinely reason about program semantics or merely associate superficial connections between natural language and code tokens. To bridge this gap, we introduce TF-Bench, a benchmark designed to evaluate LLM reasoning based on type inference in System F, a task we refer to as *program semantics reasoning*. By employing verified transformations to remove semantically irrelevant natural language,we construct TF-Bench_pure, a purely semantics-driven variant of TF-Bench. Our analysis reveals substantial limitations in state-of-the-art LLMs, with the best-performing LLM (Claude-3.7-sonnet) achieving only $55.85\%$ accuracy on TF-Bench_pure. Additionally, we propose two novel metrics to assess the robustness and effectiveness of extended reasoning,underscoring the critical limitation in current LLM capabilities and highlighting essential directions for future research.