Deep Learning · Generative Models and Autoencoders
Are LLMs a proof that the 'bitter lesson' holds for NLP? Perhaps the opposite is true: they work due to the scale of human data, and not just computation.
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Applications · Genetics, Cell Biology, Health, etc
The transcriptional response to genetic perturbation reveals fundamental insights into complex cellular systems. While current approaches have made progress in predicting genetic perturbation responses, they provide limited biological understanding and cannot systematically refine existing knowledge. Overcoming these limitations requires an end-to-end integration of data-driven learning and existing knowledge. However, this integration is challenging due to inconsistencies between data and knowledge bases, such as noise, misannotation, and incompleteness. To address this challenge, we propose ALIGNED (Adaptive aLignment for Inconsistent Genetic kNowledgE and Data), a neuro-symbolic framework based on the Abductive Learning (ABL) paradigm. This end-to-end framework aligns neural and symbolic components and performs systematic knowledge refinement. We introduce a balanced consistency metric to evaluate the predictions' consistency against both data and knowledge. Our results show that ALIGNED outperforms state-of-the-art methods by achieving the highest balanced consistency, while also re-discovering biologically meaningful knowledge. Our work advances beyond existing methods to enable both the transparency and the evolution of mechanistic biological understanding.
Deep Learning · Attention Mechanisms
While 4-bit quantization has emerged as a memory-optimal choice for non-reasoning models and zero-shot tasks across scales, we show that this universal prescription fails for reasoning models, where KV cache rather than model size can dominate memory. Through systematic experiments on mathematical, code generation, and knowledge-intensive reasoning tasks, we find a scale-dependent trade-off: models with an effective size below 8-bit 4B parameters achieve better accuracy by allocating memory to larger weights, rather than longer generation, while larger models benefit from the opposite strategy. This scale threshold also determines when parallel scaling becomes memory-efficient and whether KV cache eviction outperforms KV quantization. Our findings show that memory optimization for LLMs cannot be scale-agnostic, while providing principled guidelines: for small reasoning models, prioritize model capacity over test-time compute, while for large ones, maximize test-time compute. Our results suggest that optimizing reasoning models for deployment requires fundamentally different strategies than those established for non-reasoning ones.
Applications · Chemistry and Drug Discovery
Simulation-free training frameworks have been at the forefront of the generative modelling revolution in continuous spaces, leading to large-scale diffusion and flow matching models. However, such modern generative models suffer from expensive inference, inhibiting their use in numerous scientific applications like Boltzmann Generators (BGs) for molecular conformations that require fast likelihood evaluation. In this paper, we revisit classical normalizing flows in the context of BGs that offer efficient sampling and likelihoods, but whose training via maximum likelihood is often unstable and computationally challenging. We propose Regression Training of Normalizing Flows (RegFlow), a novel and scalable regression-based training objective that bypasses the numerical instability and computational challenge of conventional maximum likelihood training in favour of a simple $\ell_2$-regression objective. Specifically, RegFlow maps prior samples under our flow to targets computed using optimal transport couplings or a pre-trained continuous normalizing flow (CNF). To enhance numerical stability, RegFlow employs effective regularization strategies such as a new forward-backward self-consistency loss that enjoys painless implementation. Empirically, we demonstrate that RegFlow unlocks a broader class of architectures that were previously intractable to train for BGs with maximum likelihood. We also show RegFlow exceeds the performance, computational cost, and stability of maximum likelihood training in equilibrium sampling in Cartesian coordinates of alanine dipeptide, tripeptide, and tetrapeptide, showcasing its potential in molecular systems. Code available at: https://github.com/danyalrehman/RegFlow.
Computer Vision · Image and Video Generation
We explore the role of the attention mechanism during inference in text-conditional diffusion models. Empirical observations suggest that cross-attention outputs converge to a fixed point after several inference steps. The convergence time naturally divides the entire inference process into two phases: an initial phase for planning text-oriented visual semantics, which are then translated into images in a subsequent fidelity-improving phase. Cross-attention is essential in the initial phase but almost irrelevant thereafter. Self-attention, however, initially plays a minor role but becomes increasingly important in the second phase. These findings yield a simple and training-free method called TGATE which efficiently generates images by caching and reusing attention outputs at scheduled time steps. Experiments show TGATE’s broad applicability to various existing text-conditional diffusion models which it speeds up by 10-50%. The code of TGATE is available at https://github.com/HaozheLiu-ST/T-GATE.
Theory · Learning Theory
Training recurrent neural networks (RNNs) with standard backpropagation through time (BPTT) can be challenging, especially in the presence of long input sequences. A practical alternative to reduce computational and memory overhead is to perform BPTT repeatedly over shorter segments of the training data set, corresponding to truncated BPTT. In this paper, we examine the training of RNNs when using such a truncated learning approach for time series tasks. Specifically, we establish theoretical bounds on the accuracy and performance loss when optimizing over subsequences instead of the full data sequence. This reveals that the burn-in phase of the RNN is an important tuning knob in its training, with significant impact on the performance guarantees. We validate our theoretical results through experiments on standard benchmarks from the fields of system identification and time series forecasting. In all experiments, we observe a strong influence of the burn-in phase on the training process, and proper tuning can lead to a reduction of the prediction error on the training and test data of more than 60% in some cases.
Applications · Health
Surgical triplet detection is a critical task in surgical video analysis, with significant implications for performance assessment and training novice surgeons. However, existing datasets like CholecT50 lack precise spatial bounding box annotations, rendering triplet classification at the image level insufficient for practical applications. The inclusion of bounding box annotations is essential to make this task meaningful, as they provide the spatial context necessary for accurate analysis and improved model generalizability. To address these shortcomings, we introduce ProstaTD, a large-scale, multi-institutional dataset for surgical triplet detection, developed from the technically demanding domain of robot-assisted prostatectomy. ProstaTD offers clinically defined temporal boundaries and high-precision bounding box annotations for each structured triplet activity. The dataset comprises 71,775 video frames, collected from 21 surgeries performed across multiple institutions, reflecting a broad range of surgical practices and intraoperative conditions. The annotation process was conducted under rigorous medical supervision and involved more than 60 contributors, including practicing surgeons and medically trained annotators, through multiple iterative phases of labeling and verification. To further facilitate future general-purpose surgical annotation, we developed two tailored labeling tools to improve efficiency and scalability in our annotation workflows. In addition, we created a surgical triplet detection evaluation toolkit that enables standardized and reproducible performance assessment across studies. ProstaTD is the largest and most diverse surgical triplet dataset to date, moving the field from simple classification to full detection with precise spatial and temporal boundaries and thereby providing a robust foundation for fair benchmarking.
Applications · Climate
Super-resolving climate data is crucial for fine-grained decision-making in various domains, ranging from agriculture to environmental conservation. However, existing super-resolution approaches struggle to generate the high-frequency spatial information present in climate data, especially over regions showing complex terrain variability. A key obstacle lies in a frequency bias existing in both deep neural networks (DNNs) and climate data: DNNs exhibit such bias by overfitting to low-frequency information, which is further exacerbated by the prevalence of low-frequency components in climate data (e.g., plains, oceans). As a consequence, geography-dependent high-frequency details are hard to reconstruct from coarse climate inputs with DNNs. To improve the fidelity of climate super-resolution (SR), we introduce GeoFAR: by explicitly encoding climatic patterns at different frequencies, while learning implicit geographical neural representations (i.e., related to location and elevation), our approach provides frequency-aware and geography-informed representations for climate SR, thereby reconstructing fine-grained climate information at high resolution. Experiments show that GeoFAR is a model-agnostic approach that can mitigate high-frequency prediction errors in both deterministic and generative SR models, demonstrating state-of-the-art performance across various spatial resolutions, atmospheric variables, and downscaling ratios. Datasets and code are available at https://eceo-epfl.github.io/GeoFAR/.
Theory · Domain Adaptation and Transfer Learning
The goal of domain adaptation is to make predictions for unlabeled samples from a target domain with the help of labeled samples from a different but related source domain. The performance of domain adaptation methods is highly influenced by the choice of source domain and pre-trained feature extractor. However, the selection of source data and pre-trained model is not trivial due to the absence of a labeled validation set for the target domain and the large number of available pre-trained models. In this work, we propose PAS, a novel score designed to estimate the transferability of a source domain set and a pre-trained feature extractor to a target classification task before actually performing domain adaptation. PAS leverages the generalization power of pre-trained models and assesses source-target compatibility based on the pre-trained feature embeddings. We integrate PAS into a framework that indicates the most relevant pre-trained model and source domain among multiple candidates, thus improving target accuracy while reducing the computational overhead. Extensive experiments on image classification benchmarks demonstrate that PAS correlates strongly with actual target accuracy and consistently guides the selection of the best-performing pre-trained model and source domain for adaptation.
Deep Learning · Everything Else
N:M sparsity has emerged as a hardware-friendly pruning strategy, notably supported by NVIDIA’s Sparse Tensor Cores. While efficient, its fixed sparsity ratio restricts flexibility, making it difficult to adapt pruning granularity to varying weight importance across layers and architectures. To overcome this limitation, we propose FlexHiNM, a hybrid framework that adaptively partitions each layer into three regions: dense, vector-pruned, and N:M sparse, enabling finer-grained control while preserving hardware compatibility. To better preserve salient weights, we extend this to FlexHiNM-GP, which incorporates Gyro-Permutation, an iterative channel-rearrangement algorithm. Through successive sampling, clustering, and assignment, Gyro-Permutation aligns high-importance weights with structured sparsity patterns and mitigates suboptimal configurations in multi-level pruning. During gradual pruning, FlexHiNM-GP further employs a differentiable masking mechanism based on the Hard Concrete distribution, enabling gradient-based mask learning and preventing over-aggressive early pruning. Experiments on vision and language benchmarks demonstrate that FlexHiNM-GP consistently surpasses strong structured baselines and approaches the performance of unstructured pruning, validating the effectiveness of combining hybrid sparsity with learned masks and permutation strategies.
Deep Learning · Everything Else
Aligning Large Language Models with human preferences typically requires computationally intensive training or complex reward architectures. We introduce PALC (Preference Alignment via Logit Calibration), a parameter-efficient framework that achieves test-time alignment through a novel intervention strategy: direct calibration in vocabulary space. Unlike existing methods that manipulate entangled hidden representations or rely on external reward models, PALC operates at the logit layer where each dimension corresponds to a distinct token, providing interpretable and efficient control. Our approach employs a bottleneck architecture that learns to compress the base model's hidden states and generate position-dependent calibration vectors, requiring only a fraction of the base model's parameters. Through this design, PALC sidesteps the superposition problem inherent in representation engineering while eliminating the computational overhead of guided decoding methods. A single scaling factor enables runtime adjustment of alignment strength without retraining, allowing practitioners to balance between preserving model capabilities and enforcing preferences. Experiments demonstrate that PALC outperforms most test-time alignment methods while maintaining near-baseline inference speed. Our ablations reveal that human preferences concentrate on surprisingly low-dimensional manifolds, validating our architectural choices. By establishing vocabulary-space intervention as an effective alignment paradigm, PALC makes preference alignment accessible for resource-constrained deployments where traditional methods are infeasible, opening new avenues for scalable and adaptive AI alignment.
Computer Vision · 3D Rendering & Reconstruction
Ultrasound imaging is widely used due to its safety, affordability, and real-time capabilities, but its 2D interpretation is highly operator-dependent, leading to variability and increased cognitive demand. We present $\textbf{UltraGauss}$: an ultrasound-specific Gaussian Splatting framework that serves as an efficient approximation to acoustic image formation. Unlike projection-based splatting, UltraGauss renders by $\textit{probe-plane intersection}$ with in-plane aggregation, aligning with plane-based echo sampling while remaining fast and memory-efficient. A stable parameterisation and compute-aware GPU rasterisation make this method practical at scale. On clinical datasets, UltraGauss delivers state-of-the-art 2D-to-3D reconstructions in minutes on a single GPU (reaching 0.99 SSIM within $\sim$20 minutes), and a clinical expert survey rates its reconstructions the most realistic among competing methods. To our knowledge, this is the first Gaussian Splatting approach tailored to ultrasound 2D-to-3D reconstruction. Our code is available at: https://www.robots.ox.ac.uk/~vgg/research/UltraGauss/
Deep Learning · Generative Models and Autoencoders
Geometric data and purpose-built generative models on them have become ubiquitous in high-impact deep learning application domains, ranging from protein backbone generation and computational chemistry to geospatial data. Current geometric generative models remain computationally expensive at inference---requiring many steps of complex numerical simulation---as they are derived from dynamical measure transport frameworks such as diffusion and flow-matching on Riemannian manifolds. In this paper, we propose Generalised Flow Maps (GFM), a new class of few-step generative models that generalises the Flow Map framework in Euclidean spaces to arbitrary Riemannian manifolds. We instantiate GFMs with three self-distillation-based training methods: Generalised Lagrangian Flow Maps, Generalised Eulerian Flow Maps, and Generalised Progressive Flow Maps. We theoretically show that GFMs, under specific design decisions, unify and elevate existing Euclidean few-step generative models, such as consistency models, shortcut models, and meanflows, to the Riemannian setting. We benchmark GFMs against other geometric generative models on a suite of geometric datasets, including geospatial data, RNA torsion angles, and hyperbolic manifolds, and achieve state-of-the-art sample quality for single- and few-step evaluations, and superior or competitive log-likelihoods using the implicit probability flow.
Applications · Language, Speech and Dialog
Large Language Models (LLMs) are pre-trained on large data from different sources and domains. These datasets often contain trillions of tokens, including large portions of copyrighted or proprietary content, which raises questions about the legal use of such models. This underscores the need for truly open pre-training data that complies with data security regulations. In this paper, we introduce Common Corpus, the largest open dataset for LLM pre-training. The data assembled in Common Corpus are either uncopyrighted or under permissive licenses and amount to about two trillion tokens. The dataset contains a wide variety of languages, ranging from the high-resource European languages to some low-resource languages rarely represented in pre-training datasets. In addition, it includes a large amount of code data. The diversity of data sources in terms of covered domains and time periods opens up the paths for both research and entrepreneurial needs in diverse areas of knowledge. In this paper, we present the detailed provenance of data assembling and the details of dataset filtering and curation. We train two small language models on Common Corpus and find that they perform comparably to other models of their size, indicating that our dataset is suitable for multilingual pretraining. Common Corpus represents a key contribution to the ecosystem for open science research on Large Language Models.
Deep Learning · Attention Mechanisms
Diffusion-based Large Language Models (dLLMs) parallelize text generation by framing decoding as a denoising process, but suffer from high computational overhead since they predict all future suffix tokens at each step while retaining only a small fraction. We propose $\textbf{Diffusion Scratchpad} (\textbf{\textit{DPad}})$, a training-free method that restricts attention to a structured subset of suffix tokens, preserving fidelity while eliminating redundancy. $\textit{DPad}$ integrates two strategies: (i) a $\textit{sliding window}$, which maintains a fixed-length suffix window, and (ii) $\textit{distance-decay dropout}$, which deterministically removes distant suffix tokens before attention computation. This concise design is compatible with existing optimizations such as parallel decoding and prefix caching, and lends itself to a lightweight implementation. Comprehensive evaluations across multiple benchmarks on $\texttt{LLaDA}$ and $\texttt{Dream}$ models demonstrate that $\textit{DPad}$ delivers up to $\mathbf{61.4\times}$ speedup over vanilla dLLMs while maintaining comparable accuracy, highlighting its potential for efficient and scalable long-sequence inference.
Theory · Interpretability and Visualization
We propose an alternative to sparse autoencoders (SAEs) as a simple and effective unsupervised method for extracting interpretable concepts from neural networks. The core idea is to cluster differences in activations, which we formally justify within a discriminant analysis framework. To enhance the diversity of extracted concepts, we refine the approach by weighting the clustering using the skewness of activations. The method aligns with Deleuze's modern view of concepts as differences. We evaluate the approach across five models and three modalities (vision, language, and audio), measuring concept quality, diversity, and consistency. Our results show that the proposed method achieves concept quality surpassing prior unsupervised SAE variants while approaching supervised baselines, and that the extracted concepts enable steering of a model’s inner representations, demonstrating their causal influence on downstream behavior.
Applications · Time Series
Traffic systems are inherently multi-scale: microscopic vehicle interactions and macroscopic flow co-evolve nonlinearly. Microscopic models capture local interactions but miss flow evolution; macroscopic models enforce aggregated consistency yet overlook stochastic vehicle-level dynamics. We propose Micro–Macro Coupled Koopman Modeling (MMCKM), which lifts the coupled dynamics to a high-dimensional linear observation space for a unified linear-operator representation. Unlike grid-based discretizations, MMCKM adopts a vehicle-centric dynamic graph that preserves microscopic perturbations while respecting macroscopic conservation laws by discretizing PDEs onto this graph. At the micro scale, scenario-adaptive Koopman evolvers selected by an Intent Discriminator are designed to model vehicle dynamics. A Koopman control module explicitly formulate how flow state influences individual vehicles, yielding bidirectional couplings. To our knowledge, this is the first work to jointly model vehicle trajectories and traffic flow density using a unified Koopman framework without requiring historical trajectories. The proposed MMCKM is validated for trajectory prediction on NGSIM and HighD. While MMCKM uses only real-time measurement, it achieves comparable or even higher accuracy than history-dependent baselines. We further analyze the effect of the operator interval and provide ablations to show the improvement by intent inference, macro-to-micro control, and diffusion. Code and implementation details are included to facilitate reproducibility.
Deep Learning · Attention Mechanisms
Transformers struggle with tasks that require symbolic planning loops, variable updates, and conditional branching, especially under length extrapolation. We introduce discrete controller modules that insert a small set of program primitives (ASSIGN, ADD, COMPARE, BRANCH) into Transformer blocks via a Gumbel–Softmax selector over operations and a compact program state of registers, flags, and optional memory. We prove that the augmented model can simulate any bounded-step program by mapping each primitive step to one controller step, and we bound the deviation of relaxed execution from its discrete trace by $O(\tau+\kappa^{-1})$ (selection temperature $\tau$, comparison sharpness $\kappa$). Empirically, the controller-augmented Transformer achieves strong length generalization on algorithmic benchmarks (Sorting, Sum-of-List, BFS), improving longest-length accuracy by up to $20$–$40$ points over strong baselines, and yields consistent gains on symbolic QA (DROP) and program-synthesis-style tasks (RobustFill) with reduced compositionality drop-off. The learned execution is interpretable: operation traces align with ground truth, register roles are linearly decodable, and targeted knockouts cause localized accuracy losses. The approach adds only $\sim$5–7% FLOPs and can be applied sparsely (every $p$-th layer).
Online reinforcement learning (RL) has been central to post-training language models, but its extension to diffusion models remains challenging due to intractable likelihoods. Recent works discretize the reverse sampling process to enable GRPO-style training, yet they inherit fundamental drawbacks, including solver restrictions, forward–reverse inconsistency, and complicated integration with classifier-free guidance (CFG). We introduce Diffusion Negative-aware FineTuning (DiffusionNFT), a new online RL paradigm that optimizes diffusion models directly on the forward process via flow matching. DiffusionNFT contrasts positive and negative generations to define an implicit policy improvement direction, naturally incorporating reinforcement signals into the supervised learning objective. This formulation enables training with arbitrary black-box solvers, eliminates the need for likelihood estimation, and requires only clean images rather than sampling trajectories for policy optimization. DiffusionNFT is up to $25\times$ more efficient than FlowGRPO in head-to-head comparisons, while being CFG-free. For instance, DiffusionNFT improves the GenEval score from 0.24 to 0.98 within 1k steps, while FlowGRPO achieves 0.95 with over 5k steps and additional CFG employment. By leveraging multiple reward models, DiffusionNFT significantly boosts the performance of SD3.5-Medium in every benchmark tested.
Deep Learning · Robustness
Adversarial attacks on NLP systems are designed to find inputs that fool models while minimizing perceptible changes, making them difficult to detect using similarity-based methods. We investigate whether Jacobian conditioning analysis can provide an orthogonal detection signal. Surprisingly, we find that adversarial inputs exhibit systematically lower condition numbers at early transformer layers—the opposite of our initial hypothesis that attacks exploit unstable, ill-conditioned regions. This “adversarial conditioning paradox” replicates across multiple attack types: TextFooler (AUC = 0.72, p = 0.001), DeepWordBug (AUC = 0.75, p = 0.001), and directionally for PWWS (AUC = 0.59, p = 0.29). The effect holds for both word-level and character-level perturbations, while embedding cosine distance fails completely (AUC ≈ 0.25). We propose that adversarial attacks succeed by finding wellconditioned directions that cross decision boundaries—smooth paths to misclassification rather than chaotic exploitation of instability. Our findings open new directions for adversarial detection using internal geometric properties invisible to embedding-based methods.