论文检索

Deep Learning · Large Language Models

Yue Zhang, Zhiyang Xu, Ying Shen, Parisa Kordjamshidi, Lifu Huang

Integrating the 3D world into large language models (3D-based LLMs) has been a promising research direction for 3D scene understanding. However, current 3D-based LLMs fall short in situated understanding due to two key limitations: 1) existing 3D datasets are constructed from a global perspective of the 3D scenes and lack situated context.2) the architectures of the current 3D-based LLMs lack an explicit mechanism for aligning situated spatial information between 3D representations and natural language, limiting their performance in tasks requiring precise spatial reasoning. In this work, we address these issues by introducing a scalable situated 3D dataset, named Spartun3D, that incorporates various situated spatial information.In addition, we propose a situated spatial alignment module to enhance the learning between 3D visual representations and their corresponding textual descriptions. Our experimental results demonstrate that both our dataset and alignment module enhance situated spatial understanding ability.

Deep Learning · Other Representation Learning

Ziye Wang, Yiran Qin, Lin Zeng, Ruimao Zhang

Weather nowcasting is an essential task that involves predicting future radar echo sequences based on current observations, offering significant benefits for disaster management, transportation, and urban planning. Current prediction methods are limited by training and storage efficiency, mainly focusing on 2D spatial predictions at specific altitudes. Meanwhile, 3D volumetric predictions at each timestamp remain largely unexplored. To address such a challenge, we introduce a comprehensive framework for 3D radar sequence prediction in weather nowcasting, using the newly proposed SpatioTemporal Coherent Gaussian Splatting (STC-GS) for dynamic radar representation and GauMamba for efficient and accurate forecasting. Specifically, rather than relying on a 4D Gaussian for dynamic scene reconstruction, STC-GS optimizes 3D scenes at each frame by employing a group of Gaussians while effectively capturing their movements across consecutive frames. It ensures consistent tracking of each Gaussian over time, making it particularly effective for prediction tasks. With the temporally correlated Gaussian groups established, we utilize them to train GauMamba, which integrates a memory mechanism into the Mamba framework. This allows the model to learn the temporal evolution of Gaussian groups while efficiently handling a large volume of Gaussian tokens. As a result, it achieves both efficiency and accuracy in forecasting a wide range of dynamic meteorological radar signals. The experimental results demonstrate that our STC-GS can efficiently represent 3D radar sequences with over $16\times$ higher spatial resolution compared with the existing 3D representation methods, while GauMamba outperforms state-of-the-art methods in forecasting a broad spectrum of high-dynamic weather conditions.

Applications · Genetics, Cell Biology, Health, etc

Lazar Atanackovic, Xi (Nicole) Zhang, Brandon Amos, Mathieu Blanchette, Leo J Lee, Yoshua Bengio, Alexander Tong, Kirill Neklyudov

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

Applications · Chemistry and Drug Discovery

Jiarui Lu, Xiaoyin Chen, Stephen Lu, Chence Shi, Hongyu Guo, Yoshua Bengio, Jian Tang

Proteins adopt multiple structural conformations to perform their diverse biological functions, and understanding these conformations is crucial for advancing drug discovery. Traditional physics-based simulation methods often struggle with sampling equilibrium conformations and are computationally expensive. Recently, deep generative models have shown promise in generating protein conformations as a more efficient alternative. However, these methods predominantly rely on the diffusion process within a 3D geometric space, which typically centers around the vicinity of metastable states and is often inefficient in terms of runtime. In this paper, we introduce Structure Language Modeling (SLM) as a novel framework for efficient protein conformation generation. Specifically, the protein structures are first encoded into a compact latent space using a discrete variational auto-encoder, followed by conditional language modeling that effectively captures sequence-specific conformation distributions. This enables a more efficient and interpretable exploration of diverse ensemble modes compared to existing methods. Based on this general framework, we instantiate SLM with various popular LM architectures as well as proposing the ESMDiff, a novel BERT-like structure language model fine-tuned from ESM3 with masked diffusion. We verify our approach in various scenarios, including the equilibrium dynamics of BPTI, conformational change pairs, and intrinsically disordered proteins. SLM provides a highly efficient solution, offering a 20-100x speedup than existing methods in generating diverse conformations, shedding light on promising avenues for future research.

Deep Learning · Other Representation Learning

Ziye Wang, Yiran Qin, Lin Zeng, Ruimao Zhang

Weather nowcasting is an essential task that involves predicting future radar echo sequences based on current observations, offering significant benefits for disaster management, transportation, and urban planning. Current prediction methods are limited by training and storage efficiency, mainly focusing on 2D spatial predictions at specific altitudes. Meanwhile, 3D volumetric predictions at each timestamp remain largely unexplored. To address such a challenge, we introduce a comprehensive framework for 3D radar sequence prediction in weather nowcasting, using the newly proposed SpatioTemporal Coherent Gaussian Splatting (STC-GS) for dynamic radar representation and GauMamba for efficient and accurate forecasting. Specifically, rather than relying on a 4D Gaussian for dynamic scene reconstruction, STC-GS optimizes 3D scenes at each frame by employing a group of Gaussians while effectively capturing their movements across consecutive frames. It ensures consistent tracking of each Gaussian over time, making it particularly effective for prediction tasks. With the temporally correlated Gaussian groups established, we utilize them to train GauMamba, which integrates a memory mechanism into the Mamba framework. This allows the model to learn the temporal evolution of Gaussian groups while efficiently handling a large volume of Gaussian tokens. As a result, it achieves both efficiency and accuracy in forecasting a wide range of dynamic meteorological radar signals. The experimental results demonstrate that our STC-GS can efficiently represent 3D radar sequences with over $16\times$ higher spatial resolution compared with the existing 3D representation methods, while GauMamba outperforms state-of-the-art methods in forecasting a broad spectrum of high-dynamic weather conditions.

Reinforcement Learning · Deep RL

Haque Ishfaq, Guangyuan Wang, Sami Islam, Doina Precup

Existing actor-critic algorithms, which are popular for continuous control reinforcement learning (RL) tasks, suffer from poor sample efficiency due to lack of principled exploration mechanism within them. Motivated by the success of Thompson sampling for efficient exploration in RL, we propose a novel model-free RL algorithm, \emph{Langevin Soft Actor Critic} (LSAC), which prioritizes enhancing critic learning through uncertainty estimation over policy optimization. LSAC employs three key innovations: approximate Thompson sampling through distributional Langevin Monte Carlo (LMC) based $Q$ updates, parallel tempering for exploring multiple modes of the posterior of the $Q$ function, and diffusion synthesized state-action samples regularized with $Q$ action gradients. Our extensive experiments demonstrate that LSAC outperforms or matches the performance of mainstream model-free RL algorithms for continuous control tasks.Notably, LSAC marks the first successful application of an LMC based Thompson sampling in continuous control tasks with continuous action spaces.

Applications · Computer Vision

Aniket Rajiv Didolkar, Andrii Zadaianchuk, Anirudh Goyal, Michael Mozer, Yoshua Bengio, Georg Martius, Maximilian Seitzer

The goal of object-centric representation learning is to decompose visual scenes into a structured representation that isolates the entities into individual vectors. Recent successes have shown that object-centric representation learning can be scaled to real-world scenes by utilizing features from pre-trained foundation models like DINO. However, so far, these object-centric methods have mostly been applied in-distribution, with models trained and evaluated on the same dataset. This is in contrast to the underlying foundation models, which have been shown to be applicable to a wide range of data and tasks. Thus, in this work, we answer the question of whether current real-world capable object-centric methods exhibit similar levels of transferability by introducing a benchmark comprising seven different synthetic and real-world datasets. We analyze the factors influencing performance under transfer and find that training on diverse real-world images improves generalization to unseen scenarios. Furthermore, inspired by the success of task-specific fine-tuning in foundation models, we introduce a novel fine-tuning strategy to adapt pre-trained vision encoders for the task of object discovery. We find that the proposed approach results in state-of-the-art performance for unsupervised object discovery, exhibiting strong zero-shot transfer to unseen datasets.

Deep Learning · Large Language Models

Minh Nguyen, Andrew Baker, Clement Neo, Allen Roush, Andreas Kirsch, Ravid Shwartz-Ziv

Large Language Models (LLMs) generate text by sampling the next token from a probability distribution over the vocabulary at each decoding step. Popular sampling methods like top-p (nucleus sampling) often struggle to balance quality and diversity, especially at higher temperatures which lead to incoherent or repetitive outputs. We propose min-p sampling, a dynamic truncation method that adjusts the sampling threshold based on the model's confidence by using the top token's probability as a scaling factor. Our experiments on benchmarks including GPQA, GSM8K, and AlpacaEval Creative Writing show that min-p sampling improves both the quality and diversity of generated text across different model families (Mistral and Llama 3) and model sizes (1B to 123B parameters), especially at higher temperatures. Human evaluations further show a clear preference for min-p sampling, in both text quality and creativity. Min-p sampling has been adopted by popular open-source LLM frameworks, including Hugging Face Transformers, VLLM, and many others, highlighting its significant impact on improving text generation quality.

Deep Learning · Large Language Models

Minh Nguyen, Andrew Baker, Clement Neo, Allen Roush, Andreas Kirsch, Ravid Shwartz-Ziv

Large Language Models (LLMs) generate text by sampling the next token from a probability distribution over the vocabulary at each decoding step. However, popular sampling methods like top-p (nucleus sampling) often struggle to balance quality and diversity, especially at higher temperatures, leading to incoherent or repetitive outputs. To address this challenge, we propose min-p sampling, a dynamic truncation method that adjusts the sampling threshold based on the model's confidence by scaling according to the top token's probability. We conduct extensive experiments on benchmarks including GPQA, GSM8K, and AlpacaEval Creative Writing, demonstrating that min-p sampling improves both the quality and diversity of generated text, particularly at high temperatures. Moreover, human evaluations reveal a clear preference for min-p sampling in terms of both text quality and diversity. Min-p sampling has been adopted by leading open-source LLM implementations including Hugging Face, VLLM and many others, highlighting its practical utility and potential impact.

Deep Learning · Generative Models and Autoencoders

Qijun Gan, Song Wang, Shengtao Wu, Jianke Zhu

Recently, artificial intelligence techniques for education have been received increasing attentions, while it still remains an open problem to design the effective music instrument instructing systems. Although key presses can be directly derived from sheet music, the transitional movements among key presses require more extensive guidance in piano performance. In this work, we construct a piano-hand motion generation benchmark to guide hand movements and fingerings for piano playing. To this end, we collect an annotated dataset, PianoMotion10M, consisting of 116 hours of piano playing videos from a bird's-eye view with 10 million annotated hand poses. We also introduce a powerful baseline model that generates hand motions from piano audios through a position predictor and a position-guided gesture generator. Furthermore, a series of evaluation metrics are designed to assess the performance of the baseline model, including motion similarity, smoothness, positional accuracy of left and right hands, and overall fidelity of movement distribution. Despite that piano key presses with respect to music scores or audios are already accessible, PianoMotion10M aims to provide guidance on piano fingering for instruction purposes. The source code and dataset can be accessed at https://github.com/agnJason/PianoMotion10M.

Panagiotis Theodoropoulos, Nikolaos Komianos, Vincent Pacelli, Guan-Horng Liu, Evangelos Theodorou

Recent advancements in diffusion bridges for distribution transport problems have heavily relied on matching frameworks, yet existing methods often face a trade-off between scalability and access to optimal pairings during training. Fully unsupervised methods make minimal assumptions but incur high computational costs, limiting their practicality. On the other hand, imposing full supervision of the matching process with optimal pairings improves scalability, however, it can be infeasible in most applications.To strike a balance between scalability and minimal supervision, we introduce Feedback Schrödinger Bridge Matching (FSBM), a novel semi-supervised matching framework that incorporates a small portion ($<8$% of the entire dataset) of pre-aligned pairs as state feedback to guide the transport map of non-coupled samples, thereby significantly improving efficiency. This is achieved by formulating a static Entropic Optimal Transport (EOT) problem with an additional term capturing the semi-supervised guidance. The generalized EOT objective is then recast into a dynamic formulation to leverage the scalability of matching frameworks. Extensive experiments demonstrate that FSBM accelerates training and enhances generalization by leveraging coupled pairs' guidance, opening new avenues for training matching frameworks with partially aligned datasets.

Panagiotis Theodoropoulos, Nikolaos Komianos, Vincent Pacelli, Guan-Horng Liu, Evangelos Theodorou

Recent advancements in diffusion bridges for distribution transport problems have heavily relied on matching frameworks, yet existing methods often face a trade-off between scalability and access to optimal pairings during training. Fully unsupervised methods make minimal assumptions but incur high computational costs, limiting their practicality. On the other hand, imposing full supervision of the matching process with optimal pairings improves scalability, however, it can be infeasible in most applications.To strike a balance between scalability and minimal supervision, we introduce Feedback Schrödinger Bridge Matching (FSBM), a novel semi-supervised matching framework that incorporates a small portion ($<8$% of the entire dataset) of pre-aligned pairs as state feedback to guide the transport map of non-coupled samples, thereby significantly improving efficiency. This is achieved by formulating a static Entropic Optimal Transport (EOT) problem with an additional term capturing the semi-supervised guidance. The generalized EOT objective is then recast into a dynamic formulation to leverage the scalability of matching frameworks. Extensive experiments demonstrate that FSBM accelerates training and enhances generalization by leveraging coupled pairs' guidance, opening new avenues for training matching frameworks with partially aligned datasets.

Kanika Madan, Alex Lamb, Emmanuel Bengio, Glen Berseth, Yoshua Bengio

Exploration is a key factor for the success of an active learning agent, especially when dealing with sparse extrinsic terminal rewards and long trajectories. We introduce Sibling Augmented Generative Flow Networks (SA-GFN), a novel framework designed to enhance exploration and training efficiency of Generative Flow Networks (GFlowNets). SA-GFN uses a decoupled dual network architecture, comprising of a main Behavior Network and an exploratory Sibling Network, to enable a diverse exploration of the underlying distribution using intrinsic rewards. Inspired by the ideas on exploration from reinforcement learning, SA-GFN provides a general-purpose exploration and learning paradigm that integrates with multiple GFlowNet training objectives and is especially helpful for exploration over a wide range of sparse or low reward distributions and task structures. An extensive set of experiments across a diverse range of tasks, reward structures and trajectory lengths, along with a thorough set of ablations, demonstrate the superior performance of SA-GFN in terms of exploration efficacy and convergence speed as compared to the existing methods. In addition, SA-GFN's versatility and compatibility with different GFlowNet training objectives and intrinsic reward methods underscores its broad applicability in various problem domains.

Theory · Reinforcement Learning and Planning

Audrey Huang, Wenhao Zhan, Tengyang Xie, Jason Lee, Wen Sun, Akshay Krishnamurthy, Dylan Foster

Language model alignment methods such as reinforcement learning from human feedback (RLHF) have led to impressive advances in language model capabilities, but are limited by a widely observed phenomenon known as *overoptimization*, where the quality of the language model degrades over the course of the alignment process. As the model optimizes performance on an offline reward model, it overfits to inaccuracies and drifts away from preferred responses covered by the data. To discourage such distribution shift, KL-regularization is widely employed in existing offline alignment methods, but overoptimization continues to harm performance. Lending theoretical insight into the source of these empirical observations, we first show that the KL-regularization is too weak to prevent overfitting, then ask: is it possible to design an efficient algorithm that is provably robust to overoptimization?In this paper, we advance theoretical understanding of sample-efficient offline alignment and introduce a new algorithm called $\chi^2$-Preference Optimization ($\chi$PO). $\chi$PO is a one-line change to Direct Preference Optimization (DPO; Rafailov et al. 2023), that modifies only the logarithmic link function in the DPO objective. Despite this minimal change, $\chi$PO implicitly implements the principle of *pessimism in the face of uncertainty* via regularization with the $\chi^2$-divergence---which quantifies uncertainty more effectively than KL-regularization---and provably alleviates overoptimization, achieving sample-complexity guarantees based on *single-policy concentrability*, the gold standard in offline reinforcement learning. This guarantee makes $\chi$PO the first simple, yet general-purpose offline alignment algorithm that is provably robust to overoptimization.

Applications · Computer Vision

Yankai Jiang, Wenhui Lei, Xiaofan Zhang, Shaoting Zhang

Recent advancements in medical vision-language pre-training models have driven significant progress in zero-shot disease recognition. However, transferring image-level knowledge to pixel-level tasks, such as lesion segmentation in 3D CT scans, remains a critical challenge. Due to the complexity and variability of pathological visual characteristics, existing methods struggle to align fine-grained lesion features not encountered during training with disease-related textual representations. In this paper, we present Malenia, a novel multi-scale lesion-level mask-attribute alignment framework, specifically designed for 3D zero-shot lesion segmentation. Malenia improves the compatibility between mask representations and their associated elemental attributes, explicitly linking the visual features of unseen lesions with the extensible knowledge learned from previously seen ones. Furthermore, we design a Cross-Modal Knowledge Injection module to enhance both visual and textual features with mutually beneficial information, effectively guiding the generation of segmentation results. Comprehensive experiments across three datasets and 12 lesion categories validate the superior performance of Malenia.

Applications · Health

Arvind Pillai, Dimitris Spathis, Fahim Kawsar, Mohammad Malekzadeh

Photoplethysmography (PPG) is the leading non-invasive technique for monitoring biosignals and cardiovascular health, with widespread adoption in both clinical settings and consumer wearable devices. While machine learning models trained on PPG signals have shown promise, they tend to be task-specific and struggle with generalization. Current research is limited by the use of single-device datasets, insufficient exploration of out-of-domain generalization, and a lack of publicly available models, which hampers reproducibility. To address these limitations, we present PaPaGei, the first open foundation model for PPG signals. The model is pre-trained on over 57,000 hours of data, comprising 20 million unlabeled PPG segments from publicly available datasets. We introduce a novel representation learning approach that leverages domain knowledge of PPG signal morphology across individuals, enabling the capture of richer representations compared to traditional contrastive learning methods. We evaluate PaPaGei against state-of-the-art time-series foundation models and self-supervised learning benchmarks across 20 tasks from 10 diverse datasets, spanning cardiovascular health, sleep disorders, pregnancy monitoring, and wellbeing assessment. Our model demonstrates superior performance, improving classification and regression metrics by 6.3% and 2.9% respectively in at least 14 tasks. Notably, PaPaGei achieves these results while being more data- and parameter-efficient, outperforming models that are 70x larger. Beyond accuracy, we examine model robustness across different skin tones, establishing a benchmark for bias evaluation in future models. PaPaGei can serve as both a feature extractor and an encoder for multimodal models, opening up new opportunities for multimodal health monitoring. Models, data, and code are available at: https://github.com/nokia-bell-labs/papagei-foundation-model

Applications · Neuroscience, Cognitive Science

Ziyu Lu, Wuwei Zhang, Trung Le, Hao Wang, Uygar Sümbül, Eric SheaBrown, Lu Mi

Neuronal dynamics are highly nonlinear and nonstationary. Traditional methods for extracting the underlying network structure from neuronal activity recordings mainly concentrate on modeling static connectivity, without accounting for key nonstationary aspects of biological neural systems, such as ongoing synaptic plasticity and neuronal modulation. To bridge this gap, we introduce the NetFormer model, an interpretable approach applicable to such systems. In NetFormer, the activity of each neuron across a series of historical time steps is defined as a token. These tokens are then linearly mapped through a query and key mechanism to generate a state- (and hence time-) dependent attention matrix that directly encodes nonstationary connectivity structures. We analyze our formulation from the perspective of nonstationary and nonlinear networked dynamical systems, and show both via an analytical expansion and targeted simulations how it can approximate the underlying ground truth. Next, we demonstrate NetFormer's ability to model a key feature of biological networks, spike-timing-dependent plasticity, whereby connection strengths continually change in response to local activity patterns. We further demonstrate that NetFormer can capture task-induced connectivity patterns on activity generated by task-trained recurrent neural networks. Thus informed, we apply NetFormer to a multi-modal dataset of real neural recordings, which contains neural activity, cell type, and behavioral state information. We show that the NetFormer effectively predicts neural dynamics and identifies cell-type specific, state-dependent dynamic connectivity that matches patterns measured in separate ground-truth physiology experiments, demonstrating its ability to help decode complex neural interactions based on population activity observations alone.

Reinforcement Learning · Everything Else

Wenye Li, Jiacai Liu, Ke Wei

Inspired by the similar update pattern of softmax natural policy gradient and Hadamard policy gradient, we propose to study a general policy update rule called $\phi$-update, where $\phi$ refers to a scaling function on advantage functions. Under very mild conditions on $\phi$, the global asymptotic state value convergence of $\phi$-update is firstly established. Then we show that the policy produced by $\phi$-update indeed converges, even when there are multiple optimal policies. This is in stark contrast to existing results where explicit regularizations are required to guarantee the convergence of the policy. Since softmax natural policy gradient is an instance of $\phi$-update, it provides an affirmative answer to the question whether the policy produced by softmax natural policy gradient converges. The exact asymptotic convergence rate of state values is further established based on the policy convergence. Lastly, we establish the global linear convergence of $\phi$-update.

Theory · Domain Adaptation and Transfer Learning

Zhen Zhang, Xin Liu, Shaoli Wang, Jiaye Teng

Covariate shift occurs when the distribution of input features differs between the training and testing phases. In covariate shift, estimating an unknown function's moment is a classical problem that remains under-explored, despite its common occurrence in real-world scenarios. In this paper, we investigate the minimax lower bound of the problem when the source and target distributions are known. To achieve the minimax optimal bound (up to a logarithmic factor), we propose a two-stage algorithm. Specifically, it first trains an optimal estimator for the function under the source distribution, and then uses a likelihood ratio reweighting procedure to calibrate the moment estimator. In practice, the source and target distributions are typically unknown, and estimating the likelihood ratio may be unstable. To solve this problem, we propose a truncated version of the estimator that ensures double robustness and provide the corresponding upper bound. Extensive numerical studies on synthetic examples confirm our theoretical findings and further illustrate the effectiveness of our proposed method.

Deep Learning · Other Representation Learning

Sanghyuk Chun, Wonjae Kim, Song Park, Sangdoo Yun

Vision-language models (VLMs) embed aligned image-text pairs into a joint space but often rely on deterministic embeddings, assuming a one-to-one correspondence between images and texts. This oversimplifies real-world relationships, which are inherently many-to-many, with multiple captions describing a single image and vice versa. We introduce Probabilistic Language-Image Pre-training (ProLIP), the first probabilistic VLM pre-trained on a billion-scale image-text dataset using only probabilistic objectives, achieving a strong zero-shot capability (e.g., 74.6% ImageNet zero-shot accuracy with ViT-B/16). ProLIP efficiently estimates uncertainty by an ``uncertainty token'' without extra parameters. We also introduce a novel inclusion loss that enforces distributional inclusion relationships between image-text pairs and between original and masked inputs. Experiments demonstrate that, by leveraging uncertainty estimates, ProLIP benefits downstream tasks and aligns with intuitive notions of uncertainty, e.g., shorter texts being more uncertain and more general inputs including specific ones. Utilizing text uncertainties, we further improve ImageNet accuracy from 74.6% to 75.8% (under a few-shot setting), supporting the practical advantages of our probabilistic approach. The code is available at https://github.com/naver-ai/prolip