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Probabilistic Methods · Variational Inference

Charles Dawson, Van Tran, Max Li, Chuchu Fan

Increased deployment of autonomous systems in fields like transportation and robotics have seen a corresponding increase in safety-critical failures. These failures can be difficult to model and debug due to the relative lack of data: compared to tens of thousands of examples from normal operations, we may have only seconds of data leading up to the failure. This scarcity makes it challenging to train generative models of rare failure events, as existing methods risk either overfitting to noise in the limited failure dataset or underfitting due to an overly strong prior. We address this challenge with CalNF, or calibrated normalizing flows, a self-regularized framework for posterior learning from limited data. CalNF achieves state-of-the-art performance on data-limited failure modeling and inverse problems and enables a first-of-a-kind case study into the root causes of the 2022 Southwest Airlines scheduling crisis.

Saptarshi Roy, Vansh Bansal, Purnamrita Sarkar, Alessandro Rinaldo

Diffusion models have emerged as a powerful tool for image generation and denoising. Typically, generative models learn a trajectory between the starting noise distribution and the target data distribution. Recently Liu et al. (2023b) designed a novel alternative generative model Rectified Flow(RF), which aims to learn straight flow trajectories from noise to data using a sequence of convex optimization problems with close ties to optimal transport. If the trajectory is curved, one must use many Euler discretization steps or novel strategies, such as exponential integrators, to achieve a satisfactory generation quality. In contrast, RF has been shown to theoretically straighten the trajectory through successive rectifications, reducing the number of function evaluations (NFEs) while sampling. It has also been shown empirically that RF may improve the straightness in two rectifications if one can solve the underlying optimization problem within a sufficiently small error. In this paper, we make two key theoretical contributions: 1) we provide the first theoretical analysis of theWasserstein distance between the sampling distribution of RF and the target distribution. Our error rate is characterized by the number of discretization steps and a new formulation of straightness stronger than that in the original work. 2) under a mild regularity assumption, we show that for a rectified flow from a Gaussian to any general target distribution with finite first moment (e.g. mixture of Gaussians), two rectifications are sufficient to achieve a straight flow, which is in line with the previous empirical findings. Additionally, we also present empirical results on both simulated and real datasets to validate our theoretical findings.

Social Aspects · Trustworthy Machine Learning

Botong Zhang, Shuo Li, Osbert Bastani

Conformal prediction has recently emerged as a promising strategy for quantifying the uncertainty of a predictive model; these algorithms modify the model to output sets of labels that are guaranteed to contain the true label with high probability. However, existing conformal prediction algorithms have largely targeted classification and regression settings, where the structure of the prediction set has a simple form as a level set of the scoring function. However, for complex structured outputs such as text generation, these prediction sets might include a large number of labels and therefore be hard for users to interpret. In this paper, we propose a general framework for conformal prediction in the structured prediction setting, that modifies existing conformal prediction algorithms to output structured prediction sets that implicitly represent sets of labels. In addition, we demonstrate how our approach can be applied in domains where the prediction sets can be represented as a set of nodes in a directed acyclic graph; for instance, for hierarchical labels such as image classification, a prediction set might be a small subset of coarse labels implicitly representing the prediction set of all their more fine-descendants. We demonstrate how our algorithm can be used to construct prediction sets that satisfy a desired coverage guarantee in several domains.

Miscellaneous Aspects of Machine Learning · Representation Learning

Han-Hung Lee, Yiming Zhang, Angel Chang

We introduce Duoduo CLIP, a model for 3D representation learning that learns shape encodings from multi-view images instead of point-clouds. The choice of multi-view images allows us to leverage 2D priors from off-the-shelf CLIP models to facilitate fine-tuning with 3D data. Our approach not only shows better generalization compared to existing point cloud methods, but also reduces GPU requirements and training time. In addition, the model is modified with cross-view attention to leverage information across multiple frames of the object which further boosts performance. Notably, our model is permutation invariant to the order of multi-view images while being pose-free. Compared to the current SOTA point cloud method that requires 480 A100 hours to train 1 billion model parameters we only require 57 A5000 hours and 87 million parameters. Multi-view images also provide more flexibility including being able to encode objects with a variable number of images, and performance scales when more views are used. In contrast, point cloud based methods require an entire scan or model of the object. We showcase this flexibility with benchmarks from images of real-world objects. Our model also achieves better performance in more fine-grained text to shape retrieval, demonstrating better text-and-shape alignment than point cloud based models.

Deep Learning · Graph Neural Networks

Hannah Lawrence, Vasco Portilheiro, Yan Zhang, Sékou-Oumar Kaba

Equivariance encodes known symmetries into neural networks, often enhancing generalization. However, equivariant networks cannot *break* symmetries: the output of an equivariant network must, by definition, have at least the same self-symmetries as its input. This poses an important problem, both (1) for prediction tasks on domains where self-symmetries are common, and (2) for generative models, which must break symmetries in order to reconstruct from highly symmetric latent spaces. This fundamental limitation can in fact be addressed by considering *equivariant conditional distributions*, instead of equivariant functions. We therefore present novel theoretical results that establish necessary and sufficient conditions for representing such distributions. Concretely, this representation provides a practical framework for breaking symmetries in any equivariant network via randomized canonicalization. Our method, SymPE (Symmetry-breaking Positional Encodings), admits a simple interpretation in terms of positional encodings. This approach expands the representational power of equivariant networks while retaining the inductive bias of symmetry, which we justify through generalization bounds. Experimental results demonstrate that SymPE significantly improves performance of group-equivariant and graph neural networks across diffusion models for graphs, graph autoencoders, and lattice spin system modeling.

Deep Learning · Other Representation Learning

Naoya Hasegawa, Issei Sato

Real-world data distributions are often highly skewed. This has spurred a growing body of research on long-tailed recognition, aimed at addressing the imbalance in training classification models. Among the methods studied, multiplicative logit adjustment (MLA) stands out as a simple and effective method. What theoretical foundation explains the effectiveness of this heuristic method?We provide a justification for the effectiveness of MLA with the following two-step process. First, we develop a theory that adjusts optimal decision boundaries by estimating feature spread on the basis of neural collapse. Second, we demonstrate that MLA approximates this optimal method. Additionally, through experiments on long-tailed datasets, we illustrate the practical usefulness of MLA under more realistic conditions. We also offer experimental insights to guide the tuning of MLA hyperparameters.

Deep Learning · Large Language Models

Chengyu Du, Jinyi Han, Yizhou Ying, Aili Chen, Qianyu He, Haokun Zhao, Haoran Guo, Sirui Xia, Jiaqing Liang, zulong chen 等

Recent advancements in large language models (LLMs) have demonstrated that progressive refinement, rather than providing a single answer, results in more accurate and thoughtful outputs. However, existing methods often rely heavily on supervision signals to evaluate previous responses, making it difficult to effectively assess output quality in more open-ended scenarios. Additionally, these methods are typically designed for specific tasks, which limits their generalization to new domains. To address these limitations, we propose Progressive Thought Refinement (PTR), a framework that enables LLMs to progressively refine their responses. PTR operates in two phases: (1) Thought data construction stage: We propose a weak and strong model collaborative selection strategy to build a high-quality progressive refinement dataset to ensure logical consistency from thought to answers, and the answers are gradually refined in each round. (2) Thought-Mask Fine-Tuning Phase: We design a training structure to mask the "thought" and adjust loss weights to encourage LLMs to refine prior thought, teaching them to implicitly understand "how to improve" rather than "what is correct." Experimental results show that PTR significantly enhances LLM performance across ten diverse tasks (avg. from 49.6% to 53.5%) without task-specific fine-tuning. Notably, in more open-ended tasks, LLMs also demonstrate substantial improvements in the quality of responses beyond mere accuracy, suggesting that PTR truly teaches LLMs to self-improve over time. Our work is now open-source. https://github.com/cydu24/Progressive-Thought-Refinement

Applications · Chemistry and Drug Discovery

Raul Fernandez-Diaz, Hoang Thanh Lam, Vanessa Lopez, Denis Shields

Quantifying model generalization to out-of-distribution data has been a longstanding challenge in machine learning. Addressing this issue is crucial for leveraging machine learning in scientific discovery, where models must generalize to new molecules or materials. Current methods typically split data into train and test sets using various criteria — temporal, sequence identity, scaffold, or random cross-validation — before evaluating model performance. However, with so many splitting criteria available, existing approaches offer limited guidance on selecting the most appropriate one, and they do not provide mechanisms for incorporating prior knowledge about the target deployment distribution(s).To tackle this problem, we have developed a novel metric, AU-GOOD, which quantifies expected model performance under conditions of increasing dissimilarity between train and test sets, while also accounting for prior knowledge about the target deployment distribution(s), when available. This metric is broadly applicable to biochemical entities, including proteins, small molecules, nucleic acids, or cells; as long as a relevant similarity function is defined for them. Recognizing the wide range of similarity functions used in biochemistry, we propose criteria to guide the selection of the most appropriate metric for partitioning. We also introduce a new partitioning algorithm that generates more challenging test sets, and we propose statistical methods for comparing models based on AU-GOOD.Finally, we demonstrate the insights that can be gained from this framework by applying it to two different use cases: developing predictors for pharmaceutical properties of small molecules, and using protein language models as embeddings to build biophysical property predictors.

Johannes von Oswald, Seijin Kobayashi, Yassir Akram, Angelika Steger

Randomization is a powerful tool that endows algorithms with remarkable properties. For instance, randomized algorithms excel in adversarial settings, often surpassing the worst-case performance of deterministic algorithms with large margins. Furthermore, their success probability can be amplified by simple strategies such as repetition and majority voting. In this paper, we enhance deep neural networks, in particular transformer models, with randomization. We demonstrate for the first time that randomized algorithms can be instilled in transformers through learning, in a purely data- and objective-driven manner. First, we analyze known adversarial objectives for which randomized algorithms offer a distinct advantage over deterministic ones. We then show that common optimization techniques, such as gradient descent or evolutionary strategies, can effectively learn transformer parameters that make use of the randomness provided to the model. To illustrate the broad applicability of randomization in empowering neural networks, we study three conceptual tasks: associative recall, graph coloring, and agents that explore grid worlds. In addition to demonstrating increased robustness against oblivious adversaries through learned randomization, our experiments reveal remarkable performance improvements due to the inherently random nature of the neural networks' computation and predictions.

Reinforcement Learning · Everything Else

Guangchen (Eric) Lan, Dong-Jun Han, Abolfazl Hashemi, Vaneet Aggarwal, Christopher Brinton

To improve the efficiency of reinforcement learning (RL), we propose a novel asynchronous federated reinforcement learning (FedRL) framework termed AFedPG, which constructs a global model through collaboration among $N$ agents using policy gradient (PG) updates. To address the challenge of lagged policies in asynchronous settings, we design a delay-adaptive lookahead technique *specifically for FedRL* that can effectively handle heterogeneous arrival times of policy gradients. We analyze the theoretical global convergence bound of AFedPG, and characterize the advantage of the proposed algorithm in terms of both the sample complexity and time complexity. Specifically, our AFedPG method achieves $\mathcal{O}(\frac{{\epsilon}^{-2.5}}{N})$ sample complexity for global convergence at each agent on average. Compared to the single agent setting with $\mathcal{O}(\epsilon^{-2.5})$ sample complexity, it enjoys a linear speedup with respect to the number of agents. Moreover, compared to synchronous FedPG, AFedPG improves the time complexity from $\mathcal{O}(\frac{t_{\max}}{N})$ to $\mathcal{O}({\sum_{i=1}^{N} \frac{1}{t_{i}}})^{-1}$, where $t_{i}$ denotes the time consumption in each iteration at agent $i$, and $t_{\max}$ is the largest one. The latter complexity $\mathcal{O}({\sum_{i=1}^{N} \frac{1}{t_{i}}})^{-1}$ is always smaller than the former one, and this improvement becomes significant in large-scale federated settings with heterogeneous computing powers ($t_{\max}\gg t_{\min}$). Finally, we empirically verify the improved performance of AFedPG in four widely used MuJoCo environments with varying numbers of agents. We also demonstrate the advantages of AFedPG in various computing heterogeneity scenarios.

Beining Yang, Qingyun Sun, Cheng Ji, Xingcheng Fu, Jianxin Li

The increasing scale of graph datasets significantly enhances deep learning models but also presents substantial training challenges. Graph dataset condensation has emerged to condense large datasets into smaller yet informative ones that maintain similar test performance. However, these methods require downstream usage to match the original dataset and task, which is impractical in real-world scenarios. Our empirical studies show that existing methods fail in "cross-task" and "cross-dataset" scenarios, often performing worse than training from scratch. To address these challenges, we propose a novel method: Self-supervised and Transferable Graph dataset Condensation (ST-GCond). For cross-task transferability, we propose a task-disentangled meta optimization strategy to adaptively update the condensed graph according to the task relevance, encouraging information preservation for various tasks. For cross-dataset transferability, we propose a multi-teacher self-supervised optimization strategy to incorporate auxiliary self-supervised tasks to inject universal knowledge into the condensed graph. Additionally, we incorporate mutual information guided joint condensation mitigating the potential conflicts and ensure the condensing stability. Experiments on both node-level and graph-level datasets show that ST-GCond outperforms existing methods by 2.5% to 18.7% in all cross-task and cross-dataset scenarios, and also achieves state-of-the-art performance on 5 out of 6 datasets in the single dataset and task scenario.

Deep Learning · Large Language Models

Tong Chen, Hao Fang, Patrick Xia, Xiaodong Liu, Ben Van Durme, Luke Zettlemoyer, Jianfeng Gao, Hao Cheng

Large language models (LLMs) acquire substantial knowledge during pretraining but often need adaptation to new contexts, tasks, or domains, typically achieved through fine-tuning or prompting. However, fine-tuning incurs significant training costs, while prompting increases inference overhead. Inspired by fast weight memory, we introduce GenerativeAdapter, an effective and efficient adaptation method that encode test-time context into language model parameters with a single forward pass.GenerativeAdapter augments a frozen pretrained LM with a lightweight adapter generator, trained via self-supervised learning, to produce parameter-efficient adapters.Notably, our generator is general-purpose, i.e., one generator can adapt the corresponding base model for all langauge processing scenarios.We apply GenerativeAdapter to two pretrained LMs (Mistral-7B-Instruct and Llama2-7B-Chat) and evaluate the adapted models across knowledge acquisition from documents, learning from demonstrations, and personalization for users.In StreamingQA, our approach is effective in injecting knowledge into the LM's parameters, achieving a 63.5\% improvement in F1 score over the model with supervised fine-tuning (from $19.5$ to $31.5$) for contexts as long as 32K tokens.In the MetaICL in-context learning evaluation, our method achieves an average accuracy of $44.9$ across 26 tasks, outperforming the base model. On MSC, our method proves to be highly competitive in memorizing user information from conversations with a 4x reduction in computation and memory costs compared to prompting with full conversation history.Overall, GenerativeAdapter provides a viable solution for adapting large LMs to evolving information and providing tailored user experience, while reducing training and inference costs relative to traditional fine-tuning and prompting techniques.

Deep Learning · Large Language Models

Zhiyang He, Sashrika Pandey, Mariah Schrum, Anca Dragan

To deliver high-quality, personalized responses, large language models (LLMs) must effectively incorporate context — personal, demographic, and cultural information specific to an end-user. For example, asking the model to explain Newton's second law with the context "I am a toddler'' should produce a response different from when the context is "I am a physics professor''. However, leveraging the context in practice is a nuanced and challenging task, and is often dependent on the specific situation or user base. The model must strike a balance between providing specific, personalized responses and maintaining general applicability. Current solutions, such as prompt-engineering and fine-tuning, require collection of contextually appropriate responses as examples, making them time-consuming and less flexible to use across different contexts. In this work, we introduce Context Steering (CoS) —a simple, training-free decoding approach that amplifies the influence of the context in next token predictions. CoS computes contextual influence by comparing the output probabilities from two LLM forward passes: one that includes the context and one that does not. By linearly scaling the contextual influence, CoS allows practitioners to flexibly control the degree of personalization for different use cases. We show that CoS can be applied to autoregressive LLMs, and demonstrates strong performance in personalized recommendations. Additionally, we show that CoS can function as a Bayesian Generative model to infer and quantify correlations between open-ended texts, broadening its potential applications.

Applications · Computer Vision

Neel Dey, Benjamin Billot, Hallee Wong, Clinton Wang, Mengwei Ren, Ellen Grant, Adrian Dalca, Polina Golland

Current volumetric biomedical foundation models struggle to generalize as public 3D datasets are small and do not cover the broad diversity of medical procedures, conditions, anatomical regions, and imaging protocols. We address this by creating a representation learning method that instead anticipates strong domain shifts at training time itself. We first propose a data engine that synthesizes highly variable training samples that would enable generalization to new biomedical contexts. To then train a single 3D network for any voxel-level task, we develop a contrastive learning method that pretrains the network to be stable against nuisance imaging variation simulated by the data engine, a key inductive bias for generalization. This network's features can be used as robust representations of input images for downstream tasks and its weights provide a strong, _dataset-agnostic_ initialization for finetuning on new datasets. As a result, we set new standards across _both_ multimodality registration and few-shot segmentation, a first for any 3D biomedical vision model, all without (pre-)training on any existing dataset of real images.

Deep Learning · Large Language Models

Jingyu Zhang, Ahmed Elgohary Ghoneim, Ahmed Magooda, Daniel Khashabi, Ben Van Durme

The current paradigm for safety alignment of large language models (LLMs) follows a _one-size-fits-all_ approach: the model refuses to interact with any content deemed unsafe by the model provider. This approach lacks flexibility in the face of varying social norms across cultures and regions. In addition, users may have diverse safety needs, making a model with _static_ safety standards too restrictive to be useful, as well as too costly to be re-aligned.We propose _Controllable Safety Alignment_ (CoSA), a framework designed to adapt models to diverse safety requirements without re-training. Instead of aligning a fixed model, we align models to follow _safety configs_—free-form natural language descriptions of the desired safety behaviors—that are provided as part of the system prompt. To adjust model safety behavior, authorized users only need to modify such safety configs at inference time. To enable that, we propose CoSAlign, a data-centric method for aligning LLMs to easily adapt to diverse safety configs. Furthermore, we devise a novel controllability evaluation protocol that considers both helpfulness and configured safety, summarizing them into CoSA-Score, and construct CoSApien, a _human-authored_ benchmark that consists of real-world LLM use cases with diverse safety requirements and corresponding evaluation prompts. We show that CoSAlign leads to substantial gains of controllability over strong baselines including in-context alignment. Our framework encourages better representation and adaptation to pluralistic human values in LLMs, and thereby increasing their practicality.

Applications · Genetics, Cell Biology, Health, etc

Sichen Zhu, Yuchen Zhu, Molei Tao, Peng Qiu

Spatial Transcriptomics (ST) allows a high-resolution measurement of RNA sequence abundance by systematically connecting cell morphology depicted in Hematoxylin and eosin (H\&E) stained histology images to spatially resolved gene expressions. ST is a time-consuming, expensive yet powerful experimental technique that provides new opportunities to understand cancer mechanisms at a fine-grained molecular level, which is critical for uncovering new approaches for disease diagnosis and treatments. Here, we present $\textbf{Stem}$ ($\underline{\textbf{S}}$pa$\underline{\textbf{T}}$ially resolved gene $\underline{\textbf{E}}$xpression inference with diffusion $\underline{\textbf{M}}$odel), a novel computational tool that leverages a conditional diffusion generative model to enable in silico gene expression inference from H&E stained images. Through better capturing the inherent stochasticity and heterogeneity in ST data, $\textbf{Stem}$ achieves state-of-the-art performance on spatial gene expression prediction and generates biologically meaningful gene profiles for new H&E stained images at test time. We evaluate the proposed algorithm on datasets with various tissue sources and sequencing platforms, where it demonstrates clear improvement over existing approaches. $\textbf{Stem}$ generates high-fidelity gene expression predictions that share similar gene variation levels as ground truth data, suggesting that our method preserves the underlying biological heterogeneity. Our proposed pipeline opens up the possibility of analyzing existing, easily accessible H&E stained histology images from a genomics point of view without physically performing gene expression profiling and empowers potential biological discovery from H&E stained histology images. Code is available at: https://github.com/SichenZhu/Stem.

Millicent Li, Tongfei Chen, Ben Van Durme, Patrick Xia

Document retrieval for tasks such as search and retrieval-augmented generation typically involves datasets that are _unstructured_: free-form text without explicit internal structure in each document. However, documents can have some structure, containing fields such as an article title, a message body, or an HTML header. To address this gap, we introduce Multi-Field Adaptive Retrieval (mFAR), a flexible framework that accommodates any number and any type of document indices on _semi-structured_ data. Our framework consists of two main steps: (1) the decomposition of an existing document into fields, each indexed independently through dense and lexical methods, and (2) learning a model which adaptively predicts the importance of a field by conditioning on the document query, allowing on-the-fly weighting of the most likely field(s). We find that our approach allows for the optimized use of dense versus lexical representations across field types, significantly improves in document ranking over a number of existing retrievers, and achieves state-of-the-art performance for multi-field structured data.

Deep Learning · Generative Models and Autoencoders

Yuchen Zhu, Tianrong Chen, Lingkai Kong, Evangelos Theodorou, Molei Tao

The generative modeling of data on manifolds is an important task, for which diffusion models in flat spaces typically need nontrivial adaptations. This article demonstrates how a technique called `trivialization' can transfer the effectiveness of diffusion models in Euclidean spaces to Lie groups. In particular, an auxiliary momentum variable was algorithmically introduced to help transport the position variable between data distribution and a fixed, easy-to-sample distribution. Normally, this would incur further difficulty for manifold data because momentum lives in a space that changes with the position. However, our trivialization technique creates a new momentum variable that stays in a simple fixed vector space. This design, together with a manifold preserving integrator, simplifies implementation and avoids inaccuracies created by approximations such as projections to tangent space and manifold, which were typically used in prior work, hence facilitating generation with high-fidelity and efficiency. The resulting method achieves state-of-the-art performance on protein and RNA torsion angle generation and sophisticated torus datasets. We also, arguably for the first time, tackle the generation of data on high-dimensional Special Orthogonal and Unitary groups, the latter essential for quantum problems. Code is available at https://github.com/yuchen-zhu-zyc/TDM.

Applications · Time Series

Yizi Zhang, Jingyan Shen, Xiaoxue Xiong, Yongchan Kwon

Evaluating the contribution of individual data points to a model's prediction is critical for interpreting model predictions and improving model performance. Existing data contribution methods have been applied to various data types, including tabular data, images, and text; however, their primary focus has been on i.i.d. settings. Despite the pressing need for principled approaches tailored to time series datasets, the problem of estimating data contribution in such settings remains under-explored, possibly due to challenges associated with handling inherent temporal dependencies. This paper introduces TimeInf, a model-agnostic data contribution estimation method for time-series datasets. By leveraging influence scores, TimeInf attributes model predictions to individual time points while preserving temporal structures between the time points. Our empirical results show that TimeInf effectively detects time series anomalies and outperforms existing data attribution techniques as well as state-of-the-art anomaly detection methods. Moreover, TimeInf offers interpretable attributions of data values, allowing us to distinguish diverse anomalous patterns through visualizations. We also showcase a potential application of TimeInf in identifying mislabeled anomalies in the ground truth annotations.

Applications · Computer Vision

Amandine Brunetto, Sascha Hornauer, Fabien Moutarde

Sound plays a major role in human perception. Along with vision, it provides essential information for understanding our surroundings. Despite advances in neural implicit representations, learning acoustics that align with visual scenes remains a challenge. We propose NeRAF, a method that jointly learns acoustic and radiance fields. NeRAF synthesizes both novel views and spatialized room impulse responses (RIR) at new positions by conditioning the acoustic field on 3D scene geometric and appearance priors from the radiance field. The generated RIR can be applied to auralize any audio signal. Each modality can be rendered independently and at spatially distinct positions, offering greater versatility. We demonstrate that NeRAF generates high-quality audio on SoundSpaces and RAF datasets, achieving significant performance improvements over prior methods while being more data-efficient. Additionally, NeRAF enhances novel view synthesis of complex scenes trained with sparse data through cross-modal learning.NeRAF is designed as a Nerfstudio module, providing convenient access to realistic audio-visual generation. Project page: https://amandinebtto.github.io/NeRAF