ICLR 2025 论文列表

The interrogation of cellular states and interactions in immunology research is an ever-evolving task, requiring adaptation to the current levels of high dimensionality. Cytometry enables high-dimensional profiling of immune cells, but its analysis is hindered by the complexity and variability of the data. We present MAESTRO, a self-supervised set representation learning model that generates vector representations of set-structured data, which we apply to learn immune profiles from cytometry data. Unlike previous studies only learn cell-level representations, whereas MAESTRO uses all of a sample's cells to learn a set representation. MAESTRO leverages specialized attention mechanisms to handle sets of variable number of cells and ensure permutation invariance, coupled with an online tokenizer by self-distillation framework. We benchmarked our model against existing cytometry approaches and other existing machine learning methods that have never been applied in cytometry. Our model outperforms existing approaches in retrieving cell-type proportions and capturing clinically relevant features for downstream tasks such as disease diagnosis and immune cell profiling.

The performance of unsupervised methods such as clustering depends on the choice of distance metric between features, or ground metric. Commonly, ground metrics are decided with heuristics or learned via supervised algorithms. However, since many interesting datasets are unlabelled, unsupervised ground metric learning approaches have been introduced. One promising option employs Wasserstein singular vectors (WSVs), which emerge when computing optimal transport distances between features and samples simultaneously. WSVs are effective, but can be prohibitively computationally expensive in some applications: $\mathcal{O}(n^2m^2(n \log(n) + m \log(m))$ for $n$ samples and $m$ features. In this work, we propose to augment the WSV method by embedding samples and features on trees, on which we compute the tree-Wasserstein distance (TWD). We demonstrate theoretically and empirically that the algorithm converges to a better approximation of the standard WSV approach than the best known alternatives, and does so with $\mathcal{O}(n^3+m^3+mn)$ complexity. In addition, we prove that the initial tree structure can be chosen flexibly, since tree geometry does not constrain the richness of the approximation up to the number of edge weights. This proof suggests a fast and recursive algorithm for computing the tree parameter basis set, which we find crucial to realising the efficiency gains at scale. Finally, we employ the tree-WSV algorithm to several single-cell RNA sequencing genomics datasets, demonstrating its scalability and utility for unsupervised cell-type clustering problems. These results poise unsupervised ground metric learning with TWD as a low-rank approximation of WSV with the potential for widespread application.

$\textit{Cis}$-regulatory elements (CREs), such as promoters and enhancers, are relatively short DNA sequences that directly regulate gene expression. The fitness of CREs, measured by their ability to modulate gene expression, highly depends on the nucleotide sequences, especially specific motifs known as transcription factor binding sites (TFBSs). Designing high-fitness CREs is crucial for therapeutic and bioengineering applications. Current CRE design methods are limited by two major drawbacks: (1) they typically rely on iterative optimization strategies that modify existing sequences and are prone to local optima, and (2) they lack the guidance of biological prior knowledge in sequence optimization. In this paper, we address these limitations by proposing a generative approach that leverages reinforcement learning (RL) to fine-tune a pre-trained autoregressive (AR) model. Our method incorporates data-driven biological priors by deriving computational inference-based rewards that simulate the addition of activator TFBSs and removal of repressor TFBSs, which are then integrated into the RL process. We evaluate our method on promoter design tasks in two yeast media conditions and enhancer design tasks for three human cell types, demonstrating its ability to generate high-fitness CREs while maintaining sequence diversity. The code is available at https://github.com/yangzhao1230/TACO.

As a neural network's depth increases, it can improve generalization performance. However, training deep networks is challenging due to gradient and signal propagation issues. To address these challenges, extensive theoretical research and various methods have been introduced. Despite these advances, effective weight initialization methods for tanh neural networks remain insufficiently investigated. This paper presents a novel weight initialization method for neural networks with tanh activation function. Based on an analysis of the fixed points of the function $\tanh(ax)$, the proposed method aims to determine values of $a$ that mitigate activation saturation. A series of experiments on various classification datasets and physics-informed neural networks demonstrates that the proposed method outperforms Xavier initialization methods (with or without normalization) in terms of robustness across different network sizes, data efficiency, and convergence speed. Code is available at https://github.com/1HyunwooLee/Tanh-Init.

The group of permutations $S_n$, also known as the finite symmetric groups, are essential in fields such as combinatorics, physics, and chemistry. However, learning a probability distribution over $S_n$ poses significant challenges due to its intractable size and discrete nature. In this paper, we introduce *SymmetricDiffusers*, a novel discrete diffusion model that simplifies the task of learning a complicated distribution over $S_n$ by decomposing it into learning simpler transitions of the reverse diffusion using deep neural networks. We identify the riffle shuffle as an effective forward transition and provide empirical guidelines for selecting the diffusion length based on the theory of random walks on finite groups. Additionally, we propose a generalized Plackett-Luce (PL) distribution for the reverse transition, which is provably more expressive than the PL distribution. We further introduce a theoretically grounded "denoising schedule" to improve sampling and learning efficiency. Extensive experiments show that our model achieves state-of-the-art or comparable performance on solving tasks including sorting 4-digit MNIST images, jigsaw puzzles, and traveling salesman problems. Our code is released at <https://github.com/DSL-Lab/SymmetricDiffusers>.

To build effective therapeutics, biologists iteratively mutate antibody sequences to improve binding and stability. Proposed mutations can be informed by previous measurements or by learning from large antibody databases to predict only typical antibodies. Unfortunately, the space of typical antibodies is enormous to search, and experiments often fail to find suitable antibodies on a budget. We introduce Clone-informed Bayesian Optimization (CloneBO), a Bayesian optimization procedure that efficiently optimizes antibodies in the lab by teaching a generative model how our immune system optimizes antibodies. Our immune system makes antibodies by iteratively evolving specific portions of their sequences to bind their target strongly and stably, resulting in a set of related, evolving sequences known as a *clonal family*. We train a large language model, CloneLM, on hundreds of thousands of clonal families and use it to design sequences with mutations that are most likely to optimize an antibody within the human immune system. We propose to guide our designs to fit previous measurements with a twisted sequential Monte Carlo procedure. We show that CloneBO optimizes antibodies substantially more efficiently than previous methods in realistic *in silico* experiments and designs stronger and more stable binders in *in vitro* wet lab experiments.

Large Language Models fine-tuned with Reinforcement Learning from Human Feedback (RLHF-LLMs) can over-rely on aligned preferences without truly gaining self-knowledge, leading to hallucination and biases. If an LLM can better access its knowledge and know what it knows, it can avoid making false or unsupported claims. Therefore, it is crucial to evaluate whether LLMs have the ability to know what they know, as it can help to ensure accuracy and faithfulness in real-world applications. Inspired by research in Educational Psychology, surface learners who don’t really know are easily affected by teacher and peer guidance, we treat LLM as a student, incorporate role guidance in prompts to explore whether LLMs really know. Specifically, we propose a novel strategy called Role-Guided and Self-Reflection (RoSe) to fully assess whether LLM “knows it knows”. We introduce multiple combinations of different roles and strong reminder in prompts combined with self-reflection to explore what local information in prompt LLMs rely on and whether LLMs remain unaffected by external guidance with varying roles. Our findings reveal that LLMs are very sensitive to the strong reminder information. Role guidance can help LLMs reduce their reliance on strong reminder. Meanwhile, LLMs tend to trust the role of authority more when guided by different roles. Following these findings, we propose a double-calibrated strategy with verbalized confidence to extract well-calibrated data from closed-source LLM and fine-tune open-source LLMs. Extensive experiments conducted on fine-tuning open-source LLMs demonstrate the effectiveness of double-calibrated strategy in mitigating the reliance of LLMs on local information. For a thorough comparison, we not only employ public JEC-QA and openBookQA datasets, but also construct EG-QA which contains English Grammar multiple-choice question-answering and 14 key knowledge points for assessing self-knowledge and logical reasoning.

RNA is a dynamic biomolecule crucial for cellular regulation, with its function largely determined by its folding into complex structures, while misfolding can lead to multifaceted biological sequelae. During the folding process, RNA traverses through a series of intermediate structural states, with each transition occurring at variable rates that collectively influence the time required to reach the functional form. Understanding these folding kinetics is vital for predicting RNA behavior and optimizing applications in synthetic biology and drug discovery. While in silico kinetic RNA folding simulators are often computationally intensive and time-consuming, accurate approximations of the folding times can already be very informative to assess the efficiency of the folding process. In this work, we present KinPFN, a novel approach that leverages prior-data fitted networks to directly model the posterior predictive distribution of RNA folding times. By training on synthetic data representing arbitrary prior folding times, KinPFN efficiently approximates the cumulative distribution function of RNA folding times in a single forward pass, given only a few initial folding time examples. Our method offers a modular extension to existing RNA kinetics algorithms, promising significant computational speed-ups orders of magnitude faster, while achieving comparable results. We showcase the effectiveness of KinPFN through extensive evaluations and real-world case studies, demonstrating its potential for RNA folding kinetics analysis, its practical relevance, and generalization to other biological data.

RNA secondary structure prediction is critical for understanding RNA function but remains challenging due to complex structural elements like pseudoknots and limited training data. We introduce DEPfold, a novel deep learning approach that re-frames RNA secondary structure prediction as a dependency parsing problem. DEPfold presents three key innovations: (1) a biologically motivated transformation of RNA structures into labeled dependency trees, (2) a biaffine attention mechanism for joint prediction of base pairings and their types, and (3) an optimal tree decoding algorithm that enforces valid RNA structural constraints. Unlike traditional energy-based methods, DEPfold learns directly from annotated data and leverages pretrained language models to predict RNA structure. We evaluate DEPfold on both within-family and cross-family RNA datasets, demonstrating significant performance improvements over existing methods. DEPfold shows strong performance in cross-family generalization when trained on data augmented by traditional energy-based models, outperforming existing methods on the bpRNAnew dataset. This demonstrates DEPfold’s ability to effectively learn structural information beyond what traditional methods capture. Our approach bridges natural language processing (NLP) with RNA biology, providing a computationally efficient and adaptable tool for advancing RNA structure prediction and analysis

Parametric differential equations of the form $\frac{\partial u}{\partial t} = f(u, x, t, p)$ are fundamental in science and engineering. While deep learning frameworks like the Fourier Neural Operator (FNO) efficiently approximate differential equation solutions, they struggle with inverse problems, sensitivity calculations $\frac{\partial u}{\partial p}$, and concept drift. We address these challenges by introducing a novel sensitivity loss regularizer, demonstrated through Sensitivity-Constrained Fourier Neural Operators (SC-FNO). Our approach maintains high accuracy for solution paths and outperforms both standard FNO and FNO with Physics-Informed Neural Network regularization. SC-FNO exhibits superior performance in parameter inversion tasks, accommodates more complex parameter spaces (tested with up to 82 parameters), reduces training data requirements, and decreases training time while maintaining accuracy. These improvements apply across various differential equations and neural operators, enhancing their reliability without significant computational overhead (30%–130% extra training time per epoch). Models and selected experiment code are available at: [https://github.com/AMBehroozi/SC_Neural_Operators](https://github.com/AMBehroozi/SC_Neural_Operators).

The reconstruction of physical fields from sparse measurements is pivotal in both scientific research and engineering applications. Traditional methods are increasingly supplemented by deep learning models due to their efficacy in extracting features from data. However, except for the low accuracy on complex physical systems, these models often fail to comply with essential physical constraints, such as governing equations and boundary conditions. To overcome this limitation, we introduce a novel data-driven field reconstruction framework, termed the Physics-aligned Schr\"{o}dinger Bridge (PalSB). This framework leverages a diffusion bridge mechanism that is specifically tailored to align with physical constraints. The PalSB approach incorporates a dual-stage training process designed to address both local reconstruction mapping and global physical principles. Additionally, a boundary-aware sampling technique is implemented to ensure adherence to physical boundary conditions. We demonstrate the effectiveness of PalSB through its application to three complex nonlinear systems: cylinder flow from Particle Image Velocimetry experiments, two-dimensional turbulence, and a reaction-diffusion system. The results reveal that PalSB not only achieves higher accuracy but also exhibits enhanced compliance with physical constraints compared to existing methods. This highlights PalSB's capability to generate high-quality representations of intricate physical interactions, showcasing its potential for advancing field reconstruction techniques. The source code can be found at https://github.com/lzy12301/PalSB.

Classification tasks play a fundamental role in various applications, spanning domains such as healthcare, natural language processing and computer vision. With the growing popularity and capacity of machine learning models, people can easily access trained classifiers as a service online or offline. However, model use comes with a cost and classifiers of higher capacity (such as large foundation models) usually incur higher inference costs. To harness the respective strengths of different classifiers, we propose a principled approach, OCCAM, to compute the best classifier assignment strategy over classification queries (termed as the optimal model portfolio) so that the aggregated accuracy is maximized, under user-specified cost budgets. Our approach uses an unbiased and low-variance accuracy estimator and effectively computes the optimal solution by solving an integer linear programming problem. On a variety of real-world datasets, OCCAM achieves 40% cost reduction with little to no accuracy drop.

Neural network-based odometry using accelerometer and gyroscope readings from a single IMU can achieve robust, and low-drift localization capabilities, through the use of _neural displacement priors (NDPs)_. These priors learn to produce denoised displacement measurements but need to ignore data variations due to specific IMU mount orientation and motion directions, hindering generalization. This work introduces EqNIO, which addresses this challenge with _canonical displacement priors_, i.e., priors that are invariant to the orientation of the gravity-aligned frame in which the IMU data is expressed. We train such priors on IMU measurements, that are mapped into a learnable canonical frame, which is uniquely defined via three axes: the first is gravity, making the frame gravity aligned, while the second and third are predicted from IMU data. The outputs (displacement and covariance) are mapped back to the original gravity-aligned frame. To maximize generalization, we find that these learnable frames must transform equivariantly with global gravity-preserving roto-reflections from the subgroup $O_g(3)\subset O(3)$, acting on the trajectory, rendering the NDP $O(3)$-_subequivariant_. We tailor specific linear, convolutional, and non-linear layers that commute with the actions of the group. Moreover, we introduce a bijective decomposition of angular rates into vectors that transform similarly to accelerations, allowing us to leverage both measurement types. Natively, angular rates would need to be inverted upon reflection, unlike acceleration, which hinders their joint processing. We highlight EqNIO's flexibility and generalization capabilities by applying it to both filter-based (TLIO), and end-to-end (RONIN) architectures, and outperforming existing methods that use _soft equivariance from auxiliary losses or data augmentation on various datasets. We believe this work paves the way for low-drift and generalizable neural inertial odometry on edge devices. The project details and code can be found at [https://github.com/RoyinaJayanth/EqNIO](https://github.com/RoyinaJayanth/EqNIO).

Why do biological and artificial neurons sometimes modularise, each encoding a single meaningful variable, and sometimes entangle their representation of many variables? In this work, we develop a theory of when biologically inspired networks---those that are nonnegative and energy efficient---modularise their representation of source variables (sources). We derive necessary and sufficient conditions on a sample of sources that determine whether the neurons in an optimal biologically-inspired linear autoencoder modularise. Our theory applies to any dataset, extending far beyond the case of statistical independence studied in previous work. Rather we show that sources modularise if their support is ``sufficiently spread''. From this theory, we extract and validate predictions in a variety of empirical studies on how data distribution affects modularisation in nonlinear feedforward and recurrent neural networks trained on supervised and unsupervised tasks. Furthermore, we apply these ideas to neuroscience data, showing that range independence can be used to understand the mixing or modularising of spatial and reward information in entorhinal recordings in seemingly conflicting experiments. Further, we use these results to suggest alternate origins of mixed-selectivity, beyond the predominant theory of flexible nonlinear classification. In sum, our theory prescribes precise conditions on when neural activities modularise, providing tools for inducing and elucidating modular representations in brains and machines.

Recent years have witnessed a surge in the development of protein foundation models, significantly improving performance in protein prediction and generative tasks ranging from 3D structure prediction and protein design to conformational dynamics. However, the capabilities and limitations associated with these models remain poorly understood due to the absence of a unified evaluation framework. To fill this gap, we introduce ProteinBench, a holistic evaluation framework designed to enhance the transparency of protein foundation models. Our approach consists of three key components: (i) A taxonomic classification of tasks that broadly encompass the main challenges in the protein domain, based on the relationships between different protein modalities; (ii) A multi-metric evaluation approach that assesses performance across four key dimensions: quality, novelty, diversity, and robustness; and (iii) In-depth analyses from various user objectives, providing a holistic view of model performance. Our comprehensive evaluation of protein foundation models reveals several key findings that shed light on their current capabilities and limitations. To promote transparency and facilitate further research, we release the evaluation dataset, code, and a public leaderboard publicly for further analysis and a general modular toolkit. We intend for ProteinBench to be a living benchmark for establishing a standardized, in-depth evaluation framework for protein foundation models, driving their development and application while fostering collaboration within the field.

Predicting drug efficacy and safety in vivo requires information on biological responses (e.g., cell morphology and gene expression) to small molecule perturbations. However, current molecular representation learning methods do not provide a comprehensive view of cell states under these perturbations and struggle to remove noise, hindering model generalization. We introduce the Information Alignment (InfoAlign) approach to learn molecular representations through the information bottleneck method in cells. We integrate molecules and cellular response data as nodes into a context graph, connecting them with weighted edges based on chemical, biological, and computational criteria. For each molecule in a training batch, InfoAlign optimizes the encoder's latent representation with a minimality objective to discard redundant structural information. A sufficiency objective decodes the representation to align with different feature spaces from the molecule's neighborhood in the context graph. We demonstrate that the proposed sufficiency objective for alignment is tighter than existing encoder-based contrastive methods. Empirically, we validate representations from InfoAlign in two downstream applications: molecular property prediction against up to 27 baseline methods across four datasets, plus zero-shot molecule-morphology matching. The code and model are available at https://github.com/liugangcode/InfoAlign.

The Gromov–Wasserstein (GW) problem, a variant of the classical optimal transport (OT) problem, has attracted growing interest in the machine learning and data science communities due to its ability to quantify similarity between measures in different metric spaces. However, like the classical OT problem, GW imposes an equal mass constraint between measures, which restricts its application in many machine learning tasks. To address this limitation, the partial Gromov-Wasserstein (PGW) problem has been introduced. It relaxes the equal mass constraint, allowing the comparison of general positive Radon measures. Despite this, both GW and PGW face significant computational challenges due to their non-convex nature. To overcome these challenges, we propose the linear partial Gromov-Wasserstein (LPGW) embedding, a linearized embedding technique for the PGW problem. For $K$ different metric measure spaces, the pairwise computation of the PGW distance requires solving the PGW problem $\mathcal{O}(K^2)$ times. In contrast, the proposed linearization technique reduces this to $\mathcal{O}(K)$ times. Similar to the linearization technique for the classical OT problem, we prove that LPGW defines a valid metric for metric measure spaces. Finally, we demonstrate the effectiveness of LPGW in practical applications such as shape retrieval and learning with transport-based embeddings, showing that LPGW preserves the advantages of PGW in partial matching while significantly enhancing computational efficiency. The code is available at https://github.com/mint-vu/Linearized_Partial_Gromov_Wasserstein.

Personalized federated learning (PFL) achieves high performance by assuming clients only meet test data locally, which does not meet many generic federated learning (GFL) scenarios. In this work, we theoretically show that PMs can be used to enhance GFL with a new learning problem named Selective FL (SFL), which involves optimizing PFL and model selection. However, storing and selecting whole models requires impractical computation and communication costs. To practically solve SFL, inspired by model components that attempt to edit a sub-model for specific purposes, we design an efficient and effective framework named Hot-Pluggable Federated Learning (HPFL). Specifically, clients individually train personalized plug-in modules based on a shared backbone, and upload them with a plug-in marker on the server modular store. In inference stage, an accurate selection algorithm allows clients to identify and retrieve suitable plug-in modules from the modular store to enhance their generalization performance on the target data distribution. Furthermore, we provide differential privacy protection during the selection with theoretical guarantee. Our comprehensive experiments and ablation studies demonstrate that HPFL significantly outperforms state-of-the-art GFL and PFL algorithms. Additionally, we empirically show HPFL's remarkable potential to resolve other practical FL problems such as continual federated learning and discuss its possible applications in one-shot FL, anarchic FL, and FL plug-in market. Our work is the first attempt towards improving GFL performance through a selecting mechanism with personalized plug-ins.

Weak gravitational lensing is the slight distortion of galaxy shapes caused primarily by the gravitational effects of dark matter in the universe. In our work, we seek to invert the weak lensing signal from 2D telescope images to reconstruct a 3D map of the universe's dark matter field. While inversion typically yields a 2D projection of the dark matter field, accurate 3D maps of the dark matter distribution are essential for localizing structures of interest and testing theories of our universe. However, 3D inversion poses significant challenges. First, unlike standard 3D reconstruction that relies on multiple viewpoints, in this case, images are only observed from a single viewpoint. This challenge can be partially addressed by observing how galaxy emitters throughout the volume are lensed. However, this leads to the second challenge: the shapes and exact locations of unlensed galaxies are unknown, and can only be estimated with a very large degree of uncertainty. This introduces an overwhelming amount of noise which nearly drowns out the lensing signal completely. Previous approaches tackle this by imposing strong assumptions about the structures in the volume. We instead propose a methodology using a gravitationally-constrained neural field to flexibly model the continuous matter distribution. We take an analysis-by-synthesis approach, optimizing the weights of the neural network through a fully differentiable physical forward model to reproduce the lensing signal present in image measurements. We showcase our method on simulations, including realistic simulated measurements of dark matter distributions that mimic data from upcoming telescope surveys. Our results show that our method can not only outperform previous methods, but importantly is also able to recover potentially surprising dark matter structures.