Understanding cellular responses to chemical interventions is critical to the discovery of effective therapeutics. Because individual biological techniques often measure only one axis of cellular response at a time, high-quality multimodal datasets are needed to unlock a holistic understanding of how cells respond to treatments and to advance computational methods that integrate modalities. However, many techniques destroy cells and thus preclude paired measurements, and attempts to match disparate unimodal datasets are often confounded by data being generated in incompatible experimental settings. Here we introduce scGeneScope, a multimodal single-cell RNA sequencing (scRNA-seq) and Cell Painting microscopy image dataset conditionally paired by chemical treatment, designed to facilitate the development and benchmarking of unimodal, multimodal, and multiple profile machine learning methods for cellular profiling.

While Large language models (LLMs) are driving the rapid advancement of artificial intelligence, effectively and reliably training these large models remains one of the field's most significant challenges. To address this challenge, we propose POET, a novel reParameterized training algorithm that uses Orthogonal Equivalence Transformation to optimize neurons. Specifically, POET reparameterizes each neuron with two learnable orthogonal matrices and a fixed random weight matrix. Because of its provable preservation of spectral properties of weight matrices, POET can stably optimize the objective function with improved generalization. We further develop efficient approximations that make POET flexible and scalable for training large-scale neural networks.

Despite recent advances on multi-modal models, 3D spatial reasoning remains a challenging task for state-of-the-art open-source and proprietary models. Recent studies explore data-driven approaches and achieve enhanced spatial reasoning performance by fine-tuning models on 3D-related visual question-answering data. However, these methods typically perform spatial reasoning in an implicit manner and often fail on questions that are trivial to humans, even with long chain-ofthought reasoning. In this work, we introduce SpatialReasoner, a novel large visionlanguage model (LVLM) that addresses 3D spatial reasoning with explicit 3D representations shared between multiple stages-3D perception, computation, and reasoning. Explicit 3D representations provide a coherent interface that supports advanced 3D spatial reasoning and improves the generalization ability to novel question types. Furthermore, by analyzing the explicit 3D representations in multistep reasoning traces of SpatialReasoner, we study the factual errors and identify key shortcomings of current LVLMs. Results show that our SpatialReasoner achieves improved performance on a variety of spatial reasoning benchmarks, outperforming Gemini 2.0 by 9.2% on 3DSRBench, and generalizes better when evaluating on novel 3D spatial reasoning questions.

Data duplication within large-scale corpora often impedes large language models' (LLMs) performance and privacy. In privacy-concerned federated learning scenarios, conventional deduplication methods typically rely on trusted third parties to perform uniform deletion, risking loss of informative samples while introducing privacy vulnerabilities. To address these gaps, we propose Federated ReWeighting (FedRW), the first privacy-preserving framework, to the best of our knowledge, that performs soft deduplication via sample reweighting instead of deletion in federated LLM training, without assuming a trusted third party. At its core, FedRW proposes a secure, frequency-aware reweighting protocol through secure multi-party computation, coupled with a parallel orchestration strategy to ensure efficiency and scalability. During training, FedRW utilizes an adaptive reweighting mechanism with global sample frequencies to adjust individual loss contributions, effectively improving generalization and robustness. Empirical results demonstrate that FedRW outperforms the state-of-the-art method by achieving up to 28.78 speedup in preprocessing and approximately 11.42% improvement in perplexity, while offering enhanced security guarantees. FedRW thus establishes a new paradigm for managing duplication in federated LLM training.

Table Question Answering (TableQA) combines natural language understanding and structured data reasoning, posing challenges in semantic interpretation and logical inference. Recent advances in Large Language Models (LLMs) have improved TableQA performance through Direct Prompting and Agent paradigms. However, these models often rely on spurious correlations, as they tend to overfit to token co-occurrence patterns in pretraining corpora, rather than perform genuine reasoning. To address this issue, we propose Causal Intervention TableQA (CIT), which is based on a structural causal graph and applies front-door adjustment to eliminate bias caused by token co-occurrence. CIT formalizes TableQA as a causal graph and identifies token co-occurrence patterns as confounders. By applying front-door adjustment, CIT guides question variant generation and reasoning to reduce confounding effects. Experiments on multiple benchmarks show that CIT achieves state-of-the-art performance, demonstrating its effectiveness in mitigating bias. Consistent gains across various LLMs further confirm its generalizability. We release our code here.

We study the problem of designing procurement auctions for the strategic uncapacitated facility location problem: a company needs to procure a set of facility locations in order to serve its customers and each facility location is owned by a strategic agent. Each owner has a private cost for providing access to their facility (e.g., renting it or selling it to the company) and needs to be compensated accordingly. The goal is to design truthful auctions that decide which facilities the company should procure and how much to pay the corresponding owners, aiming to minimize the total cost, i.e., the monetary cost paid to the owners and the connection cost suffered by the customers (their distance to the nearest facility). We evaluate the performance of these auctions using the frugality ratio. We first analyze the performance of the classic VCG auction in this context and prove that its frugality ratio is exactly 3. We then leverage the learning-augmented framework and design auctions that are augmented with predictions regarding the owners' private costs. Specifically, we propose a family of learning-augmented auctions that achieve significant payment reductions when the predictions are accurate, leading to much better frugality ratios. At the same time, we demonstrate that these auctions remain robust even if the predictions are arbitrarily inaccurate, and maintain reasonable frugality ratios even under adversarially chosen predictions. We finally provide a family of "error-tolerant" auctions that maintain improved frugality ratios even if the predictions are only approximately accurate, and we provide upper bounds on their frugality ratio as a function of the prediction error.

Large multimodal models (LMMs) have gained impressive performance due to their outstanding capability in various understanding tasks. However, these models still suffer from some fundamental limitations related to robustness and generalization due to the alignment and correlation between visual and textual features. In this paper, we introduce a simple but efficient learning mechanism for improving the robust alignment between visual and textual modalities by solving shuffling problems. In particular, the proposed approach can improve reasoning capability, visual understanding, and cross-modality alignment by introducing two new tasks: reconstructing the image order and the text order into the LMM's pretraining and fine-tuning phases. In addition, we propose a new directed-token approach to capture visual and textual knowledge, enabling the capability to reconstruct the correct order of visual inputs. Then, we introduce a new Image-toResponse Guided loss to further improve the visual understanding of the LMM in its responses. The proposed approach consistently achieves state-of-the-art (SoTA) performance compared with prior LMMs on academic task-oriented and instruction-following LMM benchmarks.

We present GOATEX, a diffusion-based method for 3D mesh texturing that generates methods high-quality perform te well xtures on for visible both re exterior gions, and they interior inherently surfaces.

Deployment of neural networks on resource-constrained devices demands models that are both compact and robust to adversarial inputs. However, compression and adversarial robustness often conflict. In this work, we introduce a dynamical lowrank training scheme enhanced with a novel spectral regularizer that controls the condition number of the low-rank core in each layer. This approach mitigates the sensitivity of compressed models to adversarial perturbations without sacrificing accuracy on clean data. The method is model-and data-agnostic, computationally efficient, and supports rank adaptivity to automatically compress the network at hand. Extensive experiments across standard architectures, datasets, and adversarial attacks show the regularized networks can achieve over 94% compression while recovering or improving adversarial accuracy relative to uncompressed baselines.

Understanding convergent learning--the degree to which independently trained neural systems--whether multiple artificial networks or brains and models--arrive at similar internal representations--is crucial for both neuroscience and AI. Yet, the literature remains narrow in scope--typically examining just a handful of models with one dataset, relying on one alignment metric, and evaluating networks at a single post-training checkpoint. We present a large-scale audit of convergent learning, spanning dozens of vision models and thousands of layer-pair comparisons, to close these long-standing gaps.