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Applications · Health / Medicine

Olga Ovcharenko, Florian Barkmann, Philip Toma, Imant Daunhawer, Julia Vogt, Sebastian Schelter, Valentina Boeva

Self-supervised learning (SSL) has proven to be a powerful approach for extracting biologically meaningful representations from single-cell data. To advance our understanding of SSL methods applied to single-cell data, we present scSSL-Bench, a comprehensive benchmark that evaluates nineteen SSL methods. Our evaluation spans nine datasets and focuses on three common downstream tasks: batch correction, cell type annotation, and missing modality prediction. Furthermore, we systematically assess various data augmentation strategies. Our analysis reveals task-specific trade-offs: the specialized single-cell frameworks, scVI, CLAIRE, and the finetuned scGPT excel at uni-modal batch correction, while generic SSL methods, such as VICReg and SimCLR, demonstrate superior performance in cell typing and multi-modal data integration. Random masking emerges as the most effective augmentation technique across all tasks, surpassing domain-specific augmentations. Notably, our results indicate the need for a specialized single-cell multi-modal data integration framework. scSSL-Bench provides a standardized evaluation platform and concrete recommendations for applying SSL to single-cell analysis, advancing the convergence of deep learning and single-cell genomics.

Theory · Learning Theory

Ari Karchmer, Eran Malach

We study the relationship between gradient-based optimization of parametric models (e.g., neural networks) and optimization of linear combinations of random features. Our main result shows that if a parametric model can be learned using mini-batch stochastic gradient descent (bSGD) without making assumptions about the data distribution, then with high probability, the target function can also be approximated using a polynomial-sized combination of random features. The size of this combination depends on the number of gradient steps and numerical precision used in the bSGD process. This finding reveals fundamental limitations of distribution-free learning in neural networks trained by gradient descent, highlighting why making assumptions about data distributions is often crucial in practice.Along the way, we also introduce a new theoretical framework called average probabilistic dimension complexity (adc), which extends the probabilistic dimension complexity developed by Kamath et al. (2020). We prove that adc has a polynomial relationship with statistical query dimension, and use this relationship to demonstrate an infinite separation between adc and standard dimension complexity.

Applications · Computer Vision

Sophie Ostmeier, Brian Axelrod, Maya Varma, Michael Moseley, Akshay Chaudhari, Curtis Langlotz

Transformer architectures depend on explicit position encodings to capture token positional information. Rotary Position Encoding (RoPE) has emerged as a popular choice in language models due to its efficient encoding of relative position information through key-query rotations. However, RoPE faces significant limitations beyond language processing: it is constrained to one-dimensional sequence data and, even with learnable phases, offers limited representational capacity.We address these challenges with Lie Relative Encodings (LieRE), which generalizes RoPE to high-dimensional rotation matrices by leveraging their Lie group structure. Through extensive evaluation on three image datasets across 2D and 3D classification tasks, LieRE achieves 1.5% improvement over state-of-the-art baselines on 2D tasks and 1% on 3D tasks, while demonstrating superior generalization to higher resolutions. Our implementation is computationally efficient, with results reproducible on 4 A100 GPUs in 30 minutes on CIFAR100. Our code is available at https://github.com/StanfordMIMI/LieRE.

Position · Methodology

D. Sculley, William Cukierski, Phil Culliton, Sohier Dane, Maggie Demkin, Ryan Holbrook, Addison Howard, Paul Mooney, Walter Reade, Meg Risdal 等

In this position paper, we observe that empirical evaluation in Generative AI is at a crisis point since traditional ML evaluation and benchmarking strategies are insufficient to meet the needs of evaluating modern GenAI models and systems. There are many reasons for this, including the fact that these models typically have nearly unbounded input and output spaces, typically do not have a well defined ground truth target, and typically exhibit strong feedback loops and prediction dependence based on context of previous model outputs. On top of these critical issues, we argue that the problems of *leakage* and *contamination* are in fact the most important and difficult issues to address for GenAI evaluations. Interestingly, the field of AI Competitions has developed effective measures and practices to combat leakage for the purpose of counteracting cheating by bad actors within a competition setting. This makes AI Competitions an especially valuable (but underutilized) resource. Now is time for the field to view AI Competitions as the gold standard for empirical rigor in GenAI evaluation, and to harness and harvest their results with according value.

D. Sculley, William Cukierski, Phil Culliton, Sohier Dane, Maggie Demkin, Ryan Holbrook, Addison Howard, Paul Mooney, Walter Reade, Meg Risdal 等

In this position paper, we observe that empirical evaluation in Generative AI is at a crisis point since traditional ML evaluation and benchmarking strategies are insufficient to meet the needs of evaluating modern GenAI models and systems. There are many reasons for this, including the fact that these models typically have nearly unbounded input and output spaces, typically do not have a well defined ground truth target, and typically exhibit strong feedback loops and prediction dependence based on context of previous model outputs. On top of these critical issues, we argue that the problems of *leakage* and *contamination* are in fact the most important and difficult issues to address for GenAI evaluations. Interestingly, the field of AI Competitions has developed effective measures and practices to combat leakage for the purpose of counteracting cheating by bad actors within a competition setting. This makes AI Competitions an especially valuable (but underutilized) resource. Now is time for the field to view AI Competitions as the gold standard for empirical rigor in GenAI evaluation, and to harness and harvest their results with according value.

Social Aspects · Accountability, Transparency, and Interpretability

Mateo Espinosa Zarlenga, Gabriele Dominici, Pietro Barbiero, Zohreh Shams, Mateja Jamnik

In this paper, we investigate how concept-based models (CMs) respond to out-of-distribution (OOD) inputs. CMs are interpretable neural architectures that first predict a set of high-level *concepts* (e.g., "stripes", "black") and then predict a task label from those concepts. In particular, we study the impact of *concept interventions* (i.e., operations where a human expert corrects a CM’s mispredicted concepts at test time) on CMs' task predictions when inputs are OOD. Our analysis reveals a weakness in current state-of-the-art CMs, which we term *leakage poisoning*, that prevents them from properly improving their accuracy when intervened on for OOD inputs. To address this, we introduce *MixCEM*, a new CM that learns to dynamically exploit leaked information missing from its concepts only when this information is in-distribution. Our results across tasks with and without complete sets of concept annotations demonstrate that MixCEMs outperform strong baselines by significantly improving their accuracy for both in-distribution and OOD samples in the presence and absence of concept interventions.

Clément Bonet, Christophe Vauthier, Anna Korba

Many applications in machine learning involve data represented as probability distributions. The emergence of such data requires radically novel techniques to design tractable gradient flows on probability distributions over this type of (infinite-dimensional) objects. For instance, being able to flow labeled datasets is a core task for applications ranging from domain adaptation to transfer learning or dataset distillation. In this setting, we propose to represent each class by the associated conditional distribution of features, and to model the dataset as a mixture distribution supported on these classes (which are themselves probability distributions), meaning that labeled datasets can be seen as probability distributions over probability distributions. We endow this space with a metric structure from optimal transport, namely the Wasserstein over Wasserstein (WoW) distance, derive a differential structure on this space, and define WoW gradient flows. The latter enables to design dynamics over this space that decrease a given objective functional. We apply our framework to transfer learning and dataset distillation tasks, leveraging our gradient flow construction as well as novel tractable functionals that take the form of Maximum Mean Discrepancies with Sliced-Wasserstein based kernels between probability distributions.

Applications · Health / Medicine

Yanchao Tan, Hang Lv, Yunfei Zhan, Guofang Ma, Bo Xiong, Carl Yang

Language Models (LMs) have advanced diagnosis prediction by leveraging the semantic understanding of medical concepts in Electronic Health Records (EHRs). Despite these advancements, existing LM-based methods often fail to capture the structures of medical concepts (e.g., hierarchy structure from domain knowledge). In this paper, we propose BoxLM, a novel framework that unifies the structures and semantics of medical concepts for diagnosis prediction. Specifically, we propose a structure-semantic fusion mechanism via box embeddings, which integrates both ontology-driven and EHR-driven hierarchical structures with LM-based semantic embeddings, enabling interpretable medical concept representations.Furthermore, in the box-aware diagnosis prediction module, an evolve-and-memorize patient box learning mechanism is proposed to model the temporal dynamics of patient visits, and a volume-based similarity measurement is proposed to enable accurate diagnosis prediction. Extensive experiments demonstrate that BoxLM consistently outperforms state-of-the-art baselines, especially achieving strong performance in few-shot learning scenarios, showcasing its practical utility in real-world clinical settings.

Theory · Optimization

Piyush Anand, Piotr Indyk, Ravishankar Krishnaswamy, Sepideh Mahabadi, Vikas Raykar, Kirankumar Shiragur, Haike Xu

Nearest neighbor search is a fundamental data structure problem with many applications. Although the main objective of the data structure is to quickly report data points that are closest to a given query, it has long been noted that without additional constraints the reported answers can be redundant and/or duplicative. This issue is typically addressed in two stages: in the first stage, the algorithm retrieves a (large) number $r$ of points closest to the query, while in the second stage, the $r$ points are post-processed and a small subset is selected to maximize the desired diversity objective. Although popular, this method suffers from a fundamental efficiency bottleneck, as the set of points retrieved in the first stage often needs to be much larger than the final output. In this paper we present provably efficient algorithms for approximate nearest neighbor search with diversity constraints that bypass this two stage process. Our algorithms are based on popular graph-based methods, which allows us to ``piggy-back'' on the existing efficient implementations. These are the first graph-based algorithms for nearest neighbor search with diversity constraints. For data sets with low intrinsic dimension, our data structures report a diverse set of $k$ points approximately closest to the query, in time that only depends on $k$ and $\log \Delta$, where $\Delta$ is the ratio of the diameter to the closest pair distance in the data set. This bound is qualitatively similar to the best known bounds for standard (non-diverse) graph-based algorithms. Our experiments show that the search time of our algorithms is substantially lower than that using the standard two-stage approach.

Deep Learning · Large Language Models

KaShun SHUM, Yuzhen Huang, Hongjian Zou, dingqi, YiXuan Liao, Xiaoxin Chen, Qian Liu, Junxian He

Language model pretraining involves training on extensive corpora, where data quality plays a pivotal role. In this work, we aim to directly estimate the contribution of data during pretraining and select pretraining data in an efficient manner. Specifically, we draw inspiration from recent findings showing that compression efficiency (i.e., normalized loss) of diverse models on certain text correlates strongly with their downstream performance, when the text domain aligns with the downstream benchmarks (Huang et al., 2024). Building on this observation, we hypothesize that data on which model losses are predictive of downstream abilities also contribute effectively to learning, which shares similar intuition with Thrush et al. (2024). To leverage this insight, we introduce predictive data selection (PreSelect), a lightweight and efficient data selection method that requires training and deploying only a fastText-based scorer. Through comprehensive experiments with 1B and 3B parameter models, we demonstrate that models trained on 30B tokens selected with PreSelect surpass the performance of the vanilla baseline trained on 300B tokens, achieving a 10x reduction in compute requirements. Furthermore, PreSelect significantly outperforms other competitive data selection baselines, such as DCLM and FineWeb-Edu on a scale of 3B models trained on 100B tokens. We open-source our trained data selection scorer along with the curated datasets at https://github.com/hkust-nlp/PreSelect.

Deep Learning · Other Representation Learning

Yaoqin He, Junchen Fu, Kaiwen Zheng, Songpei Xu, Fuhai Chen, Jie Li, Joemon Jose, Xuri Ge

In this paper, we present a novel approach, termed Double-Filter,to “slim down” the fine-tuning process of vision-language pre-trained (VLP) models via filtering redundancies in feature inputs and architectural components. We enhance the fine-tuning process using two approaches. First, we develop a new patch selection method incorporating image patch filtering through background and foreground separation, followed by a refined patch selection process. Second, we design a genetic algorithm to eliminate redundant fine-grained architecture layers, improving the efficiency and effectiveness of the model. The former makes patch selection semantics more comprehensive, improving inference efficiency while ensuring semantic representation. The latter’s fine-grained layer filter removes architectural redundancy to the extent possible and mitigates the impact on performance. Experimental results demonstrate that the proposed Double-Filter achieves superior efficiency of model fine-tuning and maintains competitive performance compared with the advanced efficient fine-tuning methods on three downstream tasks, VQA, NLVR and Retrieval. In addition, it has been proven to be effective under METER and ViLT VLP models.

Social Aspects · Safety

Nikolaus Howe, Ian McKenzie, Oskar Hollinsworth, Michał Zając, Tom Tseng, Aaron Tucker, Pierre-Luc Bacon, Adam Gleave

Increasing model size has unlocked a dazzling array of capabilities in language models.At the same time, even frontier models remain vulnerable to jailbreaks and prompt injections, despite concerted efforts to make them robust.As both attackers and defenders gain access to more compute, and as models become larger, what will be the effect on robustness?We argue that to answer this question requires a *scaling lens*, which we adopt in an extensive study of language model robustness across several classification tasks, model families, and adversarial attacks.We find that in the absence of explicit safety training, larger models are not consistently more robust; however, scale improves sample efficiency in adversarial training, though it worsens compute efficiency.Further, we find that increasing attack compute smoothly improves attack success rate against both undefended and adversarially trained models.Finally, after exploring robustness transfer across attacks and threat models, we combine attack and defense scaling rates to study the offense-defense balance.We find that while attack scaling outpaces adversarial training across all models studied, larger adversarially trained models might give defense the advantage in the long run.These results underscore the utility of the scaling lens, and provide a paradigm for evaluating future attacks and defenses on frontier models.Code for this project is available at https://github.com/AlignmentResearch/scaling-llm-robustness-paper.

Deep Learning · Large Language Models

Matthieu Meeus, Lukas Wutschitz, Santiago Zanella-Beguelin, Shruti Tople, Reza Shokri

How much information about training samples can be leaked through synthetic data generated by Large Language Models (LLMs)? Overlooking the subtleties of information flow in synthetic data generation pipelines can lead to a false sense of privacy. In this paper, we assume an adversary has access to some synthetic data generated by a LLM. We design membership inference attacks (MIAs) that target the training data used to fine-tune the LLM that is then used to synthesize data. The significant performance of our MIA shows that synthetic data leak information about the training data. Further, we find that canaries crafted for model-based MIAs are sub-optimal for privacy auditing when only synthetic data is released. Such out-of-distribution canaries have limited influence on the model’s output when prompted to generate useful, in-distribution synthetic data, which drastically reduces their effectiveness. To tackle this problem, we leverage the mechanics of auto-regressive models to design canaries with an in-distribution prefix and a high-perplexity suffix that leave detectable traces in synthetic data. This enhances the power of data-based MIAs and provides a better assessment of the privacy risks of releasing synthetic data generated by LLMs.

Optimization · Convex

Irmak Sivgin, Sara Fridovich-Keil, Gordon Wetzstein, Mert Pilanci

Volume parameterizations abound in recent literature, encompassing methods from classic voxel grids to implicit neural representations. While implicit representations offer impressive capacity and improved memory efficiency compared to voxel grids, they traditionally require training through nonconvex optimization, which can be slow and sensitive to initialization and hyperparameters. We introduce GA-Planes, a novel family of implicit neural volume representations inspired by Geometric Algebra that can be trained using convex optimization, addressing the limitations of nonconvex methods. GA-Planes models generalize many existing representations including any combination of features stored in tensor basis elements followed by a neural feature decoder, and can be adapted to convex or nonconvex training as needed for various inverse problems. In the 2D setting, we prove GA-Planes models are equivalent to a low-rank plus low-resolution matrix factorization that outperforms the classic low-rank plus sparse decomposition for fitting a natural image. In 3D, GA-Planes models exhibit competitive expressiveness, model size, and optimizability across tasks such as radiance field reconstruction, 3D segmentation, and video segmentation.

Michael Sucker, Peter Ochs

Learning-to-optimize leverages machine learning to accelerate optimization algorithms. While empirical results show tremendous improvements compared to classical optimization algorithms, theoretical guarantees are mostly lacking, such that the outcome cannot be reliably assured. Especially, convergence is hardly studied in learning-to-optimize, because conventional convergence guarantees in optimization are based on geometric arguments, which cannot be applied easily to learned algorithms. Thus, we develop a probabilistic framework that resembles classical optimization and allows for transferring geometric arguments into learning-to-optimize. Based on our new proof-strategy, our main theorem is a generalization result for parametric classes of potentially non-smooth, non-convex loss functions and establishes the convergence of learned optimization algorithms to critical points with high probability. This effectively generalizes the results of a worst-case analysis into a probabilistic framework, and frees the design of the learned algorithm from using safeguards.

Applications · Computer Vision

Hongbi ZHOU, Zhangkai NI

3D Gaussian Splatting (3DGS) has emerged as a powerful technique for novel view synthesis. However, existing methods struggle to adaptively optimize the distribution of Gaussian primitives based on scene characteristics, making it challenging to balance reconstruction quality and efficiency. Inspired by human perception, we propose scene-adaptive perceptual densification for Gaussian Splatting (Perceptual-GS), a novel framework that integrates perceptual sensitivity into the 3DGS training process to address this challenge. We first introduce a perception-aware representation that models human visual sensitivity while constraining the number of Gaussian primitives. Building on this foundation, we develop a perceptual sensitivity-adaptive distribution to allocate finer Gaussian granularity to visually critical regions, enhancing reconstruction quality and robustness. Extensive evaluations on multiple datasets, including BungeeNeRF for large-scale scenes, demonstrate that Perceptual-GS achieves state-of-the-art performance in reconstruction quality, efficiency, and robustness. The code is publicly available at: https://github.com/eezkni/Perceptual-GS

Applications · Health / Medicine

Aaron Wenteler, Martina Occhetta, Nikhil Branson, Victor Curean, Magdalena Huebner, William Dee, William Connell, Siu Chung, Alex Hawkins-Hooker, Yasha Ektefaie 等

*In silico* modeling of transcriptional responses to perturbations is crucial for advancing our understanding of cellular processes and disease mechanisms. We present PertEval-scFM, a standardized framework designed to evaluate models for perturbation effect prediction. We apply PertEval-scFM to benchmark zero-shot single-cell foundation model (scFM) embeddings against baseline models to assess whether these contextualized representations enhance perturbation effect prediction. Our results show that scFM embeddings offer limited improvement over simple baseline models in the zero-shot setting, particularly under distribution shift. Overall, this study provides a systematic evaluation of zero-shot scFM embeddings for perturbation effect prediction, highlighting the challenges of this task and the limitations of current-generation scFMs. Our findings underscore the need for specialized models and high-quality datasets that capture a broader range of cellular states. Source code and documentation can be found at: https://github.com/aaronwtr/PertEval.

Theory · Game Theory

Vikram Kher, Manolis Zampetakis

When can the distributional assumptions of theorems and learning algorithms be trusted? Inspired by this question, Rubinfeld and Vasilyan (2023) initiated the study of testable learning. In this schema, we always learn one of the following two things: either we have achieved the desired accuracy regardless of whether the distributional assumptions are satisfied, or the input distribution does not satisfy the original distributional assumptions. Motivated by the challenge of relying on strong distributional assumptions in many theorems in mechanism design, we develop a testable learning framework for mechanism design. Traditional models in mechanism design assume that value distributions satisfy some notion of regularity. Unfortunately, testing regularity is not possible in the original testable learning framework as we show. To bypass this impossibility, we propose a regularized version of the testable learning framework. Under this framework, we always learn one of the following two things: either we achieve high revenue compared to the best possible revenue of any regular distribution close to the input distribution, or the input distribution does not satisfy regularity. We then use this framework to provide: 1) a tester-learner pair for revenue optimal mechanisms, 2) a tester for whether the fundamental Bulow-Klemperer Theorem (Bulow and Klemperer 1996) is applicable to a given dataset, and 3) a tester to confirm the existence of an anonymous reserve price that results in the anonymous price auction securing a constant fraction of the optimal revenue.

Applications · Computer Vision

Guangting Zheng, Yehao Li, Yingwei Pan, Jiajun Deng, Ting Yao, Yanyong Zhang, Tao Mei

Autoregressive models have emerged as a powerful generative paradigm for visual generation. The current de-facto standard of next token prediction commonly operates over a single-scale sequence of dense image tokens, and is incapable of utilizing global context especially for early tokens prediction. In this paper, we introduce a new autoregressive design to model a hierarchy from a few low-resolution image tokens to the typical dense image tokens, and delve into a thorough hierarchical dependency across multi-scale image tokens. Technically, we present a Hierarchical Masked Autoregressive models (Hi-MAR) that pivot on low-resolution image tokens to trigger hierarchical autoregressive modeling in a multi-phase manner. Hi-MAR learns to predict a few image tokens in low resolution, functioning as intermediary pivots to reflect global structure, in the first phase. Such pivots act as the additional guidance to strengthen the next autoregressive modeling phase by shaping global structural awareness of typical dense image tokens. A new Diffusion Transformer head is further devised to amplify the global context among all tokens for mask token prediction. Extensive evaluations on both class-conditional and text-to-image generation tasks demonstrate that Hi-MAR outperforms typical AR baselines, while requiring fewer computational costs.

Deep Learning · Everything Else

Tianze Yang, Yucheng Shi, Mengnan Du, Xuansheng Wu, Qiaoyu Tan, Jin Sun, Ninghao Liu

Vector-Quantized Generative Models (VQGMs) have emerged as powerful tools for image generation. However, the key component of VQGMs---the codebook of discrete tokens---is still not well understood, e.g., which tokens are critical to generate an image of a certain concept?This paper introduces Concept-Oriented Token Explanation (CORTEX), a novel approach for interpreting VQGMs by identifying concept-specific token combinations. Our framework employs two methods: (1) a sample-level explanation method that analyzes token importance scores in individual images, and (2) a codebook-level explanation method that explores the entire codebook to find globally relevant tokens. Experimental results demonstrate CORTEX's efficacy in providing clear explanations of token usage in the generative process, outperforming baselines across multiple pretrained VQGMs. Besides enhancing VQGMs transparency, CORTEX is useful in applications such as targeted image editing and shortcut feature detection. Our code is available at https://github.com/YangTianze009/CORTEX.