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Optimization · Zero-order and Black-box Optimization

Lakshya A Agrawal, Shangyin Tan, Dilara Soylu, Noah Ziems, Rishi Khare, Krista Opsahl-Ong, Arnav Singhvi, Herumb Shandilya, Michael J Ryan, Meng Jiang 等

Large language models (LLMs) are increasingly adapted to downstream tasks via reinforcement learning (RL) methods like Group Relative Policy Optimization (GRPO), which often require thousands of rollouts to learn new tasks. We argue that the interpretable nature of language often provides a much richer learning medium for LLMs, compared to policy gradients derived from sparse, scalar rewards. To test this, we introduce GEPA (Genetic-Pareto), a prompt optimizer that thoroughly incorporates natural language reflection to learn high-level rules from trial and error. Given any AI system containing one or more LLM prompts, GEPA samples trajectories (e.g., reasoning, tool calls, and tool outputs) and reflects on them in natural language to diagnose problems, propose and test prompt updates, and combine complementary lessons from the Pareto frontier of its own attempts. As a result of GEPA's design, it can often turn even just a few rollouts into a large quality gain. Across six tasks, GEPA outperforms GRPO by 6 percentage points on average and by up to 19pp, while using up to 35x fewer rollouts. GEPA also outperforms the leading prompt optimizer, MIPROv2, by over 10 percentage points (e.g., +12pp on AIME-2025), and demonstrates promising results as an inference-time search strategy for code optimization. We release our code at https://github.com/gepa-ai/gepa.

Deep Learning · Everything Else

Alan Sun, Mariya Toneva

Mechanistic interpretability (MI) is an emerging framework for interpreting neural networks. Given a task and model, MI aims to discover a succinct algorithmic process, an interpretation, that explains the model's decision process on that task. However, MI is difficult to scale and generalize. This stems in part from two key challenges: there is no precise notion of a valid interpretation; and, generating interpretations is often an ad hoc process. In this paper, we address these challenges by defining and studying the problem of interpretive equivalence: determining whether two different models share a common interpretation, without requiring an explicit description of what that interpretation is. At the core of our approach, we propose and formalize the principle that two interpretations of a model are equivalent if all of their possible implementations are also equivalent. We develop an algorithm to estimate interpretive equivalence and case study its use on Transformer-based models. To analyze our algorithm, we introduce necessary and sufficient conditions for interpretive equivalence based on models' representation similarity. We provide guarantees that simultaneously relate a model's algorithmic interpretations, circuits, and representations. Our framework lays a foundation for the development of more rigorous evaluation methods of MI and automated, generalizable interpretation discovery methods.

Social Aspects · Accountability, Transparency and Interpretability

Oscar Hill, Mateo Espinosa Zarlenga, Mateja Jamnik

Modern deep neural networks remain challenging to interpret due to the opacity of their latent representations, impeding model understanding, debugging, and debiasing. Concept Embedding Models (CEMs) address this by mapping inputs to human-interpretable concept representations from which tasks can be predicted. Yet, CEMs fail to represent inter-concept relationships and require concept annotations at different granularities during training, limiting their applicability. In this paper, we introduce *Hierarchical Concept Embedding Models* (HiCEMs), a new family of CEMs that explicitly model concept relationships through hierarchical structures. To enable HiCEMs in real-world settings, we propose *Concept Splitting*, a method for automatically discovering finer-grained sub-concepts from a pretrained CEM’s embedding space without requiring additional annotations. This allows HiCEMs to generate fine-grained explanations from limited concept labels, reducing annotation burdens. Our evaluation across multiple datasets, including a user study and experiments on *PseudoKitchens*, a newly proposed concept-based dataset of 3D kitchen renders, demonstrates that (1) Concept Splitting discovers human-interpretable sub-concepts absent during training that can be used to train highly accurate HiCEMs, and (2) HiCEMs enable powerful test-time concept interventions at different granularities, leading to improved task accuracy.

Applications · Neuroscience, Cognitive Science

Franz Rieger, Jan-Matthis Lueckmann, Viren Jain, Michal Januszewski

Biological neurons come in many shapes. High-fidelity generative modeling of their varied morphologies is challenging yet underexplored in neuroscience, and crucial for the subfield of connectomics. We introduce MoGen (Neuronal Morphology Generation), a flow matching model to generate high-resolution 3D point clouds of mouse cortex axon and dendrite fragments. This is enabled by an adaptation that injects local geometric context into a scalable latent transformer backbone, allowing for the generation of high-fidelity, realistic samples. To assess MoGen's generation quality, we propose a dedicated evaluation suite with interpretable geometric and topological features tailored to neuronal structures that we validate in a user study. MoGen's practical utility is showcased through controllable generation for visualization via smooth interpolation and a direct downstream application: we augment the training set of a shape plausibility classifier from a production connectomics neuron reconstruction pipeline with millions of generated samples, thereby improving classifier accuracy and reducing the number of remaining split and merge errors by 4.4%. We estimate this can reduce manual proofreading labor by over 157 person-years for reconstruction of a full mouse brain.

General Machine Learning · Everything Else

Nicolas Salvy, Hugues Talbot, Bertrand Thirion

Although generative models have made remarkable progress in recent years, their use in critical applications has been hindered by an inability to reliably evaluate the quality of their generated samples. Quality refers to at least two complementary concepts: fidelity and coverage. Current quality metrics often lack reliable, interpretable values due to an absence of calibration or insufficient robustness to outliers. To address these shortcomings, we introduce two novel metrics: $\textit{Clipped Density}$ and $\textit{Clipped Coverage}$. By clipping individual sample contributions, as well as the radii of nearest neighbor balls for fidelity, our metrics prevent out-of-distribution samples from biasing the aggregated values. Through analytical and empirical calibration, these metrics demonstrate linear score degradation as the proportion of bad samples increases. Thus, they can be straightforwardly interpreted as equivalent proportions of good samples. Extensive experiments on synthetic and real-world datasets demonstrate that $\textit{Clipped Density}$ and $\textit{Clipped Coverage}$ outperform existing methods in terms of robustness, sensitivity, and interpretability when evaluating generative models.

Deep Learning · Generative Models and Autoencoders

Kacper Wyrwal, Ismail I Ceylan, Alexander Tong

Flow matching is a powerful generative modeling framework, valued for its simplicity and strong empirical performance. However, its standard formulation treats signals on structured spaces---such as fMRI data on brain graphs---as points in Euclidean space, overlooking the rich topological features of their domains. To address this, we introduce \emph{topological flow matching}, a topology-aware generalization of flow matching. We interpret flow matching as a framework for solving a degenerate Schrödinger bridge problem and inject topological information by augmenting the reference process with a Laplacian-derived drift. This principled modification captures the structure of the underlying domain while preserving the desirable properties of flow matching: a stable, simulation-free objective and deterministic sample paths. As a result, our framework serves as a plug-and-play replacement for standard flow matching. We demonstrate its effectiveness on diverse structured datasets, including brain fMRIs, ocean currents, seismic events, and traffic flows.

Social Aspects · Accountability, Transparency and Interpretability

Nikhil Prakash, Natalie Shapira, Arnab Sen Sharma, Christoph Riedl, Yonatan Belinkov, Tamar Shaham, David Bau, Atticus Geiger

How do language models (LMs) represent characters’ beliefs, especially when those beliefs may differ from reality? This question lies at the heart of understanding the Theory of Mind (ToM) capabilities of LMs. We analyze LMs' ability to reason about characters’ beliefs using causal mediation and abstraction. We construct a dataset, CausalToM, consisting of simple stories where two characters independently change the state of two objects, potentially unaware of each other's actions. Our investigation uncovered a pervasive algorithmic pattern that we call a lookback mechanism, which enables the LM to recall important information when it becomes necessary. The LM binds each character-object-state triple together by co-locating their reference information, represented as Ordering IDs (OIs), in low-rank subspaces of the state token's residual stream. When asked about a character's beliefs regarding the state of an object, the binding lookback retrieves the correct state OI and then the answer lookback retrieves the corresponding state token. When we introduce text specifying that one character is (not) visible to the other, we find that the LM first generates a visibility ID encoding the relation between the observing and the observed character OIs. In a visibility lookback, this ID is used to retrieve information about the observed character and update the observing character's beliefs. Our work provides insights into belief tracking mechanisms, taking a step toward reverse-engineering ToM reasoning in LMs.

Social Aspects · Accountability, Transparency and Interpretability

Arnab Sen Sharma, Giordano Rogers, Natalie Shapira, David Bau

We investigate the mechanisms underlying a range of list-processing tasks in LLMs, and we find that they have learned to encode a compact, causal representation of a general filtering operation that mirrors the generic ``filter'' function of functional programming. Using causal mediation analysis on a diverse set of list-processing tasks, we find that a small number of attention heads, which we dub *filter heads*, encode a compact representation of the filtering predicate in their query states at certain tokens. We demonstrate that this predicate representation is general and portable: it can be extracted and reapplied to execute the same filtering operation on different collections, presented in different formats, languages, or even in tasks. However, we also identify situations where LMs can exploit a different strategy for filtering: eagerly evaluating if an item satisfies the predicate and storing this intermediate result as a flag directly in the item representations. Our results reveal that transformer LMs can develop human-interpretable implementations of abstract computational operations that generalize in ways that are surprisingly similar to strategies used in traditional functional programming patterns.

Computer Vision · Vision Models & Multimodal

Maxim Kurkin, Boris Shirokikh, IRINA ABDULLAEVA, Viktoriia Chekalina, Andrey Kuznetsov

Despite recent advancements in extending context windows of large language models (LLMs) and large vision-language models (LVLMs), their ability to perform complex multi-modal reasoning over extended contexts remains critically limited. To underline this challenge, we present \textbf{MMReD}, a benchmark specifically designed to assess reasoning abilities within dense, information-rich scenarios where simple retrieval is not enough. Unlike traditional Needle-in-a-Haystack evaluations, MMReD challenges models to identify and interpret global patterns across entire contexts. Our benchmark comprises 24 tasks of varying complexity, ranging from standard passkey retrieval setups to those requiring selective or uniform attention to all context chunks. The evaluation reveals a consistent performance drop across all tested models -- including the most advanced LLMs, LVLMs, and architectures specializing in code and reasoning -- as the number of observations increases. Notably, even the leading reasoning-specialized models achieve 0\% accuracy on certain tasks at the maximum context length of 128 observations. Conventional fine-tuning techniques, such as SFT and GRPO, also fail to generalize effectively to longer contexts. These observations reveal an inherent limitation in current model architectures, emphasizing the need for innovative approaches to enable competent dense context reasoning in multi-modal AI systems.

Theory · Interpretability and Visualization

Karim Galliamov, Syed Muhammad Ahsan Raza Kazmi, Adil Khan, Adín Ramírez Rivera

Concept Bottleneck Models (CBMs) aim to deliver interpretable predictions by routing decisions through a human-understandable concept layer, yet they often suffer reduced accuracy and concept leakage that undermines faithfulness. We introduce an explicit Information Bottleneck regularizer on the concept layer that penalizes $I(X;C)$ while preserving task-relevant information in $I(C;Y)$, encouraging minimal-sufficient concept representations. We derive two practical variants (a variational objective and an entropy-based surrogate) and integrate them into standard CBM training without architectural changes or additional supervision. Evaluated across six CBM families and three benchmarks, the IB-regularized models consistently outperform their vanilla counterparts. Information-plane analyses further corroborate the intended behavior. These results indicate that enforcing a minimal-sufficient concept bottleneck improves both predictive performance and the reliability of concept-level interventions. The proposed regularizer offers a theoretic-grounded, architecture-agnostic path to more faithful and intervenable CBMs, resolving prior evaluation inconsistencies by aligning training protocols and demonstrating robust gains across model families and datasets.

Applications · Language, Speech and Dialog

Kenny Olsen, Mads Østergaard, Karl Ulbæk, Søren Føns Nielsen, Rasmus Malik Høegh Lindrup, Bjørn Jensen, Morten Mørup

In recent years, deep learning-based single-channel speech separation has improved considerably, in large part driven by increasingly compute- and parameter-efficient neural network architectures. Most such architectures are, however, designed with a fixed compute and parameter budget and consequently cannot scale to varying compute demands or resources, which limits their use in embedded and heterogeneous devices such as mobile phones and hearables. To enable such use-cases we design a neural network architecture for speech separation and enhancement capable of early-exit, and we propose an uncertainty-aware probabilistic framework to jointly model the clean speech signal and error variance which we use to derive probabilistic early-exit conditions in terms of desired signal-to-noise ratios. We evaluate our methods on both speech separation and enhancement tasks where we demonstrate that early-exit capabilities can be introduced without compromising reconstruction, and that when trained on variable-length audio our early-exit conditions are well-calibrated and lead to considerable compute savings when used to dynamically scale compute at test time while remaining directly interpretable.

Reinforcement Learning · Multi-agent

Cheng Yang, Jiaxuan Lu, Haiyuan Wan, Junchi Yu, Feiwei Qin

The chemical reaction recommendation is to select proper reaction condition parameters for chemical reactions, which is pivotal to accelerating chemical science.With the rapid development of large language models (LLMs), there is growing interest in leveraging their reasoning and planning capabilities for reaction condition recommendation.Despite their success, existing methods rarely explain the rationale behind the recommended reaction conditions, limiting their utility in high-stakes scientific workflows. In this work, we propose ChemMAS, a multi-agent system that reframes condition prediction as an evidence-based reasoning task. ChemMAS decomposes the task into mechanistic grounding, multi-channel recall, constraint-aware agentic debate, and rationale aggregation. Each decision is backed by interpretable justifications grounded in chemical knowledge and retrieved precedents. Experiments show that ChemMAS achieves 20–35\% gains over domain-specific baselines and outperforms general-purpose LLMs by 10–15\% in Top-1 similarity, while offering falsifiable, human-trustable rationales, which establishes a new paradigm for explainable AI in scientific discovery.

Jianxin Zhang, Clayton Scott

Many generative models originally developed in finite-dimensional Euclidean space have functional generalizations in infinite-dimensional settings. However, the extension of rectified flow to infinite-dimensional spaces remains unexplored. In this work, we establish a rigorous functional formulation of rectified flow in an infinite-dimensional Hilbert space. Our approach builds upon the superposition principle for continuity equations in an infinite-dimensional space. We further show that this framework extends naturally to functional flow matching and functional probability flow ODEs, interpreting them as nonlinear generalizations of rectified flow. Notably, our extension to functional flow matching removes the restrictive measure-theoretic assumptions in the existing theory of \citet{kerrigan2024functional}. Furthermore, we demonstrate experimentally that our method achieves superior performance compared to existing functional generative models.

Deep Learning · Everything Else

Shihao Zhang, Haoyu Zhang, Ian Colbert, Rayan Saab

We introduce Qronos---a new post-training quantization algorithm that not only explicitly corrects errors due to both weight and activation quantization, but also corrects errors accumulated from previously quantized layers. Our iterative algorithm is based on an interpretable and disciplined optimization framework that surpasses existing data-driven approaches. At each step, Qronos alternates between error correction and diffusion via optimal update rules. Importantly, we prove that Qronos admits an equivalent formulation that significantly improves algorithmic efficiency; we use our discovery to reduce peak memory usage by 18\times on Llama3 8B, and our scaling analysis shows a speedup of up to 13.8\times for a single-layer microbenchmark. We demonstrate compatibility with existing transformation techniques such as Hadamard-based incoherence processing and weight-activation scaling equalization, among others. We evaluate Qronos using recent language models in the Llama3 and Qwen3 families; Qronos consistently outperforms previous state-of-the-art adaptive rounding methods when quantizing the weights, activations, and/or KV caches to 4 bits or fewer.

Theory · Interpretability and Visualization

Zhihao Zhang, Qiaole Dong, Qi Zhang, Enyu Zhou, Jun Zhao, Zhiheng Xi, Senjie Jin, Xiaoran Fan, Yuhao Zhou, Mingqi Wu 等

Post-training algorithms such as Supervised Fine-Tuning (SFT) and Reinforcement Fine-Tuning (RFT) are widely used to adapt (multimodal) large language models to downstream tasks. While effective at task adaptation, their impact on retaining prior knowledge remains unclear. In this paper, we introduce jigsaw puzzles as a novel task absent from existing pretraining corpora and systematically study the behavior of SFT and RFT on the open-source Qwen2.5-VL series. Our experiments reveal a sharp trade-off: SFT enables rapid task acquisition but leads to catastrophic forgetting, whereas RFT learns more slowly but better maintains prior knowledge. We study this phenomenon through learning dynamics by examining both the magnitude and direction of how training data influence prior knowledge. Our analysis shows that RFT mainly reinforces correct samples naturally aligned with the base model’s probability landscape, leading to weaker interference with prior knowledge. Moreover, training on RFT-simulated rollouts, which exert a smaller magnitude of influence and are better aligned in direction to prior knowledge, allows SFT to preserve prior knowledge better while rapidly learning new tasks. We further validate our framework on Qwen2.5 post-training in math and scientific QA, observing consistent forgetting and learning-dynamics trends. These findings suggest that the distribution of post-training data, rather than algorithmic differences alone, plays a central role in forgetting, and highlight RFT as a promising ingredient for stable continual post-training.

Deep Learning · Algorithms

Makoto Shing, Masanori Koyama, Takuya Akiba

End-to-end backpropagation requires storing activations throughout all layers, creating memory bottlenecks that limit model scalability. Existing block-wise training methods offer means to alleviate this problem, but they rely on ad-hoc local objectives and remain largely unexplored beyond classification tasks. We propose $\textit{DiffusionBlocks}$, a principled framework for transforming transformer-based networks into genuinely independent trainable blocks that maintain competitive performance with end-to-end training. Our key insight leverages the fact that residual connections naturally correspond to updates in a dynamical system. With minimal modifications to this system, we can convert the updates to those of a denoising process, where each block can be learned independently by leveraging the score matching objective. This independence enables training with gradients for only one block at a time, thereby reducing memory requirements in proportion to the number of blocks. Our experiments on a range of transformer architectures (vision, diffusion, autoregressive, recurrent-depth, and masked diffusion) demonstrate that DiffusionBlocks training matches the performance of end-to-end training while enabling scalable block-wise training on practical tasks beyond small-scale classification. DiffusionBlocks provides a theoretically grounded approach that successfully scales to modern generative tasks across diverse architectures.

Theory · Interpretability and Visualization

Alex Ning, Vainateya Rangaraju, Yen-Ling Kuo

In this blog post, we extract, process, and visualize latent state geometries in Transformer-based language models through dimensionality reduction to build a better intuition of their internal dynamics. We demonstrate experiments with GPT-2 and LLaMa models, uncovering interesting geometric patterns in their latent spaces. Notably, we identify a clear separation between attention and MLP component outputs across intermediate layers, a pattern not documented in prior work to our knowledge.

General Machine Learning · Causality

Yuguang Liu, Luyao Xia, Hu Liu, Zhangxi Yan, Jian Liang, Han Li, Kun Gai

Consumption‑Drives‑Production (CDP) on social platforms aims to deliver interpretable incentive signals for creator‑ecosystem building and resource utilization improvement, which strongly relies on attributions. In large-scale and complex recommendation system, the absence of accurate labels together with unobserved confounding renders backdoor adjustments alone insufficient for reliable attribution. To address these problems, we propose Adversarial Learning Mediator based Multi‑Touch-Attribution (ALM-MTA), an extensible causal framework that leverages front-door identification with an adversarially learned mediator: a proxy trained to distillate outcome information to strengthen causal pathway from treatment to outcome and eliminate shortcut leakage. Then, we introduce contrastive learning that conditions front door marginalization on high match consumption upload pairs for ensuring positivity in large treatment spaces. To assess causality from non‑RCT logs, we also incorporate a non‑personalized bucketed protocol, estimating grouped uplift and computing AUUC over treatment clusters. Finally, we evaluate ALM-MTA performance using a real-world recommendation system with 400 million DAU (daily active users) and 30 billion samples. ALM-MTA has increased DAU with 0.04% and 0.6% of the daily active creators, with unit exposure efficiency increased by 670%. On causal utility, ALM-MTA achieves higher grouped AUUC than the SOTA in every propensity bucket, with a maximum gain of 0.070. In terms of accuracy, ALM-MTA improves upload AUC by 40% compared to SOTA. These results demonstrate that front -door deconfounding with adversarial mediator learning provides accurate, personalized and operationally efficient attribution for creator ecosystem optimization.

Reinforcement Learning · Online

Shan Chen, Jirui Qi, Zidi Xiong, Timothy Miller, Arianna Bisazza, Raquel Fernández, Danielle Bitterman

LLMs often reason internally in English even for non-English queries, limiting faithfulness and weakening human oversight in multilingual settings. We study budget alignment: lightweight methods to align a model’s reasoning language with the user’s language under modest data and compute. Using a 7B model, we evaluate multilingual SFT, RL for accuracy recovery, and model merging. Across Japanese, French, and Spanish tasks, these approaches markedly increase language-consistent reasoning while preserving strong accuracy, showing that faithful and interpretable multilingual reasoning can be achieved with low-cost alignment.

Applications · Neuroscience, Cognitive Science

Bahti Zakirov, Gasper Tkacik

Normative and task-driven theories offer powerful top-down explanations for biological systems, yet the goals of quantitatively arbitrating between competing theories, and utilizing them as inductive biases to improve data-driven fits of real biological datasets are prohibitively laborious, and often impossible. To this end, we introduce a Bayesian meta-learning framework designed to automatically convert raw functional predictions from normative theories into tractable probabilistic models. We employ adaptive deep kernel Gaussian processes, meta-learning a kernel on synthetic data generated from a normative theory. This Theory-Informed Kernel specifies a probabilistic model representing the predictions of a given theoretical model: usable for both fitting data and rigorously validating the theory. As a demonstration, we apply our framework to the early visual system, using efficient coding as our normative theory. We show improved response prediction accuracy in ex vivo recordings of mouse retinal ganglion cells stimulated by natural scenes compared to conventional data-driven baselines, while providing accurate uncertainty estimates and interpretable representations. Using exact Bayesian model selection, we also show that our informed kernel can accurately infer the degree of theory-match from data, confirming faithful encapsulation of theory structure. This work provides a more general, scalable, and automated approach for integrating theoretical knowledge into data-driven scientific inquiry in neuroscience and beyond.