Designing protein sequences of both high fitness and novelty is a challenging task in data-efficient protein engineering. Exploration beyond wild-type neighborhoods often leads to biologically implausible sequences or relies on surrogate models that lose fidelity in novel regions. Here, we propose ProSpero, an active learning framework in which a frozen pre-trained generative model is guided by a surrogate updated from oracle feedback. By integrating fitness-relevant residue selection with biologically-constrained Sequential Monte Carlo sampling, our approach enables exploration beyond wild-type neighborhoods while preserving biological plausibility. We show that our framework remains effective even when the surrogate is misspecified. ProSpero consistently outperforms or matches existing methods across diverse protein engineering tasks, retrieving sequences of both high fitness and novelty.

Local geometry-controllable computer-aided design (CAD) generation aims to modify local parts of CAD models automatically, enhancing design efficiency. It also ensures that the shapes of newly generated local parts follow user-specific geometric instructions (e.g., an isosceles right triangle or a rectangle with one corner cut off). However, existing methods encounter challenges in achieving this goal. Specifically, they either lack the ability to follow textual instructions or are unable to focus on the local parts. To address this limitation, we introduce GeoCAD, a user-friendly and local geometry-controllable CAD generation method. Specifically, we first propose a complementary captioning strategy to generate geometric instructions for local parts. This strategy involves vertex-based and VLLM-based captioning for systematically annotating simple and complex parts, respectively.

Graphical models have been widely used as parsimonious encoders of assumptions of the underlying causal system and provide a basis for causal inferences. Models encoding stronger constraints tend to require higher expressive power, which are also harder, and sometimes impossible to empirically falsify. In this paper, we introduce two new collections of distributions that include counterfactual quantities which are experimentally accessible under counterfactual randomizations. Correspondingly, we define two new classes of graphical models for encoding empirically testable constraints in these distributions. We further present a sound and complete calculus, based on counterfactual calculus, which licenses inferences in these two new models with rules that are within the empirically falsifiable boundary. Finally, we formulate a hierarchy over several graphical models based on the constraints they encode and study the fundamental trade-off between the expressive power and empirical falsifiability of different models across the hierarchy.

Math reasoning has been one crucial ability of large language models (LLMs), where significant advancements have been achieved in recent years. However, most efforts focus on LLMs by curating high-quality annotation data and intricate training (or inference) paradigms, while the math reasoning performance of multi-modal LLMs (MLLMs) remains lagging behind. Since the MLLM typically consists of an LLM and vision block, we wonder: \textit{Can MLLMs directly absorb math reasoning abilities from off-the-shelf math LLMs without tuning?} Recent model-merging approaches may offer insights into this question. However, they overlook the alignment between the MLLM and LLM, where we find that there is a large gap between their parameter spaces, resulting in lower performance. Our empirical evidence reveals two key factors behind this issue: the identification of crucial reasoning-associated layers in the model and the mitigation of the gaps in parameter space. Based on the empirical insights, we propose \textbf{IP-Merging} that first \textbf{I}dentifies the reasoning-associated parameters in both MLLM and Math LLM, then \textbf{P}rojects them into the subspace of MLLM aiming to maintain the alignment, finally merges parameters in this subspace. IP-Merging is a tuning-free approach since parameters are directly adjusted. Extensive experiments demonstrate that our IP-Merging method can enhance the math reasoning ability of MLLMs directly from Math LLMs without compromising their other capabilities.

Text-guided image editing involves modifying a source image based on a language instruction and, typically, requires changes to only small local regions. However, existing approaches generate the entire target image rather than selectively regenerate only the intended editing areas. This results in (1) unnecessary computational costs and (2) a bias toward reconstructing non-editing regions, which compromises the quality of the intended edits. To resolve these limitations, we propose to formulate image editing as $\textbf{N}$ext $\textbf{E}$diting-token $\textbf{P}$rediction (NEP) based on autoregressive image generation, where only regions that need to be edited are regenerated, thus avoiding unintended modification to the non-editing areas. To enable any-region editing, we propose to pre-train an any-order autoregressive text-to-image (T2I) model. Once trained, it is capable of zero-shot image editing and can be easily adapted to NEP for image editing, which achieves a new state-of-the-art on widely used image editing benchmarks. Moreover, our model naturally supports test-time scaling (TTS) through iteratively refining its generation in a zero-shot manner.

Deep graph neural networks (GNNs) often suffer from oversmoothing, where node representations become overly homogeneous with increasing depth. While techniques like normalization, residual connections, and edge dropout have been proposed to mitigate oversmoothing, they are typically developed independently, with limited theoretical understanding of their underlying mechanisms. In this work, we present a unified theoretical perspective based on the framework of signed graphs, showing that many existing strategies implicitly introduce negative edges that alter message-passing to resist oversmoothing. However, we show that merely adding negative edges in an unstructured manner is insufficient--the asymptotic behavior of signed propagation depends critically on the strength and organization of positive and negative edges. To address this limitation, we leverage the theory of structural balance, which promotes stable, cluster-preserving dynamics by connecting similar nodes with positive edges and dissimilar ones with negative edges. We propose Structural Balanced Propagation (SBP), a plug-and-play method that assigns signed edges based on either labels or feature similarity to explicitly enhance structural balance in the constructed signed graphs. Experiments on nine benchmarks across both homophilic and heterophilic settings demonstrate that SBP consistently improves classification accuracy and mitigates oversmoothing, even at depths of up to 300 layers. Our results provide a principled explanation for prior oversmoothing remedies and introduce a new direction for signed message-passing design in deep GNNs. Our code is available at https://github.com/kokolerk/sbp.

Protein language models (PLMs) are often assumed to capture evolutionary information by training on large protein sequence datasets. Yet it remains unclear whether PLMs can reason about evolution--that is, infer evolutionary relationships between sequences. We test this capability by evaluating whether standard PLM usage, frozen or fine-tuned embeddings with distance-based comparison, supports evolutionary reasoning. Existing PLMs consistently fail to recover phylogenetic structure, despite strong performance on sequence-level tasks such as masked-token and contact prediction. We present Phyla, a hybrid state-space and transformer model that jointly processes multiple sequences and is trained using a tree-based objective across 3,000 phylogenies spanning diverse protein families.

Natural disasters cause devastating damage to communities and infrastructure every year. Effective disaster response is hampered by the difficulty of accessing affected areas during and after events. Remote sensing has allowed us to monitor natural disasters in a remote way. More recently there have been advances in computer vision and deep learning that help automate satellite imagery analysis, However, they remain limited by their narrow focus on specific disaster types, reliance on manual expert interpretation, and lack of datasets with sufficient temporal granularity or natural language annotations for tracking disaster progression. We present MONITRS, a novel multimodal dataset of $\sim$10,000 FEMA disaster events with temporal satellite imagery with natural language annotations from news articles, accompanied by geotagged locations, and question-answer pairs. We demonstrate that fine-tuning existing MLLMs on our dataset yields significant performance improvements for disaster monitoring tasks, establishing a new benchmark for machine learning-assisted disaster response systems.

Large language models with Mixture-of-Experts (MoE) architectures achieve efficiency and scalability, yet their routing mechanisms introduce safety alignment challenges insufficiently addressed by techniques developed for dense models. In this work, the MoE-specific safety risk of positional vulnerability--that safety-aligned behaviors rely on specific expert modules--is formalized and systematically analyzed. An analytical framework, SAFEx, is presented to robustly identify, characterize, and validate safety-critical experts via a stability-based expert selection procedure, and to decompose them into two functional groups: the Harmful Content Detection Group (HCDG), which specializes in identifying and recognizing harmful content within user inputs, and the Harmful Response Control Group (HRCG), which specializes in controlling and enforcing model behaviors to generate appropriate safety responses. Expert-level interventions are conducted to probe causality and to test mitigation. Targeted masking of SAFEx-selected experts reveals that safety behavior is highly concentrated. On Qwen3-30B-A3B, configured with 48 MoE-FFN layers and 128 experts per layer under top-8 routing (48 128=6,144 experts in total), disabling 12 selected experts reduces the refusal rate by 22%. In addition, lightweight adaptation is performed using LoRA under three configurations--the HRCG, the union of HCDG and HRCG, and all experts--and the resulting updates are composed through negative weight merging targeted at the HRCG, leading to improved refusal under adversarial prompts without full-model retraining. These results establish positional vulnerability as a distinct MoE-specific safety challenge and provide a practical, compute-efficient pathway for expert-level safety interventions within routed architectures.

We consider the problem of detecting a community of densely connected vertices in a high-dimensional bipartite graph of size $n_1 \times n_2$. Under the null hypothesis, the observed graph is drawn from a bipartite Erdos-Renyi distribution with connection probability $p_0$. Under the alternative hypothesis, there exists an unknown bipartite subgraph of size $k_1 \times k_2$ in which edges appear with probability $p_1 = p_0 + \delta$ for some $\delta > 0$, while all other edges outside the subgraph appear with probability $p_0$. Specifically, we provide non-asymptotic upper and lower bounds on the smallest signal strength $\delta^*$ that is both necessary and sufficient to ensure the existence of a test with small enough type one and type two errors. We also derive novel minimax-optimal tests achieving these fundamental limits when the underlying graph is sufficiently dense. Our proposed tests involve a combination of hard-thresholded nonlinear statistics of the adjacency matrix, the analysis of which may be of independent interest. In contrast with previous work, our non-asymptotic upper and lower bounds match for any configuration of $n_1,n_2, k_1,k_2$.