ICLR 2025 Papers

Modern recordings of neural activity provide diverse observations of neurons across brain areas, behavioral conditions, and subjects; presenting an exciting opportunity to reveal the fundamentals of brain-wide dynamics. Current analysis methods, however, often fail to fully harness the richness of such data, as they provide either uninterpretable representations (e.g., via deep networks) or oversimplify models (e.g., by assuming stationary dynamics or analyzing each session independently). Here, instead of regarding asynchronous neural recordings that lack alignment in neural identity or brain areas as a limitation, we leverage these diverse views into the brain to learn a unified model of neural dynamics. Specifically, we assume that brain activity is driven by multiple hidden global sub-circuits. These sub-circuits represent global basis interactions between neural ensembles—functional groups of neurons—such that the time-varying decomposition of these sub-circuits defines how the ensembles' interactions evolve over time non-stationarily and non-linearly. We discover the neural ensembles underlying non-simultaneous observations, along with their non-stationary evolving interactions, with our new model, **CREIMBO** (**C**ross-**R**egional **E**nsemble **I**nteractions in **M**ulti-view **B**rain **O**bservations). CREIMBO identifies the hidden composition of per-session neural ensembles through novel graph-driven dictionary learning and models the ensemble dynamics on a low-dimensional manifold spanned by a sparse time-varying composition of the global sub-circuits. Thus, CREIMBO disentangles overlapping temporal neural processes while preserving interpretability due to the use of a shared underlying sub-circuit basis. Moreover, CREIMBO distinguishes session-specific computations from global (session-invariant) ones by identifying session covariates and variations in sub-circuit activations. We demonstrate CREIMBO's ability to recover true components in synthetic data, and uncover meaningful brain dynamics in human high-density electrode recordings, including cross-subject neural mechanisms as well as inter- vs. intra-region dynamical motifs. Furthermore, using mouse whole-brain recordings, we show CREIMBO's ability to discover dynamical interactions that capture task and behavioral variables and meaningfully align with the biological importance of the brain areas they represent.

In spite of finite dimension ReLU neural networks being a consistent factor behind recent deep learning successes, a theory of feature learning in these models remains elusive. Currently, insightful theories still rely on assumptions including the linearity of the network computations, unstructured input data and architectural constraints such as infinite width or a single hidden layer. To begin to address this gap we establish an equivalence between ReLU networks and Gated Deep Linear Networks, and use their greater tractability to derive dynamics of learning. We then consider multiple variants of a core task reminiscent of multi-task learning or contextual control which requires both feature learning and nonlinearity. We make explicit that, for these tasks, the ReLU networks possess an inductive bias towards latent representations which are *not* strictly modular or disentangled but are still highly structured and reusable between contexts. This effect is amplified with the addition of more contexts and hidden layers. Thus, we take a step towards a theory of feature learning in finite ReLU networks and shed light on how structured mixed-selective latent representations can emerge due to a bias for node-reuse and learning speed.

The increasing size of screening libraries poses a significant challenge for the development of virtual screening methods for drug discovery, necessitating a re-evaluation of traditional approaches in the era of big data. Although 3D pharmacophore screening remains a prevalent technique, its application to very large datasets is limited by the computational cost associated with matching query pharmacophores to database molecules. In this study, we introduce PharmacoMatch, a novel contrastive learning approach based on neural subgraph matching. Our method reinterprets pharmacophore screening as an approximate subgraph matching problem and enables efficient querying of conformational databases by encoding query-target relationships in the embedding space. We conduct comprehensive investigations of the learned representations and evaluate PharmacoMatch as pre-screening tool in a zero-shot setting. We demonstrate significantly shorter runtimes and comparable performance metrics to existing solutions, providing a promising speed-up for screening very large datasets.

Semi-supervised learning (SSL), exemplified by FixMatch (Sohn et al., 2020), has shown significant generalization advantages over supervised learning (SL), particularly in the context of deep neural networks (DNNs). However, it is still unclear, from a theoretical standpoint, why FixMatch-like SSL algorithms generalize better than SL on DNNs. In this work, we present the first theoretical justification for the enhanced test accuracy observed in FixMatch-like SSL applied to DNNs by taking convolutional neural networks (CNNs) on classification tasks as an example. Our theoretical analysis reveals that the semantic feature learning processes in FixMatch and SL are rather different. In particular, FixMatch learns all the discriminative features of each semantic class, while SL only randomly captures a subset of features due to the well-known lottery ticket hypothesis. Furthermore, we show that our analysis framework can be applied to other FixMatch-like SSL methods, e.g., FlexMatch, FreeMatch, Dash, and SoftMatch. Inspired by our theoretical analysis, we develop an improved variant of FixMatch, termed Semantic-Aware FixMatch (SA-FixMatch). Experimental results corroborate our theoretical findings and the enhanced generalization capability of SA-FixMatch.

This paper investigates the fundamental regression task of learning $k$ neurons (\emph{a.k.a.} teachers) from Gaussian input, using two-layer ReLU neural networks with width $m$ (\emph{a.k.a.} students) and $m, k= \mathcal{O}(1)$, trained via gradient descent under proper initialization and a small step-size. Our analysis follows a three-phase structure: \emph{alignment} after weak recovery, \emph{tangential growth}, and \emph{local convergence}, providing deeper insights into the learning dynamics of gradient descent (GD). We prove the global convergence at the rate of $\mathcal{O}(T^{-3})$ for the zero loss of excess risk. Additionally, our results show that GD automatically groups and balances student neurons, revealing an implicit bias toward achieving the minimum ``balanced'' $\ell_2$-norm in the solution. Our work extends beyond previous studies in exact-parameterization setting ($m = k = 1$, (Yehudai and Ohad, 2020)) and single-neuron setting ($m \geq k = 1$, (Xu and Du, 2023)). The key technical challenge lies in handling the interactions between multiple teachers and students during training, which we address by refining the alignment analysis in Phase 1 and introducing a new dynamic system analysis for tangential components in Phase 2. Our results pave the way for further research on optimizing neural network training dynamics and understanding implicit biases in more complex architectures.

3D Gaussian Splatting (3DGS) has shown promising results for Novel View Synthesis. However, while it is quite effective when based on high-quality images, its performance declines as image quality degrades, due to lack of resolution, motion blur, noise, compression artifacts, or other factors common in real-world data collection. While some solutions have been proposed for specific types of degradation, general techniques are still missing. To address the problem, we propose a robust HQGS that significantly enhances the 3DGS under various degradation scenarios. We first analyze that 3DGS lacks sufficient attention in some detailed regions in low-quality scenes, leading to the absence of Gaussian primitives in those areas and resulting in loss of detail in the rendered images. To address this issue, we focus on leveraging edge structural information to provide additional guidance for 3DGS, enhancing its robustness. First, we introduce an edge-semantic fusion guidance module that combines rich texture information from high-frequency edge-aware maps with semantic information from images. The fused features serve as prior guidance to capture detailed distribution across different regions, bringing more attention to areas with detailed edge information and allowing for a higher concentration of Gaussian primitives to be assigned to such areas. Additionally, we present a structural cosine similarity loss to complement pixel-level constraints, further improving the quality of the rendered images. Extensive experiments demonstrate that our method offers better robustness and achieves the best results across various degraded scenes. Source code and trained models are publicly available at: \url{https://github.com/linxin0/HQGS}.

In systems control, the dynamics of a system are governed by modulating its inputs to achieve a desired outcome. For example, to control the thrust of a quad-copter propeller the controller modulates its rotation rate, relying on a straightforward mapping between the input rotation rate and the resulting thrust. This mapping can be inverted to determine the rotation rate needed to generate a desired thrust. However, in complex systems, such as flapping-wing robots where intricate fluid motions are involved, mapping inputs (wing kinematics) to outcomes (aerodynamic forces) is nontrivial and inverting this mapping for real-time control is computationally impractical. Here, we report a machine-learning solution for the inverse mapping of a flapping-wing system based on data from an experimental system we have developed. Our model learns the input wing motion required to generate a desired aerodynamic force outcome. We used a sequence-to-sequence model tailored for time-series data and augmented it with a novel adaptive-spectrum layer that implements representation learning in the frequency domain. To train our model, we developed a flapping wing system that simultaneously measures the wing's aerodynamic force and its 3D motion using high-speed cameras. We demonstrate the performance of our system on an additional open-source dataset of a flapping wing in a different flow regime. Results show superior performance compared with more complex state-of-the-art transformer-based models, with 11\% improvement on the test datasets median loss. Moreover, our model shows superior inference time, making it practical for onboard robotic control. Our open-source data and framework may improve modeling and real-time control of systems governed by complex dynamics, from biomimetic robots to biomedical devices.

Do large language models (LLMs) have theory of mind? A plethora of papers and benchmarks have been introduced to evaluate if current models have been able to develop this key ability of social intelligence. However, all rely on limited datasets with simple patterns that can potentially lead to problematic blind spots in evaluation and an overestimation of model capabilities. We introduce ExploreToM, the first framework to allow large-scale generation of diverse and challenging theory of mind data for robust training and evaluation. Our approach leverages an A* search over a custom domain-specific language to produce complex story structures and novel, diverse, yet plausible scenarios to stress test the limits of LLMs. Our evaluation reveals that state-of-the-art LLMs, such as Llama-3.1-70B and GPT-4o, show accuracies as low as 0% and 9% on ExploreToM-generated data, highlighting the need for more robust theory of mind evaluation. As our generations are a conceptual superset of prior work, fine-tuning on our data yields a 27-point accuracy improvement on the classic ToMi benchmark (Le et al., 2019). ExploreToM also enables uncovering underlying skills and factors missing for models to show theory of mind, such as unreliable state tracking or data imbalances, which may contribute to models' poor performance on benchmarks.

Semantic text embedding is essential to many tasks in Natural Language Processing (NLP). While black-box models are capable of generating high-quality embeddings, their lack of interpretability limits their use in tasks that demand transparency. Recent approaches have improved interpretability by leveraging domain-expert-crafted or LLM-generated questions, but these methods rely heavily on expert input or well-prompt design, which restricts their generalizability and ability to generate discriminative questions across a wide range of tasks. To address these challenges, we introduce \algo{CQG-MBQA} (Contrastive Question Generation - Multi-task Binary Question Answering), a general framework for producing interpretable semantic text embeddings across diverse tasks. Our framework systematically generates highly discriminative, low cognitive load yes/no questions through the \algo{CQG} method and answers them efficiently with the \algo{MBQA} model, resulting in interpretable embeddings in a cost-effective manner. We validate the effectiveness and interpretability of \algo{CQG-MBQA} through extensive experiments and ablation studies, demonstrating that it delivers embedding quality comparable to many advanced black-box models while maintaining inherently interpretability. Additionally, \algo{CQG-MBQA} outperforms other interpretable text embedding methods across various downstream tasks. The source code is available at \url{https://github.com/dukesun99/CQG-MBQA}.

Ranking of vertices in a graph for different objectives is one of the most fundamental tasks in computer science. It is known that traditional ranking algorithms can generate unbalanced ranking when the graph has underlying communities, resulting in loss of information, polarised opinions, and reduced diversity (Celis, Straszak \& Vishnoi [ICALP 2018]). In this paper, we focus on *unsupervised ranking* on graphs and observe that popular centrality measure based ranking algorithms such as PageRank may often generate unbalanced ranking here as well. We address this issue by coining a new approach, which we term *relative centrality*. Our approach is based on an iterative graph-dependent local normalization of the centrality score, which promotes balancedness while maintaining the validity of the ranking. We further quantify reasons behind this unbalancedness of centrality measures on a novel structure that we propose is called multi-core-periphery with communities (MCPC). We also provide theoretical and extensive simulation support for our approach towards resolving the unbalancedness in MCPC. Finally, we consider graph embeddings of $11$ single-cell datasets. We observe that top-ranked as per existing centrality measures are better separable into the ground truth communities. However, due to the unbalanced ranking, the top nodes often do not contain points from some communities. Here, our relative-centrality-based approach generates a ranking that provides a similar improvement in clusterability while providing significantly higher balancedness.

The loss of plasticity in learning agents, analogous to the solidification of neural pathways in biological brains, significantly impedes learning and adaptation in reinforcement learning due to its non-stationary nature. To address this fundamental challenge, we propose a novel approach, *Neuroplastic Expansion* (NE), inspired by cortical expansion in cognitive science. NE maintains learnability and adaptability throughout the entire training process by dynamically growing the network from a smaller initial size to its full dimension. Our method is designed with three key components: (1) elastic neuron generation based on potential gradients, (2) dormant neuron pruning to optimize network expressivity, and (3) neuron consolidation via experience review to strike a balance in the plasticity-stability dilemma. Extensive experiments demonstrate that NE effectively mitigates plasticity loss and outperforms state-of-the-art methods across various tasks in MuJoCo and DeepMind Control Suite environments. NE enables more adaptive learning in complex, dynamic environments, which represents a crucial step towards transitioning deep reinforcement learning from static, one-time training paradigms to more flexible, continually adapting models.

Patient data is widely used to estimate heterogeneous treatment effects and understand the effectiveness and safety of drugs. Yet, patient data includes highly sensitive information that must be kept private. In this work, we aim to estimate the conditional average treatment effect (CATE) from observational data under differential privacy. Specifically, we present DP-CATE, a novel framework for CATE estimation that is *Neyman-orthogonal* and ensures *differential privacy* of the estimates. Our framework is highly general: it applies to any two-stage CATE meta-learner with a Neyman-orthogonal loss function and any machine learning model can be used for nuisance estimation. We further provide an extension of our DP-CATE, where we employ RKHS regression to release the complete CATE function while ensuring differential privacy. We demonstrate the effectiveness of DP-CATE across various experiments using synthetic and real-world datasets. To the best of our knowledge, we are the first to provide a framework for CATE estimation that is doubly robust and differentially private.

Rank collapse, a phenomenon where embedding vectors in sequence models rapidly converge to a uniform token or equilibrium state, has recently gained at- tention in the deep learning literature. This phenomenon leads to reduced expres- sivity and potential training instabilities due to vanishing gradients. Empirical ev- idence suggests that architectural components like skip connections, LayerNorm, and MultiLayer Perceptrons (MLPs) play critical roles in mitigating rank collapse. While this issue is well-documented for transformers, alternative sequence mod- els, such as State Space Models (SSMs), which have recently gained prominence, have not been thoroughly examined for similar vulnerabilities. This paper extends the theory of rank collapse from transformers to SSMs using a unifying frame- work that captures both architectures. We introduce a modification in the skip connection component, termed lambda-skip connections, that provides guaran- tees for rank collapse prevention. We present, via analytical results, a sufficient condition to achieve the guarantee for all of the aforementioned architectures. We also study the necessity of this condition via ablation studies and analytical exam- ples. To our knowledge, this is the first study that provides a general guarantee to prevent rank collapse, and that investigates rank collapse in the context of SSMs, offering valuable understanding for both theoreticians and practitioners. Finally, we validate our findings with experiments demonstrating the crucial role of archi- tectural components in preventing rank collapse.

A growing number of machine learning scenarios rely on knowledge distillation where one uses the output of a surrogate model as labels to supervise the training of a target model. In this work, we provide a sharp characterization of this process for ridgeless, high-dimensional regression, under two settings: *(i)* model shift, where the surrogate model is arbitrary, and *(ii)* distribution shift, where the surrogate model is the solution of empirical risk minimization with out-of-distribution data. In both cases, we characterize the precise risk of the target model through non-asymptotic bounds in terms of sample size and data distribution under mild conditions. As a consequence, we identify the form of the optimal surrogate model, which reveals the benefits and limitations of discarding weak features in a data-dependent fashion. In the context of weak-to-strong (W2S) generalization, this has the interpretation that *(i)* W2S training, with the surrogate as the weak model, can provably outperform training with strong labels under the same data budget, but *(ii)* it is unable to improve the data scaling law. We validate our results on numerical experiments both on ridgeless regression and on neural network architectures.

Recent advancements in head avatar rendering using Gaussian primitives have achieved significantly high-fidelity results. Although precise head geometry is crucial for applications like mesh reconstruction and relighting, current methods struggle to capture intricate geometric details and render unseen poses due to their reliance on similarity transformations, which cannot handle stretch and shear transforms essential for detailed deformations of geometry. To address this, we propose SurFhead, a novel method that reconstructs riggable head geometry from RGB videos using 2D Gaussian surfels, which offer well-defined geometric properties, such as precise depth from fixed ray intersections and normals derived from their surface orientation, making them advantageous over 3D counterparts. SurFhead ensures high-fidelity rendering of both normals and images, even in extreme poses, by leveraging classical mesh-based deformation transfer and affine transformation interpolation. SurFhead introduces precise geometric deformation and blends surfels through polar decomposition of transformations, including those affecting normals. Our key contribution lies in bridging classical graphics techniques, such as mesh-based deformation, with modern Gaussian primitives, achieving state-of-the-art geometry reconstruction and rendering quality. Unlike previous avatar rendering approaches, SurFhead enables efficient reconstruction driven by Gaussian primitives while preserving high-fidelity geometry.

We develop VSD, a method for conditioning a generative model of discrete, combinatorial designs on a rare desired class by efficiently evaluating a black-box (e.g. experiment, simulation) in a batch sequential manner. We call this task active generation; we formalize active generation's requirements and desiderata, and formulate a solution via variational inference. VSD uses off-the-shelf gradient based optimization routines, can learn powerful generative models for desirable designs, and can take advantage of scalable predictive models. We derive asymptotic convergence rates for learning the true conditional generative distribution of designs with certain configurations of our method. After illustrating the generative model on images, we empirically demonstrate that VSD can outperform existing baseline methods on a set of real sequence-design problems in various protein and DNA/RNA engineering tasks.

Recent text-to-image diffusion models leverage cross-attention layers, which have been effectively utilized to enhance a range of visual generative tasks. However, our understanding of cross-attention layers remains somewhat limited. In this study, we introduce a mechanistic interpretability approach for diffusion models by constructing Head Relevance Vectors (HRVs) that align with human-specified visual concepts. An HRV for a given visual concept has a length equal to the total number of cross-attention heads, with each element representing the importance of the corresponding head for the given visual concept. To validate HRVs as interpretable features, we develop an ordered weakening analysis that demonstrates their effectiveness. Furthermore, we propose concept strengthening and concept adjusting methods and apply them to enhance three visual generative tasks. Our results show that HRVs can reduce misinterpretations of polysemous words in image generation, successfully modify five challenging attributes in image editing, and mitigate catastrophic neglect in multi-concept generation. Overall, our work provides an advancement in understanding cross-attention layers and introduces new approaches for fine-controlling these layers at the head level.

Model merging has emerged as an effective approach to combining multiple single-task models into a multitask model. This process typically involves computing a weighted average of the model parameters without additional training. Existing model-merging methods focus on improving average task accuracy. However, interference and conflicts between the objectives of different tasks can lead to trade-offs during the merging process. In real-world applications, a set of solutions with various trade-offs can be more informative, helping practitioners make decisions based on diverse preferences. In this paper, we introduce a novel and low-compute algorithm, Model Merging with Amortized Pareto Front (MAP). MAP efficiently identifies a Pareto set of scaling coefficients for merging multiple models, reflecting the trade-offs involved. It amortizes the substantial computational cost of evaluations needed to estimate the Pareto front by using quadratic approximation surrogate models derived from a preselected set of scaling coefficients. Experimental results on vision and natural language processing tasks demonstrate that MAP can accurately identify the Pareto front, providing practitioners with flexible solutions to balance competing task objectives. We also introduce Bayesian MAP for scenarios with a relatively low number of tasks and Nested MAP for situations with a high number of tasks, further reducing the computational cost of evaluation.

The rapid scaling of large language models necessitates more lightweight finetuning methods to reduce the explosive GPU memory overhead when numerous customized models are served simultaneously. Targeting more parameter-efficient low-rank adaptation (LoRA), parameter sharing presents a promising solution. Empirically, our research into high-level sharing principles highlights the indispensable role of differentiation in reversing the detrimental effects of pure sharing. Guided by this finding, we propose Mixture of Shards (MoS), incorporating both inter-layer and intra-layer sharing schemes, and integrating four nearly cost-free differentiation strategies, namely subset selection, pair dissociation, vector sharding, and shard privatization. Briefly, it selects a designated number of shards from global pools with a Mixture-of-Experts (MoE)-like routing mechanism before sequentially concatenating them to low-rank matrices. Hence, it retains all the advantages of LoRA while offering enhanced parameter efficiency, and effectively circumvents the drawbacks of peer parameter-sharing methods. Our empirical experiments demonstrate approximately $8\times$ parameter savings in a standard LoRA setting. The ablation study confirms the significance of each component. Our insights into parameter sharing and MoS method may illuminate future developments of more parameter-efficient finetuning methods. The code is officially available at https://github.com/Forence1999/MoS.