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Deep Learning · Everything Else

Qingqing Cao, Mahyar Najibi, Sachin Mehta

Pretraining robust vision or multimodal foundation models (e.g., CLIP) relies on large-scale datasets that may be noisy, potentially misaligned, and have long-tail distributions. Previous works have shown promising results in augmenting datasets by generating synthetic samples. However, they only support domain-specific ad hoc use cases (e.g., either image or text only, but not both), and are limited in data diversity due to a lack of fine-grained control over the synthesis process. In this paper, we design a controllable image-text synthesis pipeline, CtrlSynth, for data-efficient and robust multimodal learning. The key idea is to decompose the visual semantics of an image into basic elements, apply user-specified control policies (e.g., remove, add, or replace operations), and recompose them to synthesize images or texts. The decompose and recompose feature in CtrlSynth allows users to control data synthesis in a fine-grained manner by defining customized control policies to manipulate the basic elements. CtrlSynth leverages the capabilities of pretrained foundation models such as large language models or diffusion models to reason and recompose basic elements such that synthetic samples are natural and composed in diverse ways. CtrlSynth is a closed-loop, training-free, and modular framework, making it easy to support different pretrained models. With extensive experiments on 31 datasets spanning different vision and vision-language tasks, we show that CtrlSynth substantially improves zero-shot classification, image-text retrieval, and compositional reasoning performance of CLIP models.

Deep Learning · Graph Neural Networks

Dooho Lee, Myeong Kong, Sagad Hamid, Cheonwoo Lee, Jaemin Yoo

We revisit DropEdge, a data augmentation technique for GNNs which randomly removes edges to expose diverse graph structures during training. While being a promising approach to effectively reduce overfitting on specific connections in the graph, we observe that its potential performance gain in supervised learning tasks is significantly limited. To understand why, we provide a theoretical analysis showing that the limited performance of DropEdge comes from the fundamental limitation that exists in many GNN architectures.Based on this analysis, we propose **Aggregation Buffer**, a parameter block specifically designed to improve the robustness of GNNs by addressing the limitation of DropEdge. Our method is compatible with any GNN model, and shows consistent performance improvements on multiple datasets. Moreover, our method effectively addresses well-known problems such as degree bias or structural disparity as a unifying solution. Code and datasets are available at https://github.com/dooho00/agg-buffer.

Deep Learning · Everything Else

Ilya Kaufman, Omri Azencot

Deep learning models with a large number of parameters, often referred to as over-parameterized models, have achieved exceptional performance across various tasks. Despite concerns about overfitting, these models frequently generalize well to unseen data, thanks to effective regularization techniques, with data augmentation being among the most widely used. While data augmentation has shown great success in classification tasks using label-preserving transformations, its application in regression problems has received less attention. Recently, a novel manifold learning approach for generating synthetic data was proposed, utilizing a first-order approximation of the data manifold. Building on this foundation, we present a theoretical framework and practical tools for approximating and sampling general data manifolds. Furthermore, we introduce the Curvature-Enhanced Manifold Sampling (CEMS) method for regression tasks. CEMS leverages a second-order representation of the data manifold to enable efficient sampling and reconstruction of new data points. Extensive evaluations across multiple datasets and comparisons with state-of-the-art methods demonstrate that CEMS delivers superior performance in both in-distribution and out-of-distribution scenarios, while introducing only minimal computational overhead. Code is available at https://github.com/azencot-group/CEMS.

Optimization

Nikolaj Jensen, Jamie Vicary

In this work, we propose a new architecture-agnostic method for training idempotent neural networks. An idempotent operator satisfies $f(x) = f(f(x))$, meaning it can be applied iteratively with no effect beyond the first application. Some neural networks used in data transformation tasks, such as image generation and augmentation, can represent non-linear idempotent projections. Using methods from perturbation theory we derive the recurrence relation ${\mathbf{K}' \leftarrow 3\mathbf{K}^2 - 2\mathbf{K}^3}$ for iteratively projecting a real-valued matrix $\mathbf{K}$ onto the manifold of idempotent matrices. Our analysis shows that for linear, single-layer MLP networks this projection 1) has idempotent fixed points, and 2) is attracting only around idempotent points. We give an extension to non-linear networks by considering our approach as a substitution of the gradient for the canonical loss function, achieving an architecture-agnostic training scheme. We provide experimental results for MLP- and CNN-based architectures with significant improvement in idempotent error over the canonical gradient-based approach. Finally, we demonstrate practical applications of the method as we train a generative network successfully using only a simple reconstruction loss paired with our method.

Deep Learning · Self-Supervised Learning

Jun Chen, Hong Chen, Yonghua Yu, Yiming Ying

In recent years, contrastive learning has achieved state-of-the-art performance in the territory of self-supervised representation learning. Many previous works have attempted to provide the theoretical understanding underlying the success of contrastive learning. Almost all of them rely on a default assumption, i.e., the label consistency assumption, which may not hold in practice (the probability of failure is called labeling error) due to the strength and randomness of common augmentation strategies, such as random resized crop (RRC). This paper investigates the theoretical impact of labeling error on the downstream classification performance of contrastive learning. We first reveal several significant negative impacts of labeling error on downstream classification risk. To mitigate these impacts, data dimensionality reduction method (e.g., singular value decomposition, SVD) is applied on original data to reduce false positive samples, and establish both theoretical and empirical evaluations. Moreover, it is also found that SVD acts as a double-edged sword, which may lead to the deterioration of downstream classification accuracy due to the reduced connectivity of the augmentation graph. Based on the above observations, we give the augmentation suggestion that we should use some moderate embedding dimension (such as $512, 1024$ in our experiments), data inflation, weak augmentation, and SVD to ensure large graph connectivity and small labeling error to improve model performance.

Social Aspects · Alignment

Jianwei Li, Jung-Eun Kim

Recent studies on the safety alignment of large language models (LLMs) have revealed that existing approaches often operate superficially, leaving models vulnerable to various adversarial attacks. Despite their significance, these studies generally fail to offer actionable solutions beyond data augmentation for achieving more robust safety mechanisms. This paper identifies a fundamental cause of this superficiality: existing alignment approaches often presume that models can implicitly learn a safety-related reasoning task during the alignment process, enabling them to refuse harmful requests. However, the learned safety signals are often diluted by other competing objectives, leading models to struggle with drawing a firm safety-conscious decision boundary when confronted with adversarial attacks. Based on this observation, by explicitly introducing a safety-related binary classification task and integrating its signals with our attention and decoding strategies, we eliminate this ambiguity and allow models to respond more responsibly to malicious queries. We emphasize that, with less than 0.2x overhead cost, our approach enables LLMs to assess the safety of both the query and the previously generated tokens at each necessary generating step. Extensive experiments demonstrate that our method significantly improves the resilience of LLMs against various adversarial attacks, offering a promising pathway toward more robust generative AI systems.

Social Aspects · Safety

Lukas Helff, Felix Friedrich, Manuel Brack, Kristian Kersting, Patrick Schramowski

This paper introduces Llavaguard, a suite of VLM-based vision safeguards that address the critical need for reliable tools in the era of large-scale data and models. To this end, we establish a novel open framework, describing a customizable safety taxonomy, data preprocessing, augmentation, and training setup. For teaching a VLM safeguard on safety, we further create a multimodal safety dataset with high-quality human expert annotations, where each image is labeled with a safety rating, category, and rationale. We also employ advanced augmentations to support context-specific assessments. The resulting Llavaguard models, ranging from 0.5B to 7B, serve as a versatile tool for evaluating the safety compliance of visual content against flexible policies. In comprehensive experiments, Llavaguard outperforms both state-of-the-art safeguards and VLMs in accuracy and in flexibly handling different policies. Additionally, we demonstrate Llavaguard's performance in two real-world applications: large-scale dataset annotation and moderation of text-to-image models. We make our entire framework, including the dataset, model weights, and training code, publicly available at https://ml-research.github.io/human-centered-genai/projects/llavaguard.

Applications · Health / Medicine

Qingtian Zhu, Yumin Zheng, Yuling Sang, Yifan Zhan, Ziyan Zhu, Jun Ding, Yinqiang Zheng

Spatial Transcriptomics (ST) is a method that captures gene expression profiles aligned with spatial coordinates. The discrete spatial distribution and the super-high dimensional sequencing results make ST data challenging to be modeled effectively. In this paper, we manage to model ST in a continuous and compact manner by the proposed tool, SUICA, empowered by the great approximation capability of Implicit Neural Representations (INRs) that can enhance both the spatial density and the gene expression. Concretely within the proposed SUICA, we incorporate a graph-augmented Autoencoder to effectively model the context information of the unstructured spots and provide informative embeddings that are structure-aware for spatial mapping. We also tackle the extremely skewed distribution in a regression-by-classification fashion and enforce classification-based loss functions for the optimization of SUICA. By extensive experiments of a wide range of common ST platforms under varying degradations, SUICA outperforms both conventional INR variants and SOTA methods regarding numerical fidelity, statistical correlation, and bio-conservation. The prediction by SUICA also showcases amplified gene signatures that enriches the bio-conservation of the raw data and benefits subsequent analysis.

General Machine Learning · Causality

Ke Zhu, Shu Yang, Xiaofei Wang

External controls from historical trials or observational data can augment randomized controlled trials when large-scale randomization is impractical or unethical, such as in drug evaluation for rare diseases. However, non-randomized external controls can introduce biases, and existing Bayesian and frequentist methods may inflate the type I error rate, particularly in small-sample trials where external data borrowing is most critical. To address these challenges, we propose a randomization inference framework that ensures finite-sample exact and model-free type I error rate control, adhering to the “analyze as you randomize” principle to safeguard against hidden biases. Recognizing that biased external controls reduce the power of randomization tests, we leverage conformal inference to develop an individualized test-then-pool procedure that selectively borrows comparable external controls to improve power. Our approach incorporates selection uncertainty into randomization tests, providing valid post-selection inference. Additionally, we propose an adaptive procedure to optimize the selection threshold by minimizing the mean squared error across a class of estimators encompassing both no-borrowing and full-borrowing approaches. The proposed methods are supported by non-asymptotic theoretical analysis, validated through simulations, and applied to a randomized lung cancer trial that integrates external controls from the National Cancer Database.

Applications · Chemistry, Physics, and Earth Sciences

Cailong Hua, Sivaraman Rajaganapathy, Rebecca Slick, Joseph Vavra, Joseph Muretta, James Ervasti, Murti Salapaka

Deciphering protein folding and unfolding pathways under tension is essential for deepening our understanding of fundamental biological mechanisms. Such insights hold the promise of developing treatments for a range of debilitating and fatal conditions, including muscular disorders like Duchenne Muscular Dystrophy and neurodegenerative diseases such as Parkinson's disease. Single molecule force spectroscopy (SMFS) is a powerful technique for investigating forces involved in protein domains folding and unfolding. However, SMFS trials often involve multiple protein molecules, necessitating filtering to isolate measurements from single-molecule trials. Currently, manual visual inspection is the primary method for classifying single-molecule data; a process that is both time-consuming and requires significant expertise. Here, we both apply state-of-the-art machine learning models and present a novel deep learning model tailored to SMFS data. The proposed model employs a dual-branch fusion strategy; one branch integrates the physics of protein molecules, and the other operates independently of physical constraints. This model automates the isolation of single-molecule measurements, significantly enhancing data processing efficiency. To train and validate our approach, we developed a physics-based Monte Carlo engine to simulate force spectroscopy datasets, including trials involving single molecules, multiple molecules, and no molecules. Our model achieves state-of-the-art performance, outperforming five baseline methods on both simulated and experimental datasets. It attains nearly 100\% accuracy across all simulated datasets and an average accuracy of $79.6 \pm 5.2$\% on experimental datasets, using only $\sim$30 training samples, surpassing baseline methods by 11.4\%. Notably, even without expert annotations on experimental data, the model achieves an average accuracy of $72.0 \pm 5.9$\% when pre-trained on corresponding simulated datasets. With our deep learning approach, the time required to extract meaningful statistics from single-molecule SMFS trials is reduced from a day to under an hour. This work results in SMFS experimental datasets from four important protein molecules crucial to many biological pathways. To support further research, we have made our datasets publicly available and provided a Python-based toolbox (https://github.com/SalapakaLab-SIMBioSys/SMFS-Identification).

Social Aspects · Privacy

Lucas Rosenblatt, Yuliia Lut, Ethan Turok, Marco Medina, Rachel Cummings

Imbalanced learning occurs in classification settings where the distribution of class-labels is highly skewed in the training data, such as when predicting rare diseases or in fraud detection. This class imbalance presents a significant algorithmic challenge, which can be further exacerbated when privacy-preserving techniques such as differential privacy are applied to protect sensitive training data. Our work formalizes these challenges and provides a number of algorithmic solutions. We consider DP variants of pre-processing methods that privately augment the original dataset to reduce the class imbalance, alongside DP variants of in-processing techniques, which adjust the learning algorithm to account for the imbalance. For each method, we either adapt an existing imbalanced learning technique to the private setting or demonstrate its incompatibility with differential privacy. Finally, we empirically evaluate these privacy-preserving imbalanced learning methods under various data and distributional settings. We find that private synthetic data methods perform well as a data pre-processing step, while class-weighted ERMs are an alternative in higher-dimensional settings where private synthetic data suffers from the curse of dimensionality.

Applications · Health / Medicine

Yuxin Zuo, Shang Qu, Yifei Li, Zhang-Ren Chen, Xuekai Zhu, Ermo Hua, Kaiyan Zhang, Ning Ding, Bowen Zhou

We introduce MedXpertQA, a highly challenging and comprehensive benchmark to evaluate expert-level medical knowledge and advanced reasoning. MedXpertQA includes 4,460 questions spanning 17 specialties and 11 body systems. It includes two subsets, Text for text evaluation and MM for multimodal evaluation. Notably, MM introduces expert-level exam questions with diverse images and rich clinical information, including patient records and examination results, setting it apart from traditional medical multimodal benchmarks with simple QA pairs generated from image captions. MedXpertQA applies rigorous filtering and augmentation to address the insufficient difficulty of existing benchmarks like MedQA, and incorporates specialty board questions to improve clinical relevance and comprehensiveness. We perform data synthesis to mitigate data leakage risk and conduct multiple rounds of expert reviews to ensure accuracy and reliability. We evaluate 18 leading models on MedXpertQA. Moreover, medicine is deeply connected to real-world decision-making, providing a rich and representative setting for assessing reasoning abilities beyond mathematics and code. To this end, we develop a reasoning-oriented subset to facilitate the assessment of o1-like models.

General Machine Learning · Representation Learning

Liang Huang, Benedict Lee, Daniel Ng, Kelin Xia

Text classification is a fundamental task in Natural Language Processing (NLP). Short text classification has recently captured much attention due to its increased amount from various sources with limited labels and its inherent challenges for its sparsity in words and semantics. Recent studies have adopted self-supervised contrastive learning across different representations to improve performance. However, most of the current models face several challenges. Firstly, the augmentation step might not be able to generate positive and negative samples that are semantically similar and dissimilar to the anchor respectively. Secondly, the text data could be enhanced with external auxiliary information that might introduce noise to the sparse text data. In addition, they are limited in capturing higher-order information such as group-wise interactions. In this work, we propose a novel document simplicial complex construction based on text data for a higher-order message-passing mechanism. We enhance the short text classification performance by contrasting the structural representation with the sequential representation generated by the transformer mechanism for improved outcomes and mitigated issues. The proposed framework, Contrastive Learning with Simplicial Convolutional Networks (C-SCN), leverages the expressive power of graph neural networks, models higher-order information beyond pair-wise relations and enriches features through contrastive learning. Experimental results on four benchmark datasets demonstrate the capability of C-SCN to outperform existing models in analysing sequential and complex short-text data.

Applications · Chemistry, Physics, and Earth Sciences

Kevin Han Huang, Ni Zhan, Elif Ertekin, Peter Orbanz, Ryan P. Adams

Incorporating group symmetries into neural networks has been a cornerstone of success in many AI-for-science applications. Diagonal groups of isometries, which describe the invariance under a simultaneous movement of multiple objects, arise naturally in many-body quantum problems. Despite their importance, diagonal groups have received relatively little attention, as they lack a natural choice of invariant maps except in special cases. We study different ways of incorporating diagonal invariance in neural network ansatze trained via variational Monte Carlo methods, and consider specifically data augmentation, group averaging and canonicalization. We show that, contrary to standard ML setups, in-training symmetrization destabilizes training and can lead to worse performance. Our theoretical and numerical results indicate that this unexpected behavior may arise from a unique computational-statistical tradeoff not found in standard ML analyses of symmetrization. Meanwhile, we demonstrate that post hoc averaging is less sensitive to such tradeoffs and emerges as a simple, flexible and effective method for improving neural network solvers.

Deep Learning · Sequential Models, Time series

Sungwon Han, Seungeon Lee, MEEYOUNG CHA, Sercan Arik, Jinsung Yoon

Time series forecasting uses historical data to predict future trends, leveraging the relationships between past observations and available features. In this paper, we propose RAFT, a retrieval-augmented time series forecasting method to provide sufficient inductive biases and complement the model's learning capacity. When forecasting the subsequent time frames, we directly retrieve historical data candidates from the training dataset with patterns most similar to the input, and utilize the future values of these candidates alongside the inputs to obtain predictions. This simple approach augments the model's capacity by externally providing information about past patterns via retrieval modules. Our empirical evaluations on ten benchmark datasets show that RAFT consistently outperforms contemporary baselines with an average win ratio of 86%.

Applications · Neuroscience, Cognitive Science

Weiyu Guo, Ziyue Qiao, Ying Sun, Yijie Xu, Hui Xiong

Gesture recognition based on surface electromyography (sEMG) has been gaining importance in many 3D Interactive Scenes. However, sEMG is easily influenced by various forms of noise in real-world environments, leading to challenges in providing long-term stable interactions through sEMG. Existing methods often struggle to enhance model noise resilience through various predefined data augmentation techniques.In this work, we revisit the problem from a short-term enhancement perspective to improve precision and robustness against various common noisy scenarios with learnable denoise using sEMG intrinsic pattern information and sliding-window attention. We propose a Short Term Enhancement Module(STEM), which can be easily integrated with various models. STEM offers several benefits: 1) Noise-resistant, enhanced robustness against noise without manual data augmentation; 2) Adaptability, adaptable to various models; and 3) Inference efficiency, achieving short-term enhancement through minimal weight-sharing in an efficient attention mechanism.In particular, we incorporate STEM into a transformer, creating the Short-Term Enhanced Transformer (STET).Compared with best-competing approaches, the impact of noise on STET is reduced by more than 20\%. We report promising results on classification and regression tasks and demonstrate that STEM generalizes across different gesture recognition tasks. The code is available at https://anonymous.4open.science/r/short_term_semg.

Reinforcement Learning · Deep RL

Adrià López Escoriza, Nicklas Hansen, Stone Tao, Tongzhou Mu, Hao Su

Long-horizon tasks in robotic manipulation present significant challenges in reinforcement learning (RL) due to the difficulty of designing dense reward functions and effectively exploring the expansive state-action space. However, despite a lack of dense rewards, these tasks often have a multi-stage structure, which can be leveraged to decompose the overall objective into manageable sub-goals. In this work, we propose DEMO³, a framework that exploits this structure for efficient learning from visual inputs. Specifically, our approach incorporates multi-stage dense reward learning, a bi-phasic training scheme, and world model learning into a carefully designed demonstration-augmented RL framework that strongly mitigates the challenge of exploration in long-horizon tasks. Our evaluations demonstrate that our method improves data-efficiency by an average of 40% and by 70% on particularly difficult taskscompared to state-of-the-art approaches. We validate this across 16 sparse-reward tasks spanning four domains, including challenging humanoid visual control tasks using as few as five demonstrations.

Reinforcement Learning

Bang You, Puze Liu, Huaping Liu, Jan Peters, Oleg Arenz

Simplicity is a powerful inductive bias. In reinforcement learning, regularization is used for simpler policies, data augmentation for simpler representations, and sparse reward functions for simpler objectives, all that, with the underlying motivation to increase generalizability and robustness by focusing on the essentials. Supplementary to these techniques, we investigate how to promote simple behavior throughout the episode. To that end, we introduce a modification of the reinforcement learning problem that additionally maximizes the total correlation within the induced trajectories. We propose a practical algorithm that optimizes all models, including policy and state representation, based on a lower-bound approximation. In simulated robot environments, our method naturally generates policies that induce periodic and compressible trajectories, and that exhibit superior robustness to noise and changes in dynamics compared to baseline methods, while also improving performance in the original tasks.

Deep Learning · Large Language Models

Xinyu Guan, Li Lyna Zhang, Yifei Liu, Ning Shang, Youran Sun, Yi Zhu, Fan Yang, Mao Yang

We present rStar-Math to demonstrate that small language models (SLMs) can rival or even surpass the math reasoning capability of OpenAI o1, without distillation from superior models. rStar-Math achieves this by exercising ``deep thinking'' through Monte Carlo Tree Search (MCTS), where a math policy SLM performs test-time search guided by an SLM-based process reward model. rStar-Math introduces three innovations to tackle the challenges in training the two SLMs: (1) a novel code-augmented CoT data synthesis method, which performs extensive MCTS rollouts to generate step-by-step verified reasoning trajectories used to train the policy SLM; (2) a novel process reward model training method that avoids na\"ive step-level score annotation, yielding a more effective process preference model (PPM); (3) a self-evolution recipe in which the policy SLM and PPM are built from scratch and iteratively evolved to improve reasoning capabilities. Through 4 rounds of self-evolution with millions of synthesized solutions for 747k math problems, rStar-Math boosts SLMs' math reasoning to state-of-the-art levels. On MATH benchmark, it improves Qwen2.5-Math-7B from 58.8% to 90.0%, surpassing o1-preview by +4.5%. On the USA Math Olympiad (AIME), rStar-Math solves an average of 53.3% (8/15) of problems, ranking among the top 20% of the brightest high school math students. Code and data are available at https://github.com/microsoft/rStar.

General Machine Learning · Scalable Algorithms

İlker Işık, Ramazan Gokberk Cinbis, Ebru Gol

Language models lack the notion of interchangeable tokens: symbols that are semantically equivalent yet distinct, such as bound variables in formal logic. This limitation prevents generalization to larger vocabularies and hinders the model's ability to recognize alpha-equivalence, where renaming bound variables preserves meaning. We formalize this machine learning problem and introduce alpha-covariance, a metric for evaluating robustness to such transformations. To tackle this task, we propose a dual-part token embedding strategy: a shared component ensures semantic consistency, while a randomized component maintains token distinguishability. Compared to a baseline that relies on alpha-renaming for data augmentation, our approach demonstrates improved generalization to unseen tokens in linear temporal logic solving, propositional logic assignment prediction, and copying with an extendable vocabulary, while introducing a favorable inductive bias for alpha-equivalence. Our findings establish a foundation for designing language models that can learn interchangeable token representations, a crucial step toward more flexible and systematic reasoning in formal domains. Our code and project page are available at https://necrashter.github.io/interchangeable-token-embeddings