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Günter Klambauer

Publications and source records attributed to Günter Klambauer.

At least 19 recordsLinked to original sources
arXiv2026

KVpop -- Key-Value Cache Compression with Predictive Online Pruning

Key-value (KV) cache growth is a major bottleneck in autoregressive decoding, as memory and bandwidth scale linearly with context length. Existing KV eviction methods often rely on static heuristics or proxy scores, which poorly track future token utility and cause brittle eviction as relevance shifts. To address this, we introduce KVpop, which learns a fixed-budget KV eviction policy by directly supervising the keep-or-drop decision. The scorer is trained against a novel future-attention target, computed efficiently without materializing dense attention maps. We further introduce a delayed memory-based scorer that, uniquely among learned eviction methods, defers scoring for a fixed number of steps to exploit near-future context. On AIME and HMMT mathematical reasoning, KVpop retains 98% of full-attention performance on Qwen3-4B at 75% KV cache compression and 97% at 88% compression, consistently outperforming established eviction baselines. Qwen3-8B shows even stronger results, reaching near-full teacher performance. These results show that supervising eviction with future-attention signals cuts memory costs while maintaining quality.

cs.LG↗
arXiv2026

Effective Distillation to Hybrid xLSTM Architectures

There have been numerous attempts to distill quadratic attention-based large language models (LLMs) into sub-quadratic linearized architectures. However, despite extensive research, such distilled models often fail to match the performance of their teacher LLMs on various downstream tasks. We set out the goal of lossless distillation, which we define in terms of tolerance-corrected Win-and-Tie rates between student and teacher on sets of tasks. To this end, we introduce an effective distillation pipeline for xLSTM-based students. We propose an additional merging stage, where individually linearized experts are combined into a single model. We show the effectiveness of this pipeline by distilling base and instruction-tuned models from the Llama, Qwen, and Olmo families. In many settings, our xLSTM-based students recover most of the teacher's performance, and even exceed it on some downstream tasks. Our contributions are an important step towards more energy-efficient and cost-effective replacements for transformer-based LLMs.

cs.LG↗
arXiv2026

G-RRM: Guiding Symbolic Solvers with Recurrent Reasoning Models

In this work, we focus on SE-RRMs, a symbol-equivariant instantiation of RRMs that exhibits improved extrapolation to larger problem sizes. We propose a neuro-symbolic approach, ``Guiding with Recurrent Reasoning Models'' (G-RRM), which integrates SE-RRMs with symbolic solvers for constraint satisfaction problems. SE-RRMs act as neural solvers that generate full solution proposals and guide classical symbolic solvers, such as backtracking or SAT-based methods like Glucose 4.1 and CaDiCaL 3.0.0, that produce globally correct solutions. Centrally, we investigate when neural guidance with G-RRM improves the search efficiency of symbolic solvers. % Our experiments show that the efficacy of G-RRM depends on two conditions: first, the problem instances must have an expansive combinatorial search space to expose potential gains, and second, the solver architecture must be capable of dynamically overwriting its branching choices to recover when neural hints are imperfect. When these conditions hold, guidance drives median conflict counts to zero and yields significant wall-clock speedups: on $9\times9$ Sudoku, where the SE-RRM correctly solves $91.1\%$ of instances, backtracking accelerates by $33.3\times$ and Glucose 4.1 by $1.70\times$ (median, $p<0.001$), with Glucose 4.1 retaining a $1.17\times$ speedup on perfect-hint $25\times25$ grids. In contrast, CaDiCaL 3.0.0, whose runtime is overhead-dominated and which always respects the injected branching hints rather than overwriting them, shows no significant speedup (median $1.02\times$, n.s.) and even a small significant mean slowdown ($0.90\times$) on $9\times9$. These results delineate the regimes in which neural guidance translates into practical speedups.

cs.AI↗
arXiv2026

TiRex-2: Generalizing TiRex to Multivariate Data and Streaming

We introduce TiRex-2, a recurrent xLSTM-based time series foundation model that generalizes the univariate TiRex to multivariate forecasting with both past and future covariates. Real-world forecasting is inherently sequential: observations arrive continuously, variables evolve jointly, and a subset of covariates is known ahead of time. Existing Transformer-based time series foundation models capture cross-variate dependencies but incur quadratic complexity in context length and require full-history recomputation as new observations arrive. TiRex-2 addresses these limitations through a memory-centric recurrent design that operates at constant per-patch cost under streaming. The model combines a bidirectional time mixer with an asymmetric grouped-attention variate mixer, enabling the integration of future-known covariates while preserving strict causality over target variables. To our knowledge, this is the first time series foundation model that achieves this combination of properties. To support scalable multivariate pretraining, we propose a synthetic coupling pipeline that composes diverse multivariate samples on the fly from large univariate corpora. Empirically, TiRex-2 achieves state-of-the-art zero-shot performance on GIFT-Eval and fev-bench, remains stable when streamed to arbitrary context lengths, and maintains constant inference cost per patch. The model uses 38.4M active parameters in univariate mode, with an additional 44.1M parameters activated for multivariate forecasting.

cs.LG↗
arXiv2026

Stabilizing In-Context Multi-Source Domain Adaptation for Biomedical Images Through Controls

Biomedical imaging data presents enormous potential for deep learning models to predict invaluable properties, such as diseases and drug effects. However, unavoidable alterations of the technical conditions cause batch effects: variations between groups of samples that are not due to any biological signal of interest. Batch effects greatly hinder the generalization abilities of deep learning models, preventing their practical use in the real world. Unsupervised Domain Adaptation (UDA) methods have been proposed to mitigate batch effects, but they usually assume that the data is comprised of only one source domain and one target domain, whereas biological datasets are comprised of multiple domains, both at training and at inference time. While Batch Normalization-based test-time and meta-learning adaptation methods offer a promising mechanism for domain alignment, we show that existing approaches exhibit degraded performance under the usual inference scenarios of small target batch sizes and label shift. We address these limitations by leveraging negative control samples, which are consistently present in every experimental batch in biological datasets, as stable context for adaptation. We propose CS-ARM-BN, a meta-learning BN adaptation method that uses controls both during training and inference to stabilize domain statistics. We perform a suite of experiments of Mechanism-Of-Action (MoA) classification, a crucial task for drug discovery, on the large JUMP-CP imaging dataset. Our experiments show that CS-ARM-BN substantially improves robustness to batch size and class distribution shifts, enabling practical use of deep learning models for biomedical images.

cs.LG↗
arXiv2026

Quantification of Uncertainty with Adversarial Models in Medical Image Segmentation

Reliable pixel-level uncertainty quantification holds the potential to transform clinical workflows by enabling high-fidelity longitudinal monitoring and distinguishing true pathological changes from artifacts. Ideally, these models provide the stability required for critical treatment planning and surgical intervention. However, standard deep learning models often suffer from miscalibration, yielding overconfident predictions that mask underlying vulnerabilities at subtle pathological boundaries. To address this, we propose QUAM-SM, a post-hoc framework using targeted adversarial search to identify "adversarially fragile" pixels. By actively seeking perturbations that expose predictive instability, our method highlights regions where decisions are most vulnerable to being flipped. Importantly, the framework disentangles epistemic uncertainty from aleatoric uncertainty. Experiments on two public datasets with multiple expert annotations demonstrate that QUAM-SM outperforms both standard and recent uncertainty estimation approaches in terms of reliability and boundary sensitivity. Code is available at https://github.com/HanaJebril/quam_sm

cs.CV↗
arXiv2026

Contrastive Geometric Learning Unlocks Unified Structure- and Ligand-Based Drug Design

Structure-based and ligand-based computational drug design have traditionally relied on disjoint data sources and modeling assumptions, limiting their joint use at scale. In this work, we introduce Contrastive Geometric Learning for Unified Computational Drug Design (ConGLUDe), a single contrastive geometric model that unifies structure- and ligand-based training. ConGLUDe couples a geometric protein encoder that produces whole-protein representations and implicit embeddings of predicted binding sites with a fast ligand encoder, removing the need for predefined pockets. By aligning ligands with both global protein representations and multiple candidate binding sites through contrastive learning, ConGLUDe supports ligand-conditioned pocket prediction in addition to virtual screening and target fishing, while being trained jointly on protein-ligand complexes and large-scale bioactivity data. Across diverse benchmarks, ConGLUDe achieves competitive zero-shot virtual screening performance, substantially outperforms existing methods on a challenging target fishing task, and demonstrates state-of-the-art ligand-conditioned pocket selection. These results highlight the advantages of unified structure-ligand training and position ConGLUDe as a step toward general-purpose foundation models for drug discovery.

cs.LG↗
arXiv2026

On Subquadratic Architectures: From Applications to Principles

Transformers dominate modern sequence modeling, but their quadratic attention incurs substantial computational cost. Subquadratic architectures offer a scalable alternative. However, it remains unclear which designs yield the most effective sequence models. We compare three leading approaches: xLSTM, Mamba-2, and Gated DeltaNet. We evaluate these models on tasks with complex dependencies: (1) code-model pre-training, (2) distillation of code models from large language models, and (3) pre-training of time-series foundation models. Across these settings, xLSTM delivers the strongest overall performance. To explain xLSTM's advantage, we present a unified formulation and analyze the underlying architectural mechanisms, focusing on state tracking and memory dynamics. Our results show that xLSTM enables more flexible and stable memory correction via its gating scheme. We corroborate these findings on controlled synthetic length-generalization tasks. Overall, our findings indicate that xLSTM's gains on complex tasks stem from robust state tracking and accumulation.

cs.LG↗
arXiv2026

Symbol-Equivariant Recurrent Reasoning Models

Reasoning problems such as Sudoku and ARC-AGI remain challenging for neural networks. The structured problem solving architecture family of Recurrent Reasoning Models (RRMs), including Hierarchical Reasoning Model (HRM) and Tiny Recursive Model (TRM), offer a compact alternative to large language models, but currently handle symbol symmetries only implicitly via costly data augmentation. We introduce Symbol-Equivariant Recurrent Reasoning Models (SE-RRMs), which enforce permutation equivariance at the architectural level through symbol-equivariant layers, guaranteeing identical solutions under symbol or color permutations. SE-RRMs outperform prior RRMs on 9x9 Sudoku and generalize from just training on 9x9 to smaller 4x4 and larger 16x16 and 25x25 instances, to which existing RRMs cannot extrapolate. On ARC-AGI-1 and ARC-AGI-2, SE-RRMs achieve competitive performance with substantially less data augmentation and only 2 million parameters, demonstrating that explicitly encoding symmetry improves the robustness and scalability of neural reasoning. Code is available at https://github.com/ml-jku/SE-RRM.

cs.LG↗
arXiv2026

MolecularIQ: Characterizing Chemical Reasoning Capabilities Through Symbolic Verification on Molecular Graphs

A molecule's properties are fundamentally determined by its composition and structure encoded in its molecular graph. Thus, reasoning about molecular properties requires the ability to parse and understand the molecular graph. Large Language Models (LLMs) are increasingly applied to chemistry, tackling tasks such as molecular name conversion, captioning, text-guided generation, and property or reaction prediction. Most existing benchmarks emphasize general chemical knowledge, rely on literature or surrogate labels that risk leakage or bias, or reduce evaluation to multiple-choice questions. We introduce MolecularIQ, a molecular structure reasoning benchmark focused exclusively on symbolically verifiable tasks. MolecularIQ enables fine-grained evaluation of reasoning over molecular graphs and reveals capability patterns that localize model failures to specific tasks and molecular structures. This provides actionable insights into the strengths and limitations of current chemistry LLMs and guides the development of models that reason faithfully over molecular structure.

cs.LG↗
arXiv2026

LaM-SLidE: Latent Space Modeling of Spatial Dynamical Systems via Linked Entities

Generative models are spearheading recent progress in deep learning, showcasing strong promise for trajectory sampling in dynamical systems as well. However, whereas latent space modeling paradigms have transformed image and video generation, similar approaches are more difficult for most dynamical systems. Such systems -- from chemical molecule structures to collective human behavior -- are described by interactions of entities, making them inherently linked to connectivity patterns, entity conservation, and the traceability of entities over time. Our approach, LaM-SLidE (Latent Space Modeling of Spatial Dynamical Systems via Linked Entities), bridges the gap between: (1) keeping the traceability of individual entities in a latent system representation, and (2) leveraging the efficiency and scalability of recent advances in image and video generation, where pre-trained encoder and decoder enable generative modeling directly in latent space. The core idea of LaM-SLidE is the introduction of identifier representations (IDs) that enable the retrieval of entity properties and entity composition from latent system representations, thus fostering traceability. Experimentally, across different domains, we show that LaM-SLidE performs favorably in terms of speed, accuracy, and generalizability. Code is available at https://github.com/ml-jku/LaM-SLidE .

cs.LG↗
arXiv2025

Measuring AI Progress in Drug Discovery: A Reproducible Leaderboard for the Tox21 Challenge

Deep learning's rise since the early 2010s has transformed fields like computer vision and natural language processing and strongly influenced biomedical research. For drug discovery specifically, a key inflection - akin to vision's "ImageNet moment" - arrived in 2015, when deep neural networks surpassed traditional approaches on the Tox21 Data Challenge. This milestone accelerated the adoption of deep learning across the pharmaceutical industry, and today most major companies have integrated these methods into their research pipelines. After the Tox21 Challenge concluded, its dataset was included in several established benchmarks, such as MoleculeNet and the Open Graph Benchmark. However, during these integrations, the dataset was altered and labels were imputed or manufactured, resulting in a loss of comparability across studies. Consequently, the extent to which bioactivity and toxicity prediction methods have improved over the past decade remains unclear. To this end, we introduce a reproducible leaderboard, hosted on Hugging Face with the original Tox21 Challenge dataset, together with a set of baseline and representative methods. The current version of the leaderboard indicates that the original Tox21 winner - the ensemble-based DeepTox method - and the descriptor-based self-normalizing neural networks introduced in 2017, continue to perform competitively and rank among the top methods for toxicity prediction, leaving it unclear whether substantial progress in toxicity prediction has been achieved over the past decade. As part of this work, we make all baselines and evaluated models publicly accessible for inference via standardized API calls to Hugging Face Spaces.

cs.LG↗
arXiv2025

TiRex: Zero-Shot Forecasting Across Long and Short Horizons with Enhanced In-Context Learning

In-context learning, the ability of large language models to perform tasks using only examples provided in the prompt, has recently been adapted for time series forecasting. This paradigm enables zero-shot prediction, where past values serve as context for forecasting future values, making powerful forecasting tools accessible to non-experts and increasing the performance when training data are scarce. Most existing zero-shot forecasting approaches rely on transformer architectures, which, despite their success in language, often fall short of expectations in time series forecasting, where recurrent models like LSTMs frequently have the edge. Conversely, while LSTMs are well-suited for time series modeling due to their state-tracking capabilities, they lack strong in-context learning abilities. We introduce TiRex that closes this gap by leveraging xLSTM, an enhanced LSTM with competitive in-context learning skills. Unlike transformers, state-space models, or parallelizable RNNs such as RWKV, TiRex retains state-tracking, a critical property for long-horizon forecasting. To further facilitate its state-tracking ability, we propose a training-time masking strategy called CPM. TiRex sets a new state of the art in zero-shot time series forecasting on the HuggingFace benchmarks GiftEval and Chronos-ZS, outperforming significantly larger models including TabPFN-TS (Prior Labs), Chronos Bolt (Amazon), TimesFM (Google), and Moirai (Salesforce) across both short- and long-term forecasts.

cs.LG↗
arXiv2025

Attribution assignment for deep-generative sequence models enables interpretability analysis using positive-only data

Generative machine learning models offer a powerful framework for therapeutic design by efficiently exploring large spaces of biological sequences enriched for desirable properties. Unlike supervised learning methods, which require both positive and negative labeled data, generative models such as LSTMs can be trained solely on positively labeled sequences, for example, high-affinity antibodies. This is particularly advantageous in biological settings where negative data are scarce, unreliable, or biologically ill-defined. However, the lack of attribution methods for generative models has hindered the ability to extract interpretable biological insights from such models. To address this gap, we developed Generative Attribution Metric Analysis (GAMA), an attribution method for autoregressive generative models based on Integrated Gradients. We assessed GAMA using synthetic datasets with known ground truths to characterize its statistical behavior and validate its ability to recover biologically relevant features. We further demonstrated the utility of GAMA by applying it to experimental antibody-antigen binding data. GAMA enables model interpretability and the validation of generative sequence design strategies without the need for negative training data.

cs.LG↗
arXiv2025

A Large Recurrent Action Model: xLSTM enables Fast Inference for Robotics Tasks

In recent years, there has been a trend in the field of Reinforcement Learning (RL) towards large action models trained offline on large-scale datasets via sequence modeling. Existing models are primarily based on the Transformer architecture, which result in powerful agents. However, due to slow inference times, Transformer-based approaches are impractical for real-time applications, such as robotics. Recently, modern recurrent architectures, such as xLSTM and Mamba, have been proposed that exhibit parallelization benefits during training similar to the Transformer architecture while offering fast inference. In this work, we study the aptitude of these modern recurrent architectures for large action models. Consequently, we propose a Large Recurrent Action Model (LRAM) with an xLSTM at its core that comes with linear-time inference complexity and natural sequence length extrapolation abilities. Experiments on 432 tasks from 6 domains show that LRAM compares favorably to Transformers in terms of performance and speed.

cs.LG↗
arXiv2025

xLSTM 7B: A Recurrent LLM for Fast and Efficient Inference

Recent breakthroughs in solving reasoning, math and coding problems with Large Language Models (LLMs) have been enabled by investing substantial computation budgets at inference time. Therefore, inference speed is one of the most critical properties of LLM architectures, and there is a growing need for LLMs that are efficient and fast at inference. Recently, LLMs built on the xLSTM architecture have emerged as a powerful alternative to Transformers, offering linear compute scaling with sequence length and constant memory usage, both highly desirable properties for efficient inference. However, such xLSTM-based LLMs have yet to be scaled to larger models and assessed and compared with respect to inference speed and efficiency. In this work, we introduce xLSTM 7B, a 7-billion-parameter LLM that combines xLSTM's architectural benefits with targeted optimizations for fast and efficient inference. Our experiments demonstrate that xLSTM 7B achieves performance on downstream tasks comparable to other similar-sized LLMs, while providing significantly faster inference speeds and greater efficiency compared to Llama- and Mamba-based LLMs. These results establish xLSTM 7B as the fastest and most efficient 7B LLM, offering a solution for tasks that require large amounts of test-time computation. Our work highlights xLSTM's potential as a foundational architecture for methods building on heavy use of LLM inference. Our model weights, model code and training code are open-source.

cs.LG↗
arXiv2024

xLSTM: Extended Long Short-Term Memory

In the 1990s, the constant error carousel and gating were introduced as the central ideas of the Long Short-Term Memory (LSTM). Since then, LSTMs have stood the test of time and contributed to numerous deep learning success stories, in particular they constituted the first Large Language Models (LLMs). However, the advent of the Transformer technology with parallelizable self-attention at its core marked the dawn of a new era, outpacing LSTMs at scale. We now raise a simple question: How far do we get in language modeling when scaling LSTMs to billions of parameters, leveraging the latest techniques from modern LLMs, but mitigating known limitations of LSTMs? Firstly, we introduce exponential gating with appropriate normalization and stabilization techniques. Secondly, we modify the LSTM memory structure, obtaining: (i) sLSTM with a scalar memory, a scalar update, and new memory mixing, (ii) mLSTM that is fully parallelizable with a matrix memory and a covariance update rule. Integrating these LSTM extensions into residual block backbones yields xLSTM blocks that are then residually stacked into xLSTM architectures. Exponential gating and modified memory structures boost xLSTM capabilities to perform favorably when compared to state-of-the-art Transformers and State Space Models, both in performance and scaling.

cs.LG↗
arXiv2024

Bio-xLSTM: Generative modeling, representation and in-context learning of biological and chemical sequences

Language models for biological and chemical sequences enable crucial applications such as drug discovery, protein engineering, and precision medicine. Currently, these language models are predominantly based on Transformer architectures. While Transformers have yielded impressive results, their quadratic runtime dependency on the sequence length complicates their use for long genomic sequences and in-context learning on proteins and chemical sequences. Recently, the recurrent xLSTM architecture has been shown to perform favorably compared to Transformers and modern state-space model (SSM) architectures in the natural language domain. Similar to SSMs, xLSTMs have a linear runtime dependency on the sequence length and allow for constant-memory decoding at inference time, which makes them prime candidates for modeling long-range dependencies in biological and chemical sequences. In this work, we tailor xLSTM towards these domains and propose a suite of architectural variants called Bio-xLSTM. Extensive experiments in three large domains, genomics, proteins, and chemistry, were performed to assess xLSTM's ability to model biological and chemical sequences. The results show that models based on Bio-xLSTM a) can serve as proficient generative models for DNA, protein, and chemical sequences, b) learn rich representations for those modalities, and c) can perform in-context learning for proteins and small molecules.

q-bio.BM↗