Daily Papers

Medical Visual Question Answering (Med-VQA) holds significant potential for clinical decision support, yet existing efforts primarily focus on 2D imaging with limited task diversity. This paper presents 3D-RAD, a large-scale dataset designed to advance 3D Med-VQA using radiology CT scans. The 3D-RAD dataset encompasses six diverse VQA tasks: anomaly detection, image observation, medical computation, existence detection, static temporal diagnosis, and longitudinal temporal diagnosis. It supports both open- and closed-ended questions while introducing complex reasoning challenges, including computational tasks and multi-stage temporal analysis, to enable comprehensive benchmarking. Extensive evaluations demonstrate that existing vision-language models (VLMs), especially medical VLMs exhibit limited generalization, particularly in multi-temporal tasks, underscoring the challenges of real-world 3D diagnostic reasoning. To drive future advancements, we release a high-quality training set 3D-RAD-T of 136,195 expert-aligned samples, showing that fine-tuning on this dataset could significantly enhance model performance. Our dataset and code, aiming to catalyze multimodal medical AI research and establish a robust foundation for 3D medical visual understanding, are publicly available at https://github.com/Tang-xiaoxiao/3D-RAD.

While machine learning has advanced through massive parallelization, we identify a critical blind spot: some problems are fundamentally sequential. These "inherently serial" problems-from mathematical reasoning to physical simulations to sequential decision-making-require dependent computational steps that cannot be parallelized. Drawing from complexity theory, we formalize this distinction and demonstrate that current parallel-centric architectures face fundamental limitations on such tasks. We argue that recognizing the serial nature of computation holds profound implications on machine learning, model design, hardware development. As AI tackles increasingly complex reasoning, deliberately scaling serial computation-not just parallel computation-is essential for continued progress.

We show that feedforward neural networks with ReLU activation generalize on low complexity data, suitably defined. Given i.i.d. data generated from a simple programming language, the minimum description length (MDL) feedforward neural network which interpolates the data generalizes with high probability. We define this simple programming language, along with a notion of description length of such networks. We provide several examples on basic computational tasks, such as checking primality of a natural number, and more. For primality testing, our theorem shows the following. Suppose that we draw an i.i.d. sample of Theta(N^{delta}ln N) numbers uniformly at random from 1 to N, where deltain (0,1). For each number x_i, let y_i = 1 if x_i is a prime and 0 if it is not. Then with high probability, the MDL network fitted to this data accurately answers whether a newly drawn number between 1 and N is a prime or not, with test error leq O(N^{-delta}). Note that the network is not designed to detect primes; minimum description learning discovers a network which does so.

We propose a novel multimodal video benchmark - the Perception Test - to evaluate the perception and reasoning skills of pre-trained multimodal models (e.g. Flamingo, BEiT-3, or GPT-4). Compared to existing benchmarks that focus on computational tasks (e.g. classification, detection or tracking), the Perception Test focuses on skills (Memory, Abstraction, Physics, Semantics) and types of reasoning (descriptive, explanatory, predictive, counterfactual) across video, audio, and text modalities, to provide a comprehensive and efficient evaluation tool. The benchmark probes pre-trained models for their transfer capabilities, in a zero-shot / few-shot or limited finetuning regime. For these purposes, the Perception Test introduces 11.6k real-world videos, 23s average length, designed to show perceptually interesting situations, filmed by around 100 participants worldwide. The videos are densely annotated with six types of labels (multiple-choice and grounded video question-answers, object and point tracks, temporal action and sound segments), enabling both language and non-language evaluations. The fine-tuning and validation splits of the benchmark are publicly available (CC-BY license), in addition to a challenge server with a held-out test split. Human baseline results compared to state-of-the-art video QA models show a significant gap in performance (91.4% vs 43.6%), suggesting that there is significant room for improvement in multimodal video understanding. Dataset, baselines code, and challenge server are available at https://github.com/deepmind/perception_test

In the fields of Optical Character Recognition (OCR) and Natural Language Processing (NLP), integrating multilingual capabilities remains a critical challenge, especially when considering languages with complex scripts such as Arabic. This paper introduces the Comprehensive Post-OCR Parsing and Receipt Understanding Dataset (CORU), a novel dataset specifically designed to enhance OCR and information extraction from receipts in multilingual contexts involving Arabic and English. CORU consists of over 20,000 annotated receipts from diverse retail settings, including supermarkets and clothing stores, alongside 30,000 annotated images for OCR that were utilized to recognize each detected line, and 10,000 items annotated for detailed information extraction. These annotations capture essential details such as merchant names, item descriptions, total prices, receipt numbers, and dates. They are structured to support three primary computational tasks: object detection, OCR, and information extraction. We establish the baseline performance for a range of models on CORU to evaluate the effectiveness of traditional methods, like Tesseract OCR, and more advanced neural network-based approaches. These baselines are crucial for processing the complex and noisy document layouts typical of real-world receipts and for advancing the state of automated multilingual document processing. Our datasets are publicly accessible (https://github.com/Update-For-Integrated-Business-AI/CORU).

Large language models (LLMs) demonstrate proficiency across numerous computational tasks, yet their inner workings remain unclear. In theory, the combination of causal self-attention and multilayer perceptron layers allows every token to access and compute information based on all preceding tokens. In practice, to what extent are such operations present? In this paper, on mental math tasks (i.e., direct math calculation via next-token prediction without explicit reasoning), we investigate this question in three steps: inhibiting input-specific token computations in the initial layers, restricting the routes of information transfer across token positions in the next few layers, and forcing all computation to happen at the last token in the remaining layers. With two proposed techniques, Context-Aware Mean Ablation (CAMA) and Attention-Based Peeking (ABP), we identify an All-for-One subgraph (AF1) with high accuracy on a wide variety of mental math tasks, where meaningful computation occurs very late (in terms of layer depth) and only at the last token, which receives information of other tokens in few specific middle layers. Experiments on a variety of models and arithmetic expressions show that this subgraph is sufficient and necessary for high model performance, transfers across different models, and works on a variety of input styles. Ablations on different CAMA and ABP alternatives reveal their unique advantages over other methods, which may be of independent interest.

With the development of LLMs as agents, there is a growing interest in connecting multiple agents into multi-agent systems to solve tasks concurrently, focusing on their role in task assignment and coordination. This paper explores how LLMs can effectively allocate computational tasks among multiple agents, considering factors such as cost, efficiency, and performance. In this work, we address key questions, including the effectiveness of LLMs as orchestrators and planners, comparing their effectiveness in task assignment and coordination. Our experiments demonstrate that LLMs can achieve high validity and accuracy in resource allocation tasks. We find that the planner method outperforms the orchestrator method in handling concurrent actions, resulting in improved efficiency and better utilization of agents. Additionally, we show that providing explicit information about worker capabilities enhances the allocation strategies of planners, particularly when dealing with suboptimal workers.

Quantum computing has promised significant improvement in solving difficult computational tasks over classical computers. Designing quantum circuits for practical use, however, is not a trivial objective and requires expert-level knowledge. To aid this endeavor, this paper proposes a machine learning-based method to construct quantum circuit architectures. Previous works have demonstrated that classical deep reinforcement learning (DRL) algorithms can successfully construct quantum circuit architectures without encoded physics knowledge. However, these DRL-based works are not generalizable to settings with changing device noises, thus requiring considerable amounts of training resources to keep the RL models up-to-date. With this in mind, we incorporated continual learning to enhance the performance of our algorithm. In this paper, we present the Probabilistic Policy Reuse with deep Q-learning (PPR-DQL) framework to tackle this circuit design challenge. By conducting numerical simulations over various noise patterns, we demonstrate that the RL agent with PPR was able to find the quantum gate sequence to generate the two-qubit Bell state faster than the agent that was trained from scratch. The proposed framework is general and can be applied to other quantum gate synthesis or control problems -- including the automatic calibration of quantum devices.

The integration of biomolecular modeling with natural language (BL) has emerged as a promising interdisciplinary area at the intersection of artificial intelligence, chemistry and biology. This approach leverages the rich, multifaceted descriptions of biomolecules contained within textual data sources to enhance our fundamental understanding and enable downstream computational tasks such as biomolecule property prediction. The fusion of the nuanced narratives expressed through natural language with the structural and functional specifics of biomolecules described via various molecular modeling techniques opens new avenues for comprehensively representing and analyzing biomolecules. By incorporating the contextual language data that surrounds biomolecules into their modeling, BL aims to capture a holistic view encompassing both the symbolic qualities conveyed through language as well as quantitative structural characteristics. In this review, we provide an extensive analysis of recent advancements achieved through cross modeling of biomolecules and natural language. (1) We begin by outlining the technical representations of biomolecules employed, including sequences, 2D graphs, and 3D structures. (2) We then examine in depth the rationale and key objectives underlying effective multi-modal integration of language and molecular data sources. (3) We subsequently survey the practical applications enabled to date in this developing research area. (4) We also compile and summarize the available resources and datasets to facilitate future work. (5) Looking ahead, we identify several promising research directions worthy of further exploration and investment to continue advancing the field. The related resources and contents are updating in https://github.com/QizhiPei/Awesome-Biomolecule-Language-Cross-Modeling.

The rapid growth of large-scale AI models, particularly large language models has brought significant challenges in data privacy, computational resources, and accessibility. Traditional centralized architectures often struggle to meet required data security and scalability needs which hinders the democratization of AI systems. Nesa introduces a model-agnostic sharding framework designed for decentralized AI inference. Our framework uses blockchain-based sequential deep neural network sharding to distribute computational tasks across a diverse network of nodes based on a personalised heuristic and routing mechanism. This enables efficient distributed training and inference for recent large-scale models even on consumer-grade hardware. We use compression techniques like dynamic blockwise quantization and mixed matrix decomposition to reduce data transfer and memory needs. We also integrate robust security measures, including hardware-based trusted execution environments to ensure data integrity and confidentiality. Evaluating our system across various natural language processing and vision tasks shows that these compression strategies do not compromise model accuracy. Our results highlight the potential to democratize access to cutting-edge AI technologies by enabling secure and efficient inference on a decentralized network.

The use of quantum computing for machine learning is among the most exciting prospective applications of quantum technologies. However, machine learning tasks where data is provided can be considerably different than commonly studied computational tasks. In this work, we show that some problems that are classically hard to compute can be easily predicted by classical machines learning from data. Using rigorous prediction error bounds as a foundation, we develop a methodology for assessing potential quantum advantage in learning tasks. The bounds are tight asymptotically and empirically predictive for a wide range of learning models. These constructions explain numerical results showing that with the help of data, classical machine learning models can be competitive with quantum models even if they are tailored to quantum problems. We then propose a projected quantum model that provides a simple and rigorous quantum speed-up for a learning problem in the fault-tolerant regime. For near-term implementations, we demonstrate a significant prediction advantage over some classical models on engineered data sets designed to demonstrate a maximal quantum advantage in one of the largest numerical tests for gate-based quantum machine learning to date, up to 30 qubits.

Reconstructing a structured vector-graphics representation from a rasterized floorplan image is typically an important prerequisite for computational tasks involving floorplans such as automated understanding or CAD workflows. However, existing techniques struggle in faithfully generating the structure and semantics conveyed by complex floorplans that depict large indoor spaces with many rooms and a varying numbers of polygon corners. To this end, we propose Raster2Seq, framing floorplan reconstruction as a sequence-to-sequence task in which floorplan elements--such as rooms, windows, and doors--are represented as labeled polygon sequences that jointly encode geometry and semantics. Our approach introduces an autoregressive decoder that learns to predict the next corner conditioned on image features and previously generated corners using guidance from learnable anchors. These anchors represent spatial coordinates in image space, hence allowing for effectively directing the attention mechanism to focus on informative image regions. By embracing the autoregressive mechanism, our method offers flexibility in the output format, enabling for efficiently handling complex floorplans with numerous rooms and diverse polygon structures. Our method achieves state-of-the-art performance on standard benchmarks such as Structure3D, CubiCasa5K, and Raster2Graph, while also demonstrating strong generalization to more challenging datasets like WAFFLE, which contain diverse room structures and complex geometric variations.

Tool use has turned large language models (LLMs) into powerful agents that can perform complex multi-step tasks by dynamically utilising external software components. However, these tools must be implemented in advance by human developers, hindering the applicability of LLM agents in domains which demand large numbers of highly specialised tools, like in life sciences and medicine. Motivated by the growing trend of scientific studies accompanied by public code repositories, we propose ToolMaker, a novel agentic framework that autonomously transforms papers with code into LLM-compatible tools. Given a short task description and a repository URL, ToolMaker autonomously installs required dependencies and generates code to perform the task, using a closed-loop self-correction mechanism to iteratively diagnose and rectify errors. To evaluate our approach, we introduce a benchmark comprising 15 diverse and complex computational tasks spanning both medical and non-medical domains with over 100 unit tests to objectively assess tool correctness and robustness. ToolMaker correctly implements 80% of the tasks, substantially outperforming current state-of-the-art software engineering agents. ToolMaker therefore is a step towards fully autonomous agent-based scientific workflows.

This paper presents a new approach that integrates deep learning with computational chess, using both the Mixture of Experts (MoE) method and Monte-Carlo Tree Search (MCTS). Our methodology employs a suite of specialized models, each designed to respond to specific changes in the game's input data. This results in a framework with sparsely activated models, which provides significant computational benefits. Our framework combines the MoE method with MCTS, in order to align it with the strategic phases of chess, thus departing from the conventional ``one-for-all'' model. Instead, we utilize distinct game phase definitions to effectively distribute computational tasks across multiple expert neural networks. Our empirical research shows a substantial improvement in playing strength, surpassing the traditional single-model framework. This validates the efficacy of our integrated approach and highlights the potential of incorporating expert knowledge and strategic principles into neural network design. The fusion of MoE and MCTS offers a promising avenue for advancing machine learning architectures.

Mathematical problem-solving is a key field in artificial intelligence (AI) and a critical benchmark for evaluating the capabilities of large language models (LLMs). While extensive research has focused on mathematical problem-solving, most existing work and datasets concentrate on computational tasks, leaving gaps in areas like mathematical analysis, which demands rigorous proofs and formal reasoning. We developed the DEMI-MathAnalysis dataset, comprising proof-based problems from mathematical analysis topics such as Sequences and Limits, Infinite Series, and Convex Functions. We also designed a guiding framework to rigorously enhance LLMs' ability to solve these problems. Through fine-tuning LLMs on this dataset and employing our framework, we observed significant improvements in their capability to generate logical, complete, and elegant proofs. This work addresses critical gaps in mathematical reasoning and contributes to advancing trustworthy AI capable of handling formalized mathematical language. The code is publicly accessible at LLMs for Mathematical Analysis.

To understand the learning process in brains, biologically plausible algorithms have been explored by modeling the detailed neuron properties and dynamics. On the other hand, simplified multi-layer models of neural networks have shown great success on computational tasks such as image classification and speech recognition. However, the computational models that can achieve good accuracy for these learning applications are very different from the bio-plausible models. This paper studies whether a bio-plausible model of a in vitro living neural network can be used to perform machine learning tasks and achieve good inference accuracy. A novel two-layer bio-hardware hybrid neural network is proposed. The biological layer faithfully models variations of synapses, neurons, and network sparsity in in vitro living neural networks. The hardware layer is a computational fully-connected layer that tunes parameters to optimize for accuracy. Several techniques are proposed to improve the inference accuracy of the proposed hybrid neural network. For instance, an adaptive pre-processing technique helps the proposed neural network to achieve good learning accuracy for different living neural network sparsity. The proposed hybrid neural network with realistic neuron parameters and variations achieves a 98.3% testing accuracy for the handwritten digit recognition task on the full MNIST dataset.

Large language models (LLMs) are increasingly being applied to financial analysis, reporting, investment decision support, risk management, compliance, and professional training. However, robust evaluation of their domain competence in finance remains incomplete. Widely used open benchmarks such as FinQA, ConvFinQA, and TAT-QA have played an important role in advancing financial question answering and numerical reasoning, but they focus primarily on question answering over financial reports and do not provide an explicit hierarchy of professional difficulty. Broader resources, including FinanceBench, PIXIU, FinBen, and FLaME, expand the coverage of financial tasks, yet the problem of evaluating the transition from foundational knowledge to expert-level financial reasoning remains open. In this work, we present FINESSE-Bench, a suite of eight specialized benchmarks comprising 3,993 questions for hierarchical evaluation of financial competencies in LLMs. FINESSE-Bench combines exam-oriented datasets inspired by professional certifications (CFA-like Levels 1-3, CMT-like Level 2, and CFTe-like Level 1), applied trading task collections, and a Russian-language olympiad benchmark. This design enables evaluation of domain breadth, performance degradation as difficulty increases, the ability to solve computational tasks, and model behavior in specialized financial domains. We also describe a unified evaluation protocol covering multiple-choice questions, numerical answers, and short open-ended responses, together with an automated scoring scheme for freeform answers based on the LLM-as-judge paradigm. FINESSE-Bench is intended both as a complement to existing open financial benchmarks and as a tool for more substantive evaluation of professionally relevant financial competencies in large language models.

Comics, as a medium, uniquely combine text and images in styles often distinct from real-world visuals. For the past three decades, computational research on comics has evolved from basic object detection to more sophisticated tasks. However, the field faces persistent challenges such as small datasets, inconsistent annotations, inaccessible model weights, and results that cannot be directly compared due to varying train/test splits and metrics. To address these issues, we aim to standardize annotations across datasets, introduce a variety of comic styles into the datasets, and establish benchmark results with clear, replicable settings. Our proposed Comics Datasets Framework standardizes dataset annotations into a common format and addresses the overrepresentation of manga by introducing Comics100, a curated collection of 100 books from the Digital Comics Museum, annotated for detection in our uniform format. We have benchmarked a variety of detection architectures using the Comics Datasets Framework. All related code, model weights, and detailed evaluation processes are available at https://github.com/emanuelevivoli/cdf, ensuring transparency and facilitating replication. This initiative is a significant advancement towards improving object detection in comics, laying the groundwork for more complex computational tasks dependent on precise object recognition.

While recent works (e.g. o1, DeepSeek R1) have demonstrated great promise of using long Chain-of-Thought (CoT) to improve reasoning capabilities of language models, scaling it up during test-time is challenging due to inefficient memory usage -- intermediate computations accumulate indefinitely in context even no longer needed for future thoughts. We propose PENCIL, which incorporates a reduction mechanism into the autoregressive generation process, allowing the model to recursively clean up intermediate thoughts based on patterns learned from training. With this reduction mechanism, PENCIL significantly reduces the maximal context length required during generation, and thus can generate longer thoughts with limited memory, solving larger-scale problems given more thinking time. For example, we demonstrate PENCIL achieves 97\% accuracy on the challenging Einstein's puzzle -- a task even large models like GPT-4 struggle with -- using only a small 25M-parameter transformer with 2048 context length. Theoretically, we prove PENCIL can perform universal space-efficient computation by simulating Turing machines with optimal time and space complexity, and thus can solve arbitrary computational tasks that would otherwise be intractable given context window constraints.

Deep Learning (DL) has the potential to optimize machine learning in both the scientific and clinical communities. However, greater expertise is required to develop DL algorithms, and the variability of implementations hinders their reproducibility, translation, and deployment. Here we present the community-driven Generally Nuanced Deep Learning Framework (GaNDLF), with the goal of lowering these barriers. GaNDLF makes the mechanism of DL development, training, and inference more stable, reproducible, interpretable, and scalable, without requiring an extensive technical background. GaNDLF aims to provide an end-to-end solution for all DL-related tasks in computational precision medicine. We demonstrate the ability of GaNDLF to analyze both radiology and histology images, with built-in support for k-fold cross-validation, data augmentation, multiple modalities and output classes. Our quantitative performance evaluation on numerous use cases, anatomies, and computational tasks supports GaNDLF as a robust application framework for deployment in clinical workflows.

Large language models (LLMs) are increasingly applied in educational, clinical, and professional settings, but their tendency for sycophancy -- prioritizing user agreement over independent reasoning -- poses risks to reliability. This study introduces a framework to evaluate sycophantic behavior in ChatGPT-4o, Claude-Sonnet, and Gemini-1.5-Pro across AMPS (mathematics) and MedQuad (medical advice) datasets. Sycophantic behavior was observed in 58.19% of cases, with Gemini exhibiting the highest rate (62.47%) and ChatGPT the lowest (56.71%). Progressive sycophancy, leading to correct answers, occurred in 43.52% of cases, while regressive sycophancy, leading to incorrect answers, was observed in 14.66%. Preemptive rebuttals demonstrated significantly higher sycophancy rates than in-context rebuttals (61.75% vs. 56.52%, Z=5.87, p<0.001), particularly in computational tasks, where regressive sycophancy increased significantly (preemptive: 8.13%, in-context: 3.54%, p<0.001). Simple rebuttals maximized progressive sycophancy (Z=6.59, p<0.001), while citation-based rebuttals exhibited the highest regressive rates (Z=6.59, p<0.001). Sycophantic behavior showed high persistence (78.5%, 95% CI: [77.2%, 79.8%]) regardless of context or model. These findings emphasize the risks and opportunities of deploying LLMs in structured and dynamic domains, offering insights into prompt programming and model optimization for safer AI applications.

Arabic has diverse dialects, where one dialect can be substantially different from the others. In the NLP literature, some assumptions about these dialects are widely adopted (e.g., ``Arabic dialects can be grouped into distinguishable regional dialects") and are manifested in different computational tasks such as Arabic Dialect Identification (ADI). However, these assumptions are not quantitatively verified. We identify four of these assumptions and examine them by extending and analyzing a multi-label dataset, where the validity of each sentence in 11 different country-level dialects is manually assessed by speakers of these dialects. Our analysis indicates that the four assumptions oversimplify reality, and some of them are not always accurate. This in turn might be hindering further progress in different Arabic NLP tasks.

We propose a new programming language called ALTA and a compiler that can map ALTA programs to Transformer weights. ALTA is inspired by RASP, a language proposed by Weiss et al. (2021), and Tracr (Lindner et al., 2023), a compiler from RASP programs to Transformer weights. ALTA complements and extends this prior work, offering the ability to express loops and to compile programs to Universal Transformers, among other advantages. ALTA allows us to constructively show how Transformers can represent length-invariant algorithms for computing parity and addition, as well as a solution to the SCAN benchmark of compositional generalization tasks, without requiring intermediate scratchpad decoding steps. We also propose tools to analyze cases where the expressibility of an algorithm is established, but end-to-end training on a given training set fails to induce behavior consistent with the desired algorithm. To this end, we explore training from ALTA execution traces as a more fine-grained supervision signal. This enables additional experiments and theoretical analyses relating the learnability of various algorithms to data availability and modeling decisions, such as positional encodings. We make the ALTA framework -- language specification, symbolic interpreter, and weight compiler -- available to the community to enable further applications and insights.

Object-centric (OC) representations, which represent the state of a visual scene by modeling it as a composition of objects, have the potential to be used in various downstream tasks to achieve systematic compositional generalization and facilitate reasoning. However, these claims have not been thoroughly analyzed yet. Recently, foundation models have demonstrated unparalleled capabilities across diverse domains from language to computer vision, marking them as a potential cornerstone of future research for a multitude of computational tasks. In this paper, we conduct an extensive empirical study on representation learning for downstream Visual Question Answering (VQA), which requires an accurate compositional understanding of the scene. We thoroughly investigate the benefits and trade-offs of OC models and alternative approaches including large pre-trained foundation models on both synthetic and real-world data, and demonstrate a viable way to achieve the best of both worlds. The extensiveness of our study, encompassing over 600 downstream VQA models and 15 different types of upstream representations, also provides several additional insights that we believe will be of interest to the community at large.

Superconductor electronics (SCE) is a promising complementary and beyond CMOS technology. However, despite its practical benefits, the realization of SCE logic faces a significant challenge due to the absence of dense and scalable nonvolatile memory designs. While various nonvolatile memory technologies, including Non-destructive readout, vortex transitional memory (VTM), and magnetic memory, have been explored, achieving a superconductor random-access memory (RAM) crossbar array remains challenging. This paper introduces a novel, nonvolatile, high-density, and scalable VTM cell design for SCE applications. Our proposed design addresses scaling issues while boasting zero static power consumption characteristics. Our design leverages current summation, enabling analog multiply-accumulate operations -an essential feature for many in-memory computational tasks. We demonstrate the efficacy of our approach with a 32 x 32 superconductor memory array operating at 20 GHz. This design effectively addresses scaling issues and utilizes current summation that can be used for analog multiply-accumulate operations. Additionally, we showcase the accumulation property of the memory through analog simulations conducted on an 8 x 8 superconductor crossbar array.

The observed similarities in the behavior of humans and Large Language Models (LLMs) have prompted researchers to consider the potential of using LLMs as models of human cognition. However, several significant challenges must be addressed before LLMs can be legitimately regarded as cognitive models. For instance, LLMs are trained on far more data than humans typically encounter, and may have been directly trained on human data in specific cognitive tasks or aligned with human preferences. Consequently, the origins of these behavioral similarities are not well understood. In this paper, we propose a novel way to enhance the utility of LLMs as cognitive models. This approach involves (i) leveraging computationally equivalent tasks that both an LLM and a rational agent need to master for solving a cognitive problem and (ii) examining the specific task distributions required for an LLM to exhibit human-like behaviors. We apply this approach to decision-making -- specifically risky and intertemporal choice -- where the key computationally equivalent task is the arithmetic of expected value calculations. We show that an LLM pretrained on an ecologically valid arithmetic dataset, which we call Arithmetic-GPT, predicts human behavior better than many traditional cognitive models. Pretraining LLMs on ecologically valid arithmetic datasets is sufficient to produce a strong correspondence between these models and human decision-making. Our results also suggest that LLMs used as cognitive models should be carefully investigated via ablation studies of the pretraining data.

Contrastive language-audio pretraining (CLAP) has recently emerged as a method for making audio analysis more generalisable. Specifically, CLAP-style models are able to `answer' a diverse set of language queries, extending the capabilities of audio models beyond a closed set of labels. However, CLAP relies on a large set of (audio, query) pairs for pretraining. While such sets are available for general audio tasks, like captioning or sound event detection, there are no datasets with matched audio and text queries for computational paralinguistic (CP) tasks. As a result, the community relies on generic CLAP models trained for general audio with limited success. In the present study, we explore training considerations for ParaCLAP, a CLAP-style model suited to CP, including a novel process for creating audio-language queries. We demonstrate its effectiveness on a set of computational paralinguistic tasks, where it is shown to surpass the performance of open-source state-of-the-art models.

Multiple instance learning (MIL) is the most widely used framework in computational pathology, encompassing sub-typing, diagnosis, prognosis, and more. However, the existing MIL paradigm typically requires an offline instance feature extractor, such as a pre-trained ResNet or a foundation model. This approach lacks the capability for feature fine-tuning within the specific downstream tasks, limiting its adaptability and performance. To address this issue, we propose a Re-embedded Regional Transformer (R^2T) for re-embedding the instance features online, which captures fine-grained local features and establishes connections across different regions. Unlike existing works that focus on pre-training powerful feature extractor or designing sophisticated instance aggregator, R^2T is tailored to re-embed instance features online. It serves as a portable module that can seamlessly integrate into mainstream MIL models. Extensive experimental results on common computational pathology tasks validate that: 1) feature re-embedding improves the performance of MIL models based on ResNet-50 features to the level of foundation model features, and further enhances the performance of foundation model features; 2) the R^2T can introduce more significant performance improvements to various MIL models; 3) R^2T-MIL, as an R^2T-enhanced AB-MIL, outperforms other latest methods by a large margin.The code is available at: https://github.com/DearCaat/RRT-MIL.

Digital cameras transform sensor RAW readings into RGB images by means of their Image Signal Processor (ISP). Computational photography tasks such as image denoising and colour constancy are commonly performed in the RAW domain, in part due to the inherent hardware design, but also due to the appealing simplicity of noise statistics that result from the direct sensor readings. Despite this, the availability of RAW images is limited in comparison with the abundance and diversity of available RGB data. Recent approaches have attempted to bridge this gap by estimating the RGB to RAW mapping: handcrafted model-based methods that are interpretable and controllable usually require manual parameter fine-tuning, while end-to-end learnable neural networks require large amounts of training data, at times with complex training procedures, and generally lack interpretability and parametric control. Towards addressing these existing limitations, we present a novel hybrid model-based and data-driven ISP that builds on canonical ISP operations and is both learnable and interpretable. Our proposed invertible model, capable of bidirectional mapping between RAW and RGB domains, employs end-to-end learning of rich parameter representations, i.e. dictionaries, that are free from direct parametric supervision and additionally enable simple and plausible data augmentation. We evidence the value of our data generation process by extensive experiments under both RAW image reconstruction and RAW image denoising tasks, obtaining state-of-the-art performance in both. Additionally, we show that our ISP can learn meaningful mappings from few data samples, and that denoising models trained with our dictionary-based data augmentation are competitive despite having only few or zero ground-truth labels.

Fundamental tasks in computational chemistry, from transition state search to vibrational analysis, rely on molecular Hessians, which are the second derivatives of the potential energy. Yet, Hessians are computationally expensive to calculate and scale poorly with system size, with both quantum mechanical methods and neural networks. In this work, we demonstrate that Hessians can be predicted directly from a deep learning model, without relying on automatic differentiation or finite differences. We observe that one can construct SE(3)-equivariant, symmetric Hessians from irreducible representations (irrep) features up to degree l=2 computed during message passing in graph neural networks. This makes HIP Hessians one to two orders of magnitude faster, more accurate, more memory efficient, easier to train, and enables more favorable scaling with system size. We validate our predictions across a wide range of downstream tasks, demonstrating consistently superior performance for transition state search, accelerated geometry optimization, zero-point energy corrections, and vibrational analysis benchmarks. We open-source the HIP codebase and model weights to enable further development of the direct prediction of Hessians at https://github.com/BurgerAndreas/hip

The quality of natural language texts in fine-tuning datasets plays a critical role in the performance of generative models, particularly in computational creativity tasks such as poem or song lyric generation. Fluency defects in generated poems significantly reduce their value. However, training texts are often sourced from internet-based platforms without stringent quality control, posing a challenge for data engineers to manage defect levels effectively. To address this issue, we propose the use of automated linguistic anomaly detection to identify and filter out low-quality texts from training datasets for creative models. In this paper, we present a comprehensive comparison of unsupervised and supervised text anomaly detection approaches, utilizing both synthetic and human-labeled datasets. We also introduce the RUPOR dataset, a collection of Russian-language human-labeled poems designed for cross-sentence grammatical error detection, and provide the full evaluation code. Our work aims to empower the community with tools and insights to improve the quality of training datasets for generative models in creative domains.

Artificial intelligence systems for scientific discovery have demonstrated remarkable potential, yet existing approaches remain largely proprietary and operate in batch-processing modes requiring hours per research cycle, precluding real-time researcher guidance. This paper introduces Deep Research, a multi-agent system enabling interactive scientific investigation with turnaround times measured in minutes. The architecture comprises specialized agents for planning, data analysis, literature search, and novelty detection, unified through a persistent world state that maintains context across iterative research cycles. Two operational modes support different workflows: semi-autonomous mode with selective human checkpoints, and fully autonomous mode for extended investigations. Evaluation on the BixBench computational biology benchmark demonstrated state-of-the-art performance, achieving 48.8% accuracy on open response and 64.4% on multiple-choice evaluation, exceeding existing baselines by 14 to 26 percentage points. Analysis of architectural constraints, including open access literature limitations and challenges inherent to automated novelty assessment, informs practical deployment considerations for AI-assisted scientific workflows.

We develop a learning framework for building deformable templates, which play a fundamental role in many image analysis and computational anatomy tasks. Conventional methods for template creation and image alignment to the template have undergone decades of rich technical development. In these frameworks, templates are constructed using an iterative process of template estimation and alignment, which is often computationally very expensive. Due in part to this shortcoming, most methods compute a single template for the entire population of images, or a few templates for specific sub-groups of the data. In this work, we present a probabilistic model and efficient learning strategy that yields either universal or conditional templates, jointly with a neural network that provides efficient alignment of the images to these templates. We demonstrate the usefulness of this method on a variety of domains, with a special focus on neuroimaging. This is particularly useful for clinical applications where a pre-existing template does not exist, or creating a new one with traditional methods can be prohibitively expensive. Our code and atlases are available online as part of the VoxelMorph library at http://voxelmorph.csail.mit.edu.

Large Language Models are expressive tools that enable complex tasks of text understanding within Computational Social Science. Their versatility, while beneficial, poses a barrier for establishing standardized best practices within the field. To bring clarity on the values of different strategies, we present an overview of the performance of modern LLM-based classification methods on a benchmark of 23 social knowledge tasks. Our results point to three best practices: select models with larger vocabulary and pre-training corpora; avoid simple zero-shot in favor of AI-enhanced prompting; fine-tune on task-specific data, and consider more complex forms instruction-tuning on multiple datasets only when only training data is more abundant.

Real-world applications of large language models (LLMs) in computational social science (CSS) tasks primarily depend on the effectiveness of instruction tuning (IT) or in-context learning (ICL). While IT has shown highly effective at fine-tuning LLMs for various tasks, ICL offers a rapid alternative for task adaptation by learning from examples without explicit gradient updates. In this paper, we evaluate the classification performance of LLMs using IT versus ICL in few-shot CSS tasks. The experimental results indicate that ICL consistently outperforms IT in most CSS tasks. Additionally, we investigate the relationship between the increasing number of training samples and LLM performance. Our findings show that simply increasing the number of samples without considering their quality does not consistently enhance the performance of LLMs with either ICL or IT and can sometimes even result in a performance decline. Finally, we compare three prompting strategies, demonstrating that ICL is more effective than zero-shot and Chain-of-Thought (CoT). Our research highlights the significant advantages of ICL in handling CSS tasks in few-shot settings and emphasizes the importance of optimizing sample quality and prompting strategies to improve LLM classification performance. The code will be made available.

We introduce neural lithography to address the 'design-to-manufacturing' gap in computational optics. Computational optics with large design degrees of freedom enable advanced functionalities and performance beyond traditional optics. However, the existing design approaches often overlook the numerical modeling of the manufacturing process, which can result in significant performance deviation between the design and the fabricated optics. To bridge this gap, we, for the first time, propose a fully differentiable design framework that integrates a pre-trained photolithography simulator into the model-based optical design loop. Leveraging a blend of physics-informed modeling and data-driven training using experimentally collected datasets, our photolithography simulator serves as a regularizer on fabrication feasibility during design, compensating for structure discrepancies introduced in the lithography process. We demonstrate the effectiveness of our approach through two typical tasks in computational optics, where we design and fabricate a holographic optical element (HOE) and a multi-level diffractive lens (MDL) using a two-photon lithography system, showcasing improved optical performance on the task-specific metrics.

Computational RNA design tasks are often posed as inverse problems, where sequences are designed based on adopting a single desired secondary structure without considering 3D geometry and conformational diversity. We introduce gRNAde, a geometric RNA design pipeline operating on 3D RNA backbones to design sequences that explicitly account for structure and dynamics. Under the hood, gRNAde is a multi-state Graph Neural Network that generates candidate RNA sequences conditioned on one or more 3D backbone structures where the identities of the bases are unknown. On a single-state fixed backbone re-design benchmark of 14 RNA structures from the PDB identified by Das et al. [2010], gRNAde obtains higher native sequence recovery rates (56% on average) compared to Rosetta (45% on average), taking under a second to produce designs compared to the reported hours for Rosetta. We further demonstrate the utility of gRNAde on a new benchmark of multi-state design for structurally flexible RNAs, as well as zero-shot ranking of mutational fitness landscapes in a retrospective analysis of a recent ribozyme. Open source code: https://github.com/chaitjo/geometric-rna-design

Central to our understanding of chemical reactivity is the principle of mass conservation, which is fundamental for ensuring physical consistency, balancing equations, and guiding reaction design. However, data-driven computational models for tasks such as reaction product prediction rarely abide by this most basic constraint. In this work, we recast the problem of reaction prediction as a problem of electron redistribution using the modern deep generative framework of flow matching. Our model, FlowER, overcomes limitations inherent in previous approaches by enforcing exact mass conservation, thereby resolving hallucinatory failure modes, recovering mechanistic reaction sequences for unseen substrate scaffolds, and generalizing effectively to out-of-domain reaction classes with extremely data-efficient fine-tuning. FlowER additionally enables estimation of thermodynamic or kinetic feasibility and manifests a degree of chemical intuition in reaction prediction tasks. This inherently interpretable framework represents a significant step in bridging the gap between predictive accuracy and mechanistic understanding in data-driven reaction outcome prediction.

Foundation models are rapidly being developed for computational pathology applications. However, it remains an open question which factors are most important for downstream performance with data scale and diversity, model size, and training algorithm all playing a role. In this work, we present the result of scaling both data and model size, surpassing previous studies in both dimensions, and introduce two new models: Virchow 2, a 632M parameter vision transformer, and Virchow 2G, a 1.85B parameter vision transformer, each trained with 3.1M histopathology whole slide images. To support this scale, we propose domain-inspired adaptations to the DINOv2 training algorithm, which is quickly becoming the default method in self-supervised learning for computational pathology. We achieve state of the art performance on twelve tile-level tasks, as compared to the top performing competing models. Our results suggest that data diversity and domain-specific training can outperform models that only scale in the number of parameters, but, on average, performance benefits from domain-tailoring, data scale, and model scale.

This paper introduces Adaptive Computation Time (ACT), an algorithm that allows recurrent neural networks to learn how many computational steps to take between receiving an input and emitting an output. ACT requires minimal changes to the network architecture, is deterministic and differentiable, and does not add any noise to the parameter gradients. Experimental results are provided for four synthetic problems: determining the parity of binary vectors, applying binary logic operations, adding integers, and sorting real numbers. Overall, performance is dramatically improved by the use of ACT, which successfully adapts the number of computational steps to the requirements of the problem. We also present character-level language modelling results on the Hutter prize Wikipedia dataset. In this case ACT does not yield large gains in performance; however it does provide intriguing insight into the structure of the data, with more computation allocated to harder-to-predict transitions, such as spaces between words and ends of sentences. This suggests that ACT or other adaptive computation methods could provide a generic method for inferring segment boundaries in sequence data.

Multiple Instance Learning (MIL) is a cornerstone approach in computational pathology (CPath) for generating clinically meaningful slide-level embeddings from gigapixel tissue images. However, MIL often struggles with small, weakly supervised clinical datasets. In contrast to fields such as NLP and conventional computer vision, where transfer learning is widely used to address data scarcity, the transferability of MIL models remains poorly understood. In this study, we systematically evaluate the transfer learning capabilities of pretrained MIL models by assessing 11 models across 21 pretraining tasks for morphological and molecular subtype prediction. Our results show that pretrained MIL models, even when trained on different organs than the target task, consistently outperform models trained from scratch. Moreover, pretraining on pancancer datasets enables strong generalization across organs and tasks, outperforming slide foundation models while using substantially less pretraining data. These findings highlight the robust adaptability of MIL models and demonstrate the benefits of leveraging transfer learning to boost performance in CPath. Lastly, we provide a resource which standardizes the implementation of MIL models and collection of pretrained model weights on popular CPath tasks, available at https://github.com/mahmoodlab/MIL-Lab

In the training of large language models (LLMs), updating parameters more efficiently and stably has always been an important challenge. To achieve efficient parameter updates, existing methods usually achieve performance comparable to full parameter updates through methods such as low-dimensional decomposition or layer-wise selective updates. In this work, we propose AlphaAdam, an optimization framework for LLM from the perspective of intra-layer parameter updates. By decoupling parameter updates and dynamically adjusting their strength, AlphaAdam accelerates convergence and improves training stability. We construct parameter masks based on the consistency of historical momentum and gradient direction and combine them with an adaptive mask strength strategy to ensure efficient optimization and theoretical convergence guarantees, which is also applicable to most momentum-based optimizers. Extensive experiments show that AlphaAdam outperforms state-of-the-art methods such as AdamW in terms of convergence speed and computational efficiency across tasks, including GPT-2 pre-trained and fine-tuned RoBERTa and Llama-7B. Our AlphaAdam implements an optimizer enhancement framework for LLMs through intra-layer asynchronous masked adaptive updates. Our code is available in this https://github.com/MaeChd/AlphaAdam.

Large Vision-Language Models (LVLMs) typically encode an image into a fixed number of visual tokens (e.g., 576) and process these tokens with a language model. Despite their strong performance, LVLMs face challenges in adapting to varying computational constraints. This raises the question: can we achieve flexibility in the number of visual tokens to suit different tasks and computational resources? We answer this with an emphatic yes. Inspired by Matryoshka Representation Learning, we introduce the Matryoshka Query Transformer (MQT), capable of encoding an image into m visual tokens during inference, where m can be any number up to a predefined maximum. This is achieved by employing a query transformer with M latent query tokens to compress the visual embeddings. During each training step, we randomly select m <= M latent query tokens and train the model using only these first m tokens, discarding the rest. Combining MQT with LLaVA, we train a single model once, and flexibly and drastically reduce the number of inference-time visual tokens while maintaining similar or better performance compared to training independent models for each number of tokens. Our model, MQT-LLAVA, matches LLaVA-1.5 performance across 11 benchmarks using a maximum of 256 tokens instead of LLaVA's fixed 576. Reducing to 16 tokens (8x less TFLOPs) only sacrifices the performance by 2.4 points on MMBench. On certain tasks such as ScienceQA and MMMU, we can even go down to only 2 visual tokens with performance drops of just 3% and 6% each. Our exploration of the trade-off between the accuracy and computational cost brought about by the number of visual tokens facilitates future research to achieve the best of both worlds.

Low-Rank Adaptation (LoRA) methods have emerged as crucial techniques for adapting large pre-trained models to downstream tasks under computational and memory constraints. However, they face a fundamental challenge in balancing task-specific performance gains against catastrophic forgetting of pre-trained knowledge, where existing methods provide inconsistent recommendations. This paper presents a comprehensive analysis of the performance-forgetting trade-offs inherent in low-rank adaptation using principal components as initialization. Our investigation reveals that fine-tuning intermediate components leads to better balance and show more robustness to high learning rates than first (PiSSA) and last (MiLoRA) components in existing work. Building on these findings, we provide a practical approach for initialization of LoRA that offers superior trade-offs. We demonstrate in a thorough empirical study on a variety of computer vision and NLP tasks that our approach improves accuracy and reduces forgetting, also in continual learning scenarios.

Courts must justify their decisions, but systematically analyzing judicial reasoning at scale remains difficult. This study tests claims about formalistic judging in Central and Eastern Europe (CEE) by developing automated methods to detect and classify judicial reasoning in decisions of Czech Supreme Courts using state-of-the-art natural language processing methods. We create the MADON dataset of 272 decisions from two Czech Supreme Courts with expert annotations of 9,183 paragraphs with eight argument types and holistic formalism labels for supervised training and evaluation. Using a corpus of 300,511 Czech court decisions, we adapt transformer LLMs to Czech legal domain through continued pretraining and we experiment with methods to address dataset imbalance including asymmetric loss and class weighting. The best models can detect argumentative paragraphs (82.6% Bal-F1), classify traditional types of legal argument (77.5% Bal-F1), and classify decisions as formalistic/non-formalistic (83.8% Bal-F1). Our three-stage pipeline combining ModernBERT, Llama 3.1, and traditional feature-based machine learning achieves promising results for decision classification while reducing computational costs and increasing explainability. Empirically, we challenge prevailing narratives about CEE formalism. We demonstrate that legal argument mining enables promising judicial philosophy classification and highlight its potential for other important tasks in computational legal studies. Our methodology can be used across jurisdictions, and our entire pipeline, datasets, guidelines, models, and source codes are available at https://github.com/trusthlt/madon.

Pre-trained language models (PLMs) have achieved great success in NLP and have recently been used for tasks in computational semantics. However, these tasks do not fully benefit from PLMs since meaning representations are not explicitly included in the pre-training stage. We introduce multilingual pre-trained language-meaning models based on Discourse Representation Structures (DRSs), including meaning representations besides natural language texts in the same model, and design a new strategy to reduce the gap between the pre-training and fine-tuning objectives. Since DRSs are language neutral, cross-lingual transfer learning is adopted to further improve the performance of non-English tasks. Automatic evaluation results show that our approach achieves the best performance on both the multilingual DRS parsing and DRS-to-text generation tasks. Correlation analysis between automatic metrics and human judgements on the generation task further validates the effectiveness of our model. Human inspection reveals that out-of-vocabulary tokens are the main cause of erroneous results.

Computational historical linguistics seeks to systematically understand processes of sound change, including during periods at which little to no formal recording of language is attested. At the same time, few computational resources exist which deeply explore phonological and morphological connections between proto-languages and their descendants. This is particularly true for the family of Italic languages. To assist historical linguists in the study of Italic sound change, we introduce the Proto-Italic to Latin (PILA) dataset, which consists of roughly 3,000 pairs of forms from Proto-Italic and Latin. We provide a detailed description of how our dataset was created and organized. Then, we exhibit PILA's value in two ways. First, we present baseline results for PILA on a pair of traditional computational historical linguistics tasks. Second, we demonstrate PILA's capability for enhancing other historical-linguistic datasets through a dataset compatibility study.

Large language models (LLMs) have shown high agreement with human raters across a variety of tasks, demonstrating potential to ease the challenges of human data collection. In computational social science (CSS), researchers are increasingly leveraging LLM annotations to complement slow and expensive human annotations. Still, guidelines for collecting and using LLM annotations, without compromising the validity of downstream conclusions, remain limited. We introduce Confidence-Driven Inference: a method that combines LLM annotations and LLM confidence indicators to strategically select which human annotations should be collected, with the goal of producing accurate statistical estimates and provably valid confidence intervals while reducing the number of human annotations needed. Our approach comes with safeguards against LLM annotations of poor quality, guaranteeing that the conclusions will be both valid and no less accurate than if we only relied on human annotations. We demonstrate the effectiveness of Confidence-Driven Inference over baselines in statistical estimation tasks across three CSS settings--text politeness, stance, and bias--reducing the needed number of human annotations by over 25% in each. Although we use CSS settings for demonstration, Confidence-Driven Inference can be used to estimate most standard quantities across a broad range of NLP problems.

In this work, we introduce ChatQA 2, a Llama3-based model designed to bridge the gap between open-access LLMs and leading proprietary models (e.g., GPT-4-Turbo) in long-context understanding and retrieval-augmented generation (RAG) capabilities. These two capabilities are essential for LLMs to process large volumes of information that cannot fit into a single prompt and are complementary to each other, depending on the downstream tasks and computational budgets. We present a detailed continued training recipe to extend the context window of Llama3-70B-base from 8K to 128K tokens, along with a three-stage instruction tuning process to enhance the model's instruction-following, RAG performance, and long-context understanding capabilities. Our results demonstrate that the Llama3-ChatQA-2-70B model achieves accuracy comparable to GPT-4-Turbo-2024-0409 on many long-context understanding tasks and surpasses it on the RAG benchmark. Interestingly, we find that the state-of-the-art long-context retriever can alleviate the top-k context fragmentation issue in RAG, further improving RAG-based results for long-context understanding tasks. We also provide extensive comparisons between RAG and long-context solutions using state-of-the-art long-context LLMs.

In this work, we propose Few Shot Domain Adapting Graph (FS-DAG), a scalable and efficient model architecture for visually rich document understanding (VRDU) in few-shot settings. FS-DAG leverages domain-specific and language/vision specific backbones within a modular framework to adapt to diverse document types with minimal data. The model is robust to practical challenges such as handling OCR errors, misspellings, and domain shifts, which are critical in real-world deployments. FS-DAG is highly performant with less than 90M parameters, making it well-suited for complex real-world applications for Information Extraction (IE) tasks where computational resources are limited. We demonstrate FS-DAG's capability through extensive experiments for information extraction task, showing significant improvements in convergence speed and performance compared to state-of-the-art methods. Additionally, this work highlights the ongoing progress in developing smaller, more efficient models that do not compromise on performance. Code : https://github.com/oracle-samples/fs-dag

Scale has opened new frontiers in natural language processing -- but at a high cost. In response, Mixture-of-Experts (MoE) and Switch Transformers have been proposed as an energy efficient path to even larger and more capable language models. But advancing the state-of-the-art across a broad set of natural language tasks has been hindered by training instabilities and uncertain quality during fine-tuning. Our work focuses on these issues and acts as a design guide. We conclude by scaling a sparse model to 269B parameters, with a computational cost comparable to a 32B dense encoder-decoder Transformer (Stable and Transferable Mixture-of-Experts or ST-MoE-32B). For the first time, a sparse model achieves state-of-the-art performance in transfer learning, across a diverse set of tasks including reasoning (SuperGLUE, ARC Easy, ARC Challenge), summarization (XSum, CNN-DM), closed book question answering (WebQA, Natural Questions), and adversarially constructed tasks (Winogrande, ANLI R3).

The motif-scaffolding problem is a central task in computational protein design: Given the coordinates of atoms in a geometry chosen to confer a desired biochemical function (a motif), the task is to identify diverse protein structures (scaffolds) that include the motif and maintain its geometry. Significant recent progress on motif-scaffolding has been made due to computational evaluation with reliable protein structure prediction and fixed-backbone sequence design methods. However, significant variability in evaluation strategies across publications has hindered comparability of results, challenged reproducibility, and impeded robust progress. In response we introduce MotifBench, comprising (1) a precisely specified pipeline and evaluation metrics, (2) a collection of 30 benchmark problems, and (3) an implementation of this benchmark and leaderboard at github.com/blt2114/MotifBench. The MotifBench test cases are more difficult compared to earlier benchmarks, and include protein design problems for which solutions are known but on which, to the best of our knowledge, state-of-the-art methods fail to identify any solution.

Models using structured state space sequence (S4) layers have achieved state-of-the-art performance on long-range sequence modeling tasks. An S4 layer combines linear state space models (SSMs), the HiPPO framework, and deep learning to achieve high performance. We build on the design of the S4 layer and introduce a new state space layer, the S5 layer. Whereas an S4 layer uses many independent single-input, single-output SSMs, the S5 layer uses one multi-input, multi-output SSM. We establish a connection between S5 and S4, and use this to develop the initialization and parameterization used by the S5 model. The result is a state space layer that can leverage efficient and widely implemented parallel scans, allowing S5 to match the computational efficiency of S4, while also achieving state-of-the-art performance on several long-range sequence modeling tasks. S5 averages 87.4% on the long range arena benchmark, and 98.5% on the most difficult Path-X task.

Early exiting has become a promising approach to improving the inference efficiency of deep networks. By structuring models with multiple classifiers (exits), predictions for ``easy'' samples can be generated at earlier exits, negating the need for executing deeper layers. Current multi-exit networks typically implement linear classifiers at intermediate layers, compelling low-level features to encapsulate high-level semantics. This sub-optimal design invariably undermines the performance of later exits. In this paper, we propose Dynamic Perceiver (Dyn-Perceiver) to decouple the feature extraction procedure and the early classification task with a novel dual-branch architecture. A feature branch serves to extract image features, while a classification branch processes a latent code assigned for classification tasks. Bi-directional cross-attention layers are established to progressively fuse the information of both branches. Early exits are placed exclusively within the classification branch, thus eliminating the need for linear separability in low-level features. Dyn-Perceiver constitutes a versatile and adaptable framework that can be built upon various architectures. Experiments on image classification, action recognition, and object detection demonstrate that our method significantly improves the inference efficiency of different backbones, outperforming numerous competitive approaches across a broad range of computational budgets. Evaluation on both CPU and GPU platforms substantiate the superior practical efficiency of Dyn-Perceiver. Code is available at https://www.github.com/LeapLabTHU/Dynamic_Perceiver.

We introduce Network Augmentation (NetAug), a new training method for improving the performance of tiny neural networks. Existing regularization techniques (e.g., data augmentation, dropout) have shown much success on large neural networks by adding noise to overcome over-fitting. However, we found these techniques hurt the performance of tiny neural networks. We argue that training tiny models are different from large models: rather than augmenting the data, we should augment the model, since tiny models tend to suffer from under-fitting rather than over-fitting due to limited capacity. To alleviate this issue, NetAug augments the network (reverse dropout) instead of inserting noise into the dataset or the network. It puts the tiny model into larger models and encourages it to work as a sub-model of larger models to get extra supervision, in addition to functioning as an independent model. At test time, only the tiny model is used for inference, incurring zero inference overhead. We demonstrate the effectiveness of NetAug on image classification and object detection. NetAug consistently improves the performance of tiny models, achieving up to 2.2% accuracy improvement on ImageNet. On object detection, achieving the same level of performance, NetAug requires 41% fewer MACs on Pascal VOC and 38% fewer MACs on COCO than the baseline.

The past several years have witnessed a huge surge in the use of social media platforms during mass convergence events such as health emergencies, natural or human-induced disasters. These non-traditional data sources are becoming vital for disease forecasts and surveillance when preparing for epidemic and pandemic outbreaks. In this paper, we present GeoCoV19, a large-scale Twitter dataset containing more than 524 million multilingual tweets posted over a period of 90 days since February 1, 2020. Moreover, we employ a gazetteer-based approach to infer the geolocation of tweets. We postulate that this large-scale, multilingual, geolocated social media data can empower the research communities to evaluate how societies are collectively coping with this unprecedented global crisis as well as to develop computational methods to address challenges such as identifying fake news, understanding communities' knowledge gaps, building disease forecast and surveillance models, among others.

As language models become capable of processing increasingly long and complex texts, there has been growing interest in their application within computational literary studies. However, evaluating the usefulness of these models for such tasks remains challenging due to the cost of fine-grained annotation for long-form texts and the data contamination concerns inherent in using public-domain literature. Current embedding similarity datasets are not suitable for evaluating literary-domain tasks because of a focus on coarse-grained similarity and primarily on very short text. We assemble and release FICSIM, a dataset of long-form, recently written fiction, including scores along 12 axes of similarity informed by author-produced metadata and validated by digital humanities scholars. We evaluate a suite of embedding models on this task, demonstrating a tendency across models to focus on surface-level features over semantic categories that would be useful for computational literary studies tasks. Throughout our data-collection process, we prioritize author agency and rely on continual, informed author consent.

Arbitrary-scale video super-resolution (AVSR) aims to enhance the resolution of video frames, potentially at various scaling factors, which presents several challenges regarding spatial detail reproduction, temporal consistency, and computational complexity. In this paper, we propose a strong baseline BasicAVSR for AVSR by integrating four key components: 1) adaptive multi-scale frequency priors generated from image Laplacian pyramids, 2) a flow-guided propagation unit to aggregate spatiotemporal information from adjacent frames, 3) a second-order motion compensation unit for more accurate spatial alignment of adjacent frames, and 4) a hyper-upsampling unit to generate scale-aware and content-independent upsampling kernels. To meet diverse application demands, we instantiate three propagation variants: (i) a unidirectional RNN unit for strictly online inference, (ii) a unidirectional RNN unit empowered with a limited lookahead that tolerates a small output delay, and (iii) a bidirectional RNN unit designed for offline tasks where computational resources are less constrained. Experimental results demonstrate the effectiveness and adaptability of our model across these different scenarios. Through extensive experiments, we show that BasicAVSR significantly outperforms existing methods in terms of super-resolution quality, generalization ability, and inference speed. Our work not only advances the state-of-the-art in AVSR but also extends its core components to multiple frameworks for diverse scenarios. The code is available at https://github.com/shangwei5/BasicAVSR.

The complexity and variability inherent in high-resolution pathological images present significant challenges in computational pathology. While pathology foundation models leveraging AI have catalyzed transformative advancements, their development demands large-scale datasets, considerable storage capacity, and substantial computational resources. Furthermore, ensuring their clinical applicability and generalizability requires rigorous validation across a broad spectrum of clinical tasks. Here, we present PathOrchestra, a versatile pathology foundation model trained via self-supervised learning on a dataset comprising 300K pathological slides from 20 tissue and organ types across multiple centers. The model was rigorously evaluated on 112 clinical tasks using a combination of 61 private and 51 public datasets. These tasks encompass digital slide preprocessing, pan-cancer classification, lesion identification, multi-cancer subtype classification, biomarker assessment, gene expression prediction, and the generation of structured reports. PathOrchestra demonstrated exceptional performance across 27,755 WSIs and 9,415,729 ROIs, achieving over 0.950 accuracy in 47 tasks, including pan-cancer classification across various organs, lymphoma subtype diagnosis, and bladder cancer screening. Notably, it is the first model to generate structured reports for high-incidence colorectal cancer and diagnostically complex lymphoma-areas that are infrequently addressed by foundational models but hold immense clinical potential. Overall, PathOrchestra exemplifies the feasibility and efficacy of a large-scale, self-supervised pathology foundation model, validated across a broad range of clinical-grade tasks. Its high accuracy and reduced reliance on extensive data annotation underline its potential for clinical integration, offering a pathway toward more efficient and high-quality medical services.

Computational pathology foundation models (CPathFMs) have emerged as a powerful approach for analyzing histopathological data, leveraging self-supervised learning to extract robust feature representations from unlabeled whole-slide images. These models, categorized into uni-modal and multi-modal frameworks, have demonstrated promise in automating complex pathology tasks such as segmentation, classification, and biomarker discovery. However, the development of CPathFMs presents significant challenges, such as limited data accessibility, high variability across datasets, the necessity for domain-specific adaptation, and the lack of standardized evaluation benchmarks. This survey provides a comprehensive review of CPathFMs in computational pathology, focusing on datasets, adaptation strategies, and evaluation tasks. We analyze key techniques, such as contrastive learning and multi-modal integration, and highlight existing gaps in current research. Finally, we explore future directions from four perspectives for advancing CPathFMs. This survey serves as a valuable resource for researchers, clinicians, and AI practitioners, guiding the advancement of CPathFMs toward robust and clinically applicable AI-driven pathology solutions.

Computational methods that operate on three-dimensional molecular structure have the potential to solve important questions in biology and chemistry. In particular, deep neural networks have gained significant attention, but their widespread adoption in the biomolecular domain has been limited by a lack of either systematic performance benchmarks or a unified toolkit for interacting with molecular data. To address this, we present ATOM3D, a collection of both novel and existing benchmark datasets spanning several key classes of biomolecules. We implement several classes of three-dimensional molecular learning methods for each of these tasks and show that they consistently improve performance relative to methods based on one- and two-dimensional representations. The specific choice of architecture proves to be critical for performance, with three-dimensional convolutional networks excelling at tasks involving complex geometries, graph networks performing well on systems requiring detailed positional information, and the more recently developed equivariant networks showing significant promise. Our results indicate that many molecular problems stand to gain from three-dimensional molecular learning, and that there is potential for improvement on many tasks which remain underexplored. To lower the barrier to entry and facilitate further developments in the field, we also provide a comprehensive suite of tools for dataset processing, model training, and evaluation in our open-source atom3d Python package. All datasets are available for download from https://www.atom3d.ai .

Recent breakthroughs in self-supervised learning have enabled the use of large unlabeled datasets to train visual foundation models that can generalize to a variety of downstream tasks. While this training paradigm is well suited for the medical domain where annotations are scarce, large-scale pre-training in the medical domain, and in particular pathology, has not been extensively studied. Previous work in self-supervised learning in pathology has leveraged smaller datasets for both pre-training and evaluating downstream performance. The aim of this project is to train the largest academic foundation model and benchmark the most prominent self-supervised learning algorithms by pre-training and evaluating downstream performance on large clinical pathology datasets. We collected the largest pathology dataset to date, consisting of over 3 billion images from over 423 thousand microscopy slides. We compared pre-training of visual transformer models using the masked autoencoder (MAE) and DINO algorithms. We evaluated performance on six clinically relevant tasks from three anatomic sites and two institutions: breast cancer detection, inflammatory bowel disease detection, breast cancer estrogen receptor prediction, lung adenocarcinoma EGFR mutation prediction, and lung cancer immunotherapy response prediction. Our results demonstrate that pre-training on pathology data is beneficial for downstream performance compared to pre-training on natural images. Additionally, the DINO algorithm achieved better generalization performance across all tasks tested. The presented results signify a phase change in computational pathology research, paving the way into a new era of more performant models based on large-scale, parallel pre-training at the billion-image scale.

Recent LLM-based agents have closed substantial portions of the scientific discovery loop in software-only machine-learning research, in chemistry, and in biology. Extending the same loop to high-fidelity physical simulators is harder, because solver completion does not imply physical validity and many failure modes appear only in field-level imagery rather than in solver logs. We present AI CFD Scientist, an open-source AI scientist for computational fluid dynamics (CFD) that, to our knowledge, is the first to span literature-grounded ideation, validated execution, vision-based physics verification, source-code modification, and figure-grounded writing within a single inspectable workflow. Three coupled pathways cover parameter sweeps within a fixed solver, case-local C++ library compilation for new physical models, and open-ended hypothesis search against a reference comparator, all running on OpenFOAM through Foam-Agent. At the center of the framework is a vision-language physics-verification gate that inspects rendered flow fields before any result is accepted, rerun, or written into a manuscript. On five tasks under a shared GPT-5.5 backbone, AI CFD Scientist autonomously discovers a Spalart-Allmaras runtime correction that reduces lower-wall Cf RMSE against DNS by 7.89% on the periodic hill at Reh=5600; under matched LLM cost, two strong general AI-scientist baselines (ARIS, DeepScientist) execute partial CFD workflows but lack the domain-specific validity gates needed to convert runs into defensible scientific claims; and a controlled planted-failure ablation shows that the vision-language gate detects 14 of 16 silent failures missed by solver-level checks. Code, prompts, and run artifacts are released at https://github.com/csml-rpi/cfd-scientist.

In this paper, we introduce a novel dynamic expert selection framework for Mixture of Experts (MoE) models, aiming to enhance computational efficiency and model performance by adjusting the number of activated experts based on input difficulty. Unlike traditional MoE approaches that rely on fixed Top-K routing, which activates a predetermined number of experts regardless of the input's complexity, our method dynamically selects experts based on the confidence level in expert selection for each input. This allows for a more efficient utilization of computational resources, activating more experts for complex tasks requiring advanced reasoning and fewer for simpler tasks. Through extensive evaluations, our dynamic routing method demonstrates substantial improvements over conventional Top-2 routing across various benchmarks, achieving an average improvement of 0.7% with less than 90% activated parameters. Further analysis shows our model dispatches more experts to tasks requiring complex reasoning skills, like BBH, confirming its ability to dynamically allocate computational resources in alignment with the input's complexity. Our findings also highlight a variation in the number of experts needed across different layers of the transformer model, offering insights into the potential for designing heterogeneous MoE frameworks. The code and models are available at https://github.com/ZhenweiAn/Dynamic_MoE.

Computational efficiency and robustness are essential in process modeling, optimization, and control for real-world engineering applications. While neural network-based approaches have gained significant attention in recent years, conventional neural networks often fail to address these two critical aspects simultaneously or even independently. Inspired by natural physical systems and established literature, input convex architectures are known to enhance computational efficiency in optimization tasks, whereas Lipschitz-constrained architectures improve robustness. However, combining these properties within a single model requires careful review, as inappropriate methods for enforcing one property can undermine the other. To overcome this, we introduce a novel network architecture, termed Input Convex Lipschitz Recurrent Neural Networks (ICLRNNs). This architecture seamlessly integrates the benefits of convexity and Lipschitz continuity, enabling fast and robust neural network-based modeling and optimization. The ICLRNN outperforms existing recurrent units in both computational efficiency and robustness. Additionally, it has been successfully applied to practical engineering scenarios, such as modeling and control of chemical process and the modeling and real-world solar irradiance prediction for solar PV system planning at LHT Holdings in Singapore. Source code is available at https://github.com/killingbear999/ICLRNN.

Computational pathology needs whole-slide image (WSI) foundation models that transfer across diverse clinical tasks, yet current approaches remain largely slide-centric, often depend on private data and expensive paired-report supervision, and do not explicitly model relationships among multiple slides from the same patient. We present MOOZY, a patient-first pathology foundation model in which the patient case, not the individual slide, is the core unit of representation. MOOZY explicitly models dependencies across all slides from the same patient via a case transformer during pretraining, combining multi-stage open self-supervision with scaled low-cost task supervision. In Stage 1, we pretrain a vision-only slide encoder on 77,134 public slide feature grids using masked self-distillation. In Stage 2, we align these representations with clinical semantics using a case transformer and multi-task supervision over 333 tasks from 56 public datasets, including 205 classification and 128 survival tasks across four endpoints. Across eight held-out tasks with five-fold frozen-feature probe evaluation, MOOZY achieves best or tied-best performance on most metrics and improves macro averages over TITAN by +7.37%, +5.50%, and +7.83% and over PRISM by +8.83%, +10.70%, and +9.78% for weighted F1, weighted ROC-AUC, and balanced accuracy, respectively. MOOZY is also parameter efficient with 85.77M parameters, 14x smaller than GigaPath. These results demonstrate that open, reproducible patient-level pretraining yields transferable embeddings, providing a practical path toward scalable patient-first histopathology foundation models.

AI agents have the potential to aid users on a variety of consequential tasks, including conducting scientific research. To spur the development of useful agents, we need benchmarks that are challenging, but more crucially, directly correspond to real-world tasks of interest. This paper introduces such a benchmark, designed to measure the accuracy of AI agents in tackling a crucial yet surprisingly challenging aspect of scientific research: computational reproducibility. This task, fundamental to the scientific process, involves reproducing the results of a study using the provided code and data. We introduce CORE-Bench (Computational Reproducibility Agent Benchmark), a benchmark consisting of 270 tasks based on 90 scientific papers across three disciplines (computer science, social science, and medicine). Tasks in CORE-Bench consist of three difficulty levels and include both language-only and vision-language tasks. We provide an evaluation system to measure the accuracy of agents in a fast and parallelizable way, saving days of evaluation time for each run compared to a sequential implementation. We evaluated two baseline agents: the general-purpose AutoGPT and a task-specific agent called CORE-Agent. We tested both variants using two underlying language models: GPT-4o and GPT-4o-mini. The best agent achieved an accuracy of 21% on the hardest task, showing the vast scope for improvement in automating routine scientific tasks. Having agents that can reproduce existing work is a necessary step towards building agents that can conduct novel research and could verify and improve the performance of other research agents. We hope that CORE-Bench can improve the state of reproducibility and spur the development of future research agents.

Pathology plays a critical role in diagnosing a wide range of diseases, yet existing approaches often rely heavily on task-specific models trained on extensive, well-labeled datasets. These methods face sustainability challenges due to the diversity of pathologies and the labor-intensive nature of data collection. To address these limitations, we highlight the need for universal multimodal embeddings that can support multiple downstream tasks. Previous approaches often involve fine-tuning CLIP-based models, which handle images and text separately, limiting their ability to capture complex multimodal relationships. Additionally, these models are evaluated across diverse datasets without a unified benchmark for assessing multimodal embeddings in pathology. To address these challenges, we propose MLLM4PUE, a novel framework that leverages Multimodal Large Language Models (MLLMs) to generate Pathology Universal Embeddings. The MLLM4PUE framework not only facilitates robust integration of images and text but also enhances understanding and fusion capabilities across various tasks. We further introduce the Pathology Multimodal Embedding Benchmark (PMEB), a comprehensive benchmark designed to assess the quality of pathology multimodal embeddings. PMEB comprises 15 original tasks drawn from 14 datasets, organized into three meta-tasks: retrieval, classification, and composed retrieval. Experimental results demonstrate the superiority of MLLM4PUE, illustrating MLLM-based models can effectively support a wide range of downstream tasks and unify the research direction for foundation models in pathology.

Image-to-Image translation (I2I) is a subtype of Machine Learning (ML) that has tremendous potential in applications where two domains of images and the need for translation between the two exist, such as the removal of fog. For example, this could be useful for autonomous vehicles, which currently struggle with adverse weather conditions like fog. However, datasets for I2I tasks are not abundant and typically hard to acquire. Here, we introduce STEREOFOG, a dataset comprised of 10,067 paired fogged and clear images, captured using a custom-built device, with the purpose of exploring I2I's potential in this domain. It is the only real-world dataset of this kind to the best of our knowledge. Furthermore, we apply and optimize the pix2pix I2I ML framework to this dataset. With the final model achieving an average Complex Wavelet-Structural Similarity (CW-SSIM) score of 0.76, we prove the technique's suitability for the problem.

We address the challenge of getting efficient yet accurate recognition systems with limited labels. While recognition models improve with model size and amount of data, many specialized applications of computer vision have severe resource constraints both during training and inference. Transfer learning is an effective solution for training with few labels, however often at the expense of a computationally costly fine-tuning of large base models. We propose to mitigate this unpleasant trade-off between compute and accuracy via semi-supervised cross-domain distillation from a set of diverse source models. Initially, we show how to use task similarity metrics to select a single suitable source model to distill from, and that a good selection process is imperative for good downstream performance of a target model. We dub this approach DistillNearest. Though effective, DistillNearest assumes a single source model matches the target task, which is not always the case. To alleviate this, we propose a weighted multi-source distillation method to distill multiple source models trained on different domains weighted by their relevance for the target task into a single efficient model (named DistillWeighted). Our methods need no access to source data, and merely need features and pseudo-labels of the source models. When the goal is accurate recognition under computational constraints, both DistillNearest and DistillWeighted approaches outperform both transfer learning from strong ImageNet initializations as well as state-of-the-art semi-supervised techniques such as FixMatch. Averaged over 8 diverse target tasks our multi-source method outperforms the baselines by 5.6%-points and 4.5%-points, respectively.

Large Language Models (LLMs) like ChatGPT are capable of successfully performing many language processing tasks zero-shot (without the need for training data). If this capacity also applies to the coding of social phenomena like persuasiveness and political ideology, then LLMs could effectively transform Computational Social Science (CSS). This work provides a road map for using LLMs as CSS tools. Towards this end, we contribute a set of prompting best practices and an extensive evaluation pipeline to measure the zero-shot performance of 13 language models on 24 representative CSS benchmarks. On taxonomic labeling tasks (classification), LLMs fail to outperform the best fine-tuned models but still achieve fair levels of agreement with humans. On free-form coding tasks (generation), LLMs produce explanations that often exceed the quality of crowdworkers' gold references. We conclude that today's LLMs can radically augment the CSS research pipeline in two ways: (1) serving as zero-shot data annotators on human annotation teams, and (2) bootstrapping challenging creative generation tasks (e.g., explaining the hidden meaning behind text). In summary, LLMs can significantly reduce costs and increase efficiency of social science analysis in partnership with humans.

Polarization-based underwater 3D imaging exploits polarization cues to suppress background scattering, exhibiting distinct advantages in turbid water. Although data-driven polarization-based underwater 3D reconstruction methods show great potential, existing public datasets lack sufficient diversity in scattering and observation conditions, hindering fair comparisons among different approaches, including single-view and multi-view polarization imaging methods. To address this limitation, we construct MuS-Polar3D, a benchmark dataset comprising polarization images of 42 objects captured under seven quantitatively controlled scattering conditions and five viewpoints, together with high-precision 3D models (+/- 0.05 mm accuracy), normal maps, and foreground masks. The dataset supports multiple vision tasks, including normal estimation, object segmentation, descattering, and 3D reconstruction. Inspired by computational imaging, we further decouple underwater 3D reconstruction under scattering into a two-stage pipeline, namely descattering followed by 3D reconstruction, from an imaging-chain perspective. Extensive evaluations using multiple baseline methods under complex scattering conditions demonstrate the effectiveness of the proposed benchmark, achieving a best mean angular error of 15.49 degrees. To the best of our knowledge, MuS-Polar3D is the first publicly available benchmark dataset for quantitative turbidity underwater polarization-based 3D imaging, enabling accurate reconstruction and fair algorithm evaluation under controllable scattering conditions. The dataset and code are publicly available at https://github.com/WangPuyun/MuS-Polar3D.

Training models for Natural Language Processing (NLP) requires substantial computational resources and time, posing significant challenges, especially for NLP development in Bangla, where access to high-end hardware is often limited. In this work, we explore automatic mixed precision (AMP) training as a means to improve computational efficiency without sacrificing model performance. By leveraging a dynamic mix of 16-bit and 32-bit floating-point computations, AMP lowers GPU memory requirements and speeds up training without degrading model performance. We evaluate AMP across four standard Bangla NLP tasks, namely sentiment analysis, named entity recognition, error classification, and question answering, using four transformer-based models: BanglaBERT, BanglishBERT, XLM-R, and mBERT. Our results demonstrate that AMP accelerates training by 44.5% and reduces memory consumption by 17.6%, while maintaining F-1 score within 99.7% of the full-precision baselines. This empirical study highlights AMP's potential to democratize access to state-of-the-art NLP capabilities in hardware-constrained settings by lowering computational barriers.

Generative modeling has recently achieved remarkable success across image, video, and audio domains, demonstrating powerful capabilities for unified representation learning. Yet speech front-end tasks such as speech enhancement (SE), target speaker extraction (TSE), acoustic echo cancellation (AEC), and language-queried source separation (LASS) remain largely tackled by disparate, task-specific solutions. This fragmentation leads to redundant engineering effort, inconsistent performance, and limited extensibility. To address this gap, we introduce UniFlow, a unified framework that employs continuous generative modeling to tackle diverse speech front-end tasks in a shared latent space. Specifically, UniFlow utilizes a waveform variational autoencoder (VAE) to learn a compact latent representation of raw audio, coupled with a Diffusion Transformer (DiT) that predicts latent updates. To differentiate the speech processing task during the training, learnable condition embeddings indexed by a task ID are employed to enable maximal parameter sharing while preserving task-specific adaptability. To balance model performance and computational efficiency, we investigate and compare three generative objectives: denoising diffusion, flow matching, and mean flow within the latent domain. We validate UniFlow on multiple public benchmarks, demonstrating consistent gains over state-of-the-art baselines. UniFlow's unified latent formulation and conditional design make it readily extensible to new tasks, providing an integrated foundation for building and scaling generative speech processing pipelines. To foster future research, we will open-source our codebase.

Intermediate task transfer learning can greatly improve model performance. If, for example, one has little training data for emotion detection, first fine-tuning a language model on a sentiment classification dataset may improve performance strongly. But which task to choose for transfer learning? Prior methods producing useful task rankings are infeasible for large source pools, as they require forward passes through all source language models. We overcome this by introducing Embedding Space Maps (ESMs), light-weight neural networks that approximate the effect of fine-tuning a language model. We conduct the largest study on NLP task transferability and task selection with 12k source-target pairs. We find that applying ESMs on a prior method reduces execution time and disk space usage by factors of 10 and 278, respectively, while retaining high selection performance (avg. regret@5 score of 2.95).

We develop a novel policy synthesis algorithm, RMPflow, based on geometrically consistent transformations of Riemannian Motion Policies (RMPs). RMPs are a class of reactive motion policies designed to parameterize non-Euclidean behaviors as dynamical systems in intrinsically nonlinear task spaces. Given a set of RMPs designed for individual tasks, RMPflow can consistently combine these local policies to generate an expressive global policy, while simultaneously exploiting sparse structure for computational efficiency. We study the geometric properties of RMPflow and provide sufficient conditions for stability. Finally, we experimentally demonstrate that accounting for the geometry of task policies can simplify classically difficult problems, such as planning through clutter on high-DOF manipulation systems.

Computational pathology (CPath) digitizes pathology slides into whole slide images (WSIs), enabling analysis for critical healthcare tasks such as cancer diagnosis and prognosis. However, WSIs possess extremely long sequence lengths (up to 200K), significant length variations (from 200 to 200K), and limited supervision. These extreme variations in sequence length lead to high data heterogeneity and redundancy. Conventional methods often compromise on training efficiency and optimization to preserve such heterogeneity under limited supervision. To comprehensively address these challenges, we propose a pack-based MIL framework. It packs multiple sampled, variable-length feature sequences into fixed-length ones, enabling batched training while preserving data heterogeneity. Moreover, we introduce a residual branch that composes discarded features from multiple slides into a hyperslide which is trained with tailored labels. It offers multi-slide supervision while mitigating feature loss from sampling. Meanwhile, an attention-driven downsampler is introduced to compress features in both branches to reduce redundancy. By alleviating these challenges, our approach achieves an accuracy improvement of up to 8% while using only 12% of the training time in the PANDA(UNI). Extensive experiments demonstrate that focusing data challenges in CPath holds significant potential in the era of foundation models. The code is https://github.com/FangHeng/PackMIL

Large language models(LLMs) have shown its outperforming ability on various tasks and question answering. However, LLMs require high computation cost and large memory cost. At the same time, LLMs may cause privacy leakage when training or prediction procedure contains sensitive information. In this paper, we propose SPA(Side Plugin Adaption), a lightweight architecture for fast on-devices inference and privacy retaining on the constraints of strict on-devices computation and memory constraints. Compared with other on-devices seq2seq generation, SPA could make a fast and stable inference on low-resource constraints, allowing it to obtain cost effiency. Our method establish an interaction between a pretrained LLMs on-cloud and additive parameters on-devices, which could provide the knowledge on both pretrained LLMs and private personal feature.Further more, SPA provides a framework to keep feature-base parameters on private guaranteed but low computational devices while leave the parameters containing general information on the high computational devices.

Categorical variables often appear in datasets for classification and regression tasks, and they need to be encoded into numerical values before training. Since many encoders have been developed and can significantly impact performance, choosing the appropriate encoder for a task becomes a time-consuming yet important practical issue. This study broadly classifies machine learning models into three categories: 1) ATI models that implicitly perform affine transformations on inputs, such as multi-layer perceptron neural network; 2) Tree-based models that are based on decision trees, such as random forest; and 3) the rest, such as kNN. Theoretically, we prove that the one-hot encoder is the best choice for ATI models in the sense that it can mimic any other encoders by learning suitable weights from the data. We also explain why the target encoder and its variants are the most suitable encoders for tree-based models. This study conducted comprehensive computational experiments to evaluate 14 encoders, including one-hot and target encoders, along with eight common machine-learning models on 28 datasets. The computational results agree with our theoretical analysis. The findings in this study shed light on how to select the suitable encoder for data scientists in fields such as fraud detection, disease diagnosis, etc.

We propose that small pretrained foundational generative language models with millions of parameters can be utilized as a general learning framework for sequence-based tasks. Our proposal overcomes the computational resource, skill set, and timeline challenges associated with training neural networks and language models from scratch. Further, our approach focuses on creating small and highly specialized models that can accurately execute a challenging task of which the base model is incapable of performing. We demonstrate that 125M, 350M, and 1.3B parameter pretrained foundational language models can be instruction fine-tuned with 10,000-to-1,000,000 instruction examples to achieve near state-of-the-art results on challenging cheminformatics tasks. We also demonstrate the role of successive language model fine-tuning epochs on improved outcomes, as well as the importance of both data formatting and pretrained foundational language model selection for instruction fine-tuning success.

Classification algorithms have recently found applications in computational physics for the selection of numerical methods or models adapted to the environment and the state of the physical system. For such classification tasks, labeled training data come from numerical simulations and generally correspond to physical fields discretized on a mesh. Three challenging difficulties arise: the lack of training data, their high dimensionality, and the non-applicability of common data augmentation techniques to physics data. This article introduces two algorithms to address these issues, one for dimensionality reduction via feature selection, and one for data augmentation. These algorithms are combined with a wide variety of classifiers for their evaluation. When combined with a stacking ensemble made of six multilayer perceptrons and a ridge logistic regression, they enable reaching an accuracy of 90% on our classification problem for nonlinear structural mechanics.

LLMs have shown promise in replicating human-like behavior in crowdsourcing tasks that were previously thought to be exclusive to human abilities. However, current efforts focus mainly on simple atomic tasks. We explore whether LLMs can replicate more complex crowdsourcing pipelines. We find that modern LLMs can simulate some of crowdworkers' abilities in these "human computation algorithms," but the level of success is variable and influenced by requesters' understanding of LLM capabilities, the specific skills required for sub-tasks, and the optimal interaction modality for performing these sub-tasks. We reflect on human and LLMs' different sensitivities to instructions, stress the importance of enabling human-facing safeguards for LLMs, and discuss the potential of training humans and LLMs with complementary skill sets. Crucially, we show that replicating crowdsourcing pipelines offers a valuable platform to investigate (1) the relative strengths of LLMs on different tasks (by cross-comparing their performances on sub-tasks) and (2) LLMs' potential in complex tasks, where they can complete part of the tasks while leaving others to humans.

Large Language Models (LLMs) have demonstrated considerable proficiency in general natural language processing (NLP) tasks. Instruction tuning, a successful paradigm, enhances the ability of LLMs to follow natural language instructions and exhibit robust generalization across a wide range of tasks. However, these models often encounter performance limitations across multiple tasks due to constrained model capacity. Expanding this capacity during the instruction tuning phase poses significant challenges. To address this issue, we introduce a novel approach, Parameter-Efficient Sparsity Crafting (PESC), which transitions dense models to sparse models using a Mixture of Experts (MoE) architecture. PESC integrates adapters into the MoE layers of sparse models, differentiating experts without altering the individual weights within these layers. This method significantly reduces computational costs and GPU memory requirements, facilitating model capacity expansion through a minimal increase in parameters via the inserted adapters. Our empirical evaluation demonstrates the effectiveness of the PESC method. Using PESC during instruction tuning, our sparse models, dubbed Camelidae outperform all other opensource sparse models and exhibit superior general capabilities compared to GPT3.5.

Multiple Instance Learning (MIL) has emerged as a dominant paradigm to extract discriminative feature representations within Whole Slide Images (WSIs) in computational pathology. Despite driving notable progress, existing MIL approaches suffer from limitations in facilitating comprehensive and efficient interactions among instances, as well as challenges related to time-consuming computations and overfitting. In this paper, we incorporate the Selective Scan Space State Sequential Model (Mamba) in Multiple Instance Learning (MIL) for long sequence modeling with linear complexity, termed as MambaMIL. By inheriting the capability of vanilla Mamba, MambaMIL demonstrates the ability to comprehensively understand and perceive long sequences of instances. Furthermore, we propose the Sequence Reordering Mamba (SR-Mamba) aware of the order and distribution of instances, which exploits the inherent valuable information embedded within the long sequences. With the SR-Mamba as the core component, MambaMIL can effectively capture more discriminative features and mitigate the challenges associated with overfitting and high computational overhead. Extensive experiments on two public challenging tasks across nine diverse datasets demonstrate that our proposed framework performs favorably against state-of-the-art MIL methods. The code is released at https://github.com/isyangshu/MambaMIL.

Large Language Models (LLMs) have demonstrated strong performance across general NLP tasks, but their utility in automating numerical experiments of complex physical system -- a critical and labor-intensive component -- remains underexplored. As the major workhorse of computational science over the past decades, Computational Fluid Dynamics (CFD) offers a uniquely challenging testbed for evaluating the scientific capabilities of LLMs. We introduce CFDLLMBench, a benchmark suite comprising three complementary components -- CFDQuery, CFDCodeBench, and FoamBench -- designed to holistically evaluate LLM performance across three key competencies: graduate-level CFD knowledge, numerical and physical reasoning of CFD, and context-dependent implementation of CFD workflows. Grounded in real-world CFD practices, our benchmark combines a detailed task taxonomy with a rigorous evaluation framework to deliver reproducible results and quantify LLM performance across code executability, solution accuracy, and numerical convergence behavior. CFDLLMBench establishes a solid foundation for the development and evaluation of LLM-driven automation of numerical experiments for complex physical systems. Code and data are available at https://github.com/NREL-Theseus/cfdllmbench/.

Large Language Models have significantly advanced natural language processing, achieving remarkable performance in tasks such as language generation, translation, and reasoning. However, their substantial computational requirements restrict deployment to high-end systems, limiting accessibility on consumer-grade devices. This challenge is especially pronounced for under-resourced languages like those spoken in the Iberian Peninsula, where relatively limited linguistic resources and benchmarks hinder effective evaluation. This work presents a comprehensive evaluation of compact state-of-the-art LLMs across several essential NLP tasks tailored for Iberian languages. The results reveal that while some models consistently excel in certain tasks, significant performance gaps remain, particularly for languages such as Basque. These findings highlight the need for further research on balancing model compactness with robust multilingual performance

In recent years, large language models (LLMs) have emerged as promising candidates for graph tasks. Many studies leverage natural language to describe graphs and apply LLMs for reasoning, yet most focus narrowly on performance benchmarks without fully comparing LLMs to graph learning models or exploring their broader potential. In this work, we present a comprehensive study of LLMs on graph learning tasks, evaluating both off-the-shelf and instruction-tuned models across a variety of scenarios. Beyond accuracy, we discuss data leakage concerns and computational overhead, and assess their performance under few-shot/zero-shot settings, domain transfer, structural understanding, and robustness. Our findings show that LLMs, particularly those with instruction tuning, greatly outperform traditional graph learning models in few-shot settings, exhibit strong domain transferability, and demonstrate excellent generalization and robustness. Our study highlights the broader capabilities of LLMs in graph learning and provides a foundation for future research.

How to efficiently serve Large Language Models (LLMs) has become a pressing issue because of their huge computational cost in their autoregressive generation process. To mitigate computational costs, LLMs often employ the KV Cache technique to improve the generation speed. While improving the computational efficiency, the storage requirements of the KV cache are substantial, particularly in long-context scenarios, leading to significant memory consumption. Existing KV cache eviction methods often degrade the performance of LLMs in long-context scenarios due to the information loss introduced by eviction. In this paper, we propose a novel KV cache merging approach, called KVMerger, to achieve adaptive KV cache compression for long-context tasks without significant performance degradation under constrained memory budgets. Our approach is inspired by the intriguing observation that key states exhibit high similarity at the token level within a single sequence. To facilitate merging, we develop an effective yet straightforward merging set identification algorithm to identify suitable KV states for merging. Our merging set identification algorithm stimulates the second observation that KV cache sparsity, from similarity perspective, is independent of the dataset and remains persistent at the model level. Subsequently, we propose a Gaussian kernel weighted merging algorithm to selectively merge all states within each merging set. We conduct extensive experiments to demonstrate the effectiveness of KVMerger for long-context tasks under constrained memory budgets, applying it to models including Llama2-7B-chat and Llama2-13B-chat. Using the LongBench and ZeroScroll benchmarks, we compare our method with other KV cache compression techniques, including H2O and CaM, showing that our method achieves superior performance across tasks with both 50% and 35% KV cache budgets.

Computational pathology relies on effective representation learning to support cancer research and precision medicine. Although self-supervised learning has driven major progress at the patch and whole-slide image levels, representation learning at the single-cell level remains comparatively underexplored, despite its importance for characterizing cell types and cellular phenotypes. We introduce LEMON (Learning Embeddings from Morphology Of Nuclei), a self-supervised foundation model for scalable single-cell image representation learning. Trained on millions of cell images from diverse tissues and cancer types, LEMON learns robust and versatile morphological representations that support large-scale single-cell analyses in pathology. We evaluate LEMON on five benchmark datasets across a range of prediction tasks and show that it provides strong performance, highlighting its potential as a new paradigm for cell-level computational pathology. Model weights are available at https://huggingface.co/aliceblondel/LEMON.

Representation learning of pathology whole-slide images (WSIs) has been has primarily relied on weak supervision with Multiple Instance Learning (MIL). However, the slide representations resulting from this approach are highly tailored to specific clinical tasks, which limits their expressivity and generalization, particularly in scenarios with limited data. Instead, we hypothesize that morphological redundancy in tissue can be leveraged to build a task-agnostic slide representation in an unsupervised fashion. To this end, we introduce PANTHER, a prototype-based approach rooted in the Gaussian mixture model that summarizes the set of WSI patches into a much smaller set of morphological prototypes. Specifically, each patch is assumed to have been generated from a mixture distribution, where each mixture component represents a morphological exemplar. Utilizing the estimated mixture parameters, we then construct a compact slide representation that can be readily used for a wide range of downstream tasks. By performing an extensive evaluation of PANTHER on subtyping and survival tasks using 13 datasets, we show that 1) PANTHER outperforms or is on par with supervised MIL baselines and 2) the analysis of morphological prototypes brings new qualitative and quantitative insights into model interpretability.

Webpages have been a rich, scalable resource for vision-language and language only tasks. Yet only pieces of webpages are kept: image-caption pairs, long text articles, or raw HTML, never all in one place. Webpage tasks have resultingly received little attention and structured image-text data left underused. To study multimodal webpage understanding, we introduce the Wikipedia Webpage suite (WikiWeb2M) of 2M pages. We verify its utility on three generative tasks: page description generation, section summarization, and contextual image captioning. We design a novel attention mechanism Prefix Global, which selects the most relevant image and text content as global tokens to attend to the rest of the webpage for context. By using page structure to separate such tokens, it performs better than full attention with lower computational complexity. Experiments show that the new annotations from WikiWeb2M improve task performance compared to data from prior work. We also include ablations on sequence length, input features, and model size.

Surrogate models are necessary to optimize meaningful quantities in physical dynamics as their recursive numerical resolutions are often prohibitively expensive. It is mainly the case for fluid dynamics and the resolution of Navier-Stokes equations. However, despite the fast-growing field of data-driven models for physical systems, reference datasets representing real-world phenomena are lacking. In this work, we develop AirfRANS, a dataset for studying the two-dimensional incompressible steady-state Reynolds-Averaged Navier-Stokes equations over airfoils at a subsonic regime and for different angles of attacks. We also introduce metrics on the stress forces at the surface of geometries and visualization of boundary layers to assess the capabilities of models to accurately predict the meaningful information of the problem. Finally, we propose deep learning baselines on four machine learning tasks to study AirfRANS under different constraints for generalization considerations: big and scarce data regime, Reynolds number, and angle of attack extrapolation.

Access to external knowledge is essential for many natural language processing tasks, such as question answering and dialogue. Existing methods often rely on a parametric model that stores knowledge in its parameters, or use a retrieval-augmented model that has access to an external knowledge source. Parametric and retrieval-augmented models have complementary strengths in terms of computational efficiency and predictive accuracy. To combine the strength of both approaches, we propose the Efficient Memory-Augmented Transformer (EMAT) -- it encodes external knowledge into a key-value memory and exploits the fast maximum inner product search for memory querying. We also introduce pre-training tasks that allow EMAT to encode informative key-value representations, and to learn an implicit strategy to integrate multiple memory slots into the transformer. Experiments on various knowledge-intensive tasks such as question answering and dialogue datasets show that, simply augmenting parametric models (T5-base) using our method produces more accurate results (e.g., 25.8 -> 44.3 EM on NQ) while retaining a high throughput (e.g., 1000 queries/s on NQ). Compared to retrieval-augmented models, EMAT runs substantially faster across the board and produces more accurate results on WoW and ELI5. Our code and datasets are available at https://github. com/uclnlp/EMAT.

Developing large-scale foundational datasets is a critical milestone in advancing artificial intelligence (AI)-driven scientific innovation. However, unlike AI-mature fields such as natural language processing, materials science, particularly polymer research, has significantly lagged in developing extensive open datasets. This lag is primarily due to the high costs of polymer synthesis and property measurements, along with the vastness and complexity of the chemical space. This study presents PolyOmics, an omics-scale computational database generated through fully automated molecular dynamics simulation pipelines that provide diverse physical properties for over 10^5 polymeric materials. The PolyOmics database is collaboratively developed by approximately 260 researchers from 48 institutions to bridge the gap between academia and industry. Machine learning models pretrained on PolyOmics can be efficiently fine-tuned for a wide range of real-world downstream tasks, even when only limited experimental data are available. Notably, the generalisation capability of these simulation-to-real transfer models improve significantly as the size of the PolyOmics database increases, exhibiting power-law scaling. The emergence of scaling laws supports the "more is better" principle, highlighting the significance of ultralarge-scale computational materials data for improving real-world prediction performance. This unprecedented omics-scale database reveals vast unexplored regions of polymer materials, providing a foundation for AI-driven polymer science.

Building generalist models has recently demonstrated remarkable capabilities in diverse scientific domains. Within the realm of molecular learning, several studies have explored unifying diverse tasks across diverse domains. However, negative conflicts and interference between molecules and knowledge from different domain may have a worse impact in threefold. First, conflicting molecular representations can lead to optimization difficulties for the models. Second, mixing and scaling up training data across diverse tasks is inherently challenging. Third, the computational cost of refined pretraining is prohibitively high. To address these limitations, this paper presents Omni-Mol, a scalable and unified LLM-based framework for direct instruction tuning. Omni-Mol builds on three key components to tackles conflicts: (1) a unified encoding mechanism for any task input; (2) an active-learning-driven data selection strategy that significantly reduces dataset size; (3) a novel design of the adaptive gradient stabilization module and anchor-and-reconcile MoE framework that ensures stable convergence. Experimentally, Omni-Mol achieves state-of-the-art performance across 15 molecular tasks, demonstrates the presence of scaling laws in the molecular domain, and is supported by extensive ablation studies and analyses validating the effectiveness of its design. The code and weights of the powerful AI-driven chemistry generalist are open-sourced at: https://anonymous.4open.science/r/Omni-Mol-8EDB.

Recent advances in Retrieval-Augmented Generation (RAG) systems have popularized semantic chunking, which aims to improve retrieval performance by dividing documents into semantically coherent segments. Despite its growing adoption, the actual benefits over simpler fixed-size chunking, where documents are split into consecutive, fixed-size segments, remain unclear. This study systematically evaluates the effectiveness of semantic chunking using three common retrieval-related tasks: document retrieval, evidence retrieval, and retrieval-based answer generation. The results show that the computational costs associated with semantic chunking are not justified by consistent performance gains. These findings challenge the previous assumptions about semantic chunking and highlight the need for more efficient chunking strategies in RAG systems.

This paper presents a novel approach to generating behavior trees for robots using lightweight large language models (LLMs) with a maximum of 7 billion parameters. The study demonstrates that it is possible to achieve satisfying results with compact LLMs when fine-tuned on a specific dataset. The key contributions of this research include the creation of a fine-tuning dataset based on existing behavior trees using GPT-3.5 and a comprehensive comparison of multiple LLMs (namely llama2, llama-chat, and code-llama) across nine distinct tasks. To be thorough, we evaluated the generated behavior trees using static syntactical analysis, a validation system, a simulated environment, and a real robot. Furthermore, this work opens the possibility of deploying such solutions directly on the robot, enhancing its practical applicability. Findings from this study demonstrate the potential of LLMs with a limited number of parameters in generating effective and efficient robot behaviors.

Understanding the internal representations learned by neural networks is a cornerstone challenge in the science of machine learning. While there have been significant recent strides in some cases towards understanding how neural networks implement specific target functions, this paper explores a complementary question -- why do networks arrive at particular computational strategies? Our inquiry focuses on the algebraic learning tasks of modular addition, sparse parities, and finite group operations. Our primary theoretical findings analytically characterize the features learned by stylized neural networks for these algebraic tasks. Notably, our main technique demonstrates how the principle of margin maximization alone can be used to fully specify the features learned by the network. Specifically, we prove that the trained networks utilize Fourier features to perform modular addition and employ features corresponding to irreducible group-theoretic representations to perform compositions in general groups, aligning closely with the empirical observations of Nanda et al. and Chughtai et al. More generally, we hope our techniques can help to foster a deeper understanding of why neural networks adopt specific computational strategies.

Biological cortical neurons are remarkably sophisticated computational devices, temporally integrating their vast synaptic input over an intricate dendritic tree, subject to complex, nonlinearly interacting internal biological processes. A recent study proposed to characterize this complexity by fitting accurate surrogate models to replicate the input-output relationship of a detailed biophysical cortical pyramidal neuron model and discovered it needed temporal convolutional networks (TCN) with millions of parameters. Requiring these many parameters, however, could stem from a misalignment between the inductive biases of the TCN and cortical neuron's computations. In light of this, and to explore the computational implications of leaky memory units and nonlinear dendritic processing, we introduce the Expressive Leaky Memory (ELM) neuron model, a biologically inspired phenomenological model of a cortical neuron. Remarkably, by exploiting such slowly decaying memory-like hidden states and two-layered nonlinear integration of synaptic input, our ELM neuron can accurately match the aforementioned input-output relationship with under ten thousand trainable parameters. To further assess the computational ramifications of our neuron design, we evaluate it on various tasks with demanding temporal structures, including the Long Range Arena (LRA) datasets, as well as a novel neuromorphic dataset based on the Spiking Heidelberg Digits dataset (SHD-Adding). Leveraging a larger number of memory units with sufficiently long timescales, and correspondingly sophisticated synaptic integration, the ELM neuron displays substantial long-range processing capabilities, reliably outperforming the classic Transformer or Chrono-LSTM architectures on LRA, and even solving the Pathfinder-X task with over 70% accuracy (16k context length).

A user-generated text on social media enables health workers to keep track of information, identify possible outbreaks, forecast disease trends, monitor emergency cases, and ascertain disease awareness and response to official health correspondence. This exchange of health information on social media has been regarded as an attempt to enhance public health surveillance (PHS). Despite its potential, the technology is still in its early stages and is not ready for widespread application. Advancements in pretrained language models (PLMs) have facilitated the development of several domain-specific PLMs and a variety of downstream applications. However, there are no PLMs for social media tasks involving PHS. We present and release PHS-BERT, a transformer-based PLM, to identify tasks related to public health surveillance on social media. We compared and benchmarked the performance of PHS-BERT on 25 datasets from different social medial platforms related to 7 different PHS tasks. Compared with existing PLMs that are mainly evaluated on limited tasks, PHS-BERT achieved state-of-the-art performance on all 25 tested datasets, showing that our PLM is robust and generalizable in the common PHS tasks. By making PHS-BERT available, we aim to facilitate the community to reduce the computational cost and introduce new baselines for future works across various PHS-related tasks.

Bangla -- ranked as the 6th most widely spoken language across the world (https://www.ethnologue.com/guides/ethnologue200), with 230 million native speakers -- is still considered as a low-resource language in the natural language processing (NLP) community. With three decades of research, Bangla NLP (BNLP) is still lagging behind mainly due to the scarcity of resources and the challenges that come with it. There is sparse work in different areas of BNLP; however, a thorough survey reporting previous work and recent advances is yet to be done. In this study, we first provide a review of Bangla NLP tasks, resources, and tools available to the research community; we benchmark datasets collected from various platforms for nine NLP tasks using current state-of-the-art algorithms (i.e., transformer-based models). We provide comparative results for the studied NLP tasks by comparing monolingual vs. multilingual models of varying sizes. We report our results using both individual and consolidated datasets and provide data splits for future research. We reviewed a total of 108 papers and conducted 175 sets of experiments. Our results show promising performance using transformer-based models while highlighting the trade-off with computational costs. We hope that such a comprehensive survey will motivate the community to build on and further advance the research on Bangla NLP.

What is the current state-of-the-art for image restoration and enhancement applied to degraded images acquired under less than ideal circumstances? Can the application of such algorithms as a pre-processing step to improve image interpretability for manual analysis or automatic visual recognition to classify scene content? While there have been important advances in the area of computational photography to restore or enhance the visual quality of an image, the capabilities of such techniques have not always translated in a useful way to visual recognition tasks. Consequently, there is a pressing need for the development of algorithms that are designed for the joint problem of improving visual appearance and recognition, which will be an enabling factor for the deployment of visual recognition tools in many real-world scenarios. To address this, we introduce the UG^2 dataset as a large-scale benchmark composed of video imagery captured under challenging conditions, and two enhancement tasks designed to test algorithmic impact on visual quality and automatic object recognition. Furthermore, we propose a set of metrics to evaluate the joint improvement of such tasks as well as individual algorithmic advances, including a novel psychophysics-based evaluation regime for human assessment and a realistic set of quantitative measures for object recognition performance. We introduce six new algorithms for image restoration or enhancement, which were created as part of the IARPA sponsored UG^2 Challenge workshop held at CVPR 2018. Under the proposed evaluation regime, we present an in-depth analysis of these algorithms and a host of deep learning-based and classic baseline approaches. From the observed results, it is evident that we are in the early days of building a bridge between computational photography and visual recognition, leaving many opportunities for innovation in this area.

Scaling the size of language models usually leads to remarkable advancements in NLP tasks. But it often comes with a price of growing computational cost. Although a sparse Mixture of Experts (MoE) can reduce the cost by activating a small subset of parameters (e.g., one expert) for each input, its computation escalates significantly if increasing the number of activated experts, limiting its practical utility. Can we retain the advantages of adding more experts without substantially increasing the computational costs? In this paper, we first demonstrate the superiority of selecting multiple experts and then propose a computation-efficient approach called \texttt{Merging Experts into One} (MEO), which reduces the computation cost to that of a single expert. Extensive experiments show that MEO significantly improves computational efficiency, e.g., FLOPS drops from 72.0G of vanilla MoE to 28.6G (MEO). Moreover, we propose a token-level attention block that further enhances the efficiency and performance of token-level MEO, e.g., 83.3\% (MEO) vs. 82.6\% (vanilla MoE) average score on the GLUE benchmark. Our code will be released upon acceptance. Code will be released at: https://github.com/Shwai-He/MEO.

Deep learning's recent history has been one of achievement: from triumphing over humans in the game of Go to world-leading performance in image classification, voice recognition, translation, and other tasks. But this progress has come with a voracious appetite for computing power. This article catalogs the extent of this dependency, showing that progress across a wide variety of applications is strongly reliant on increases in computing power. Extrapolating forward this reliance reveals that progress along current lines is rapidly becoming economically, technically, and environmentally unsustainable. Thus, continued progress in these applications will require dramatically more computationally-efficient methods, which will either have to come from changes to deep learning or from moving to other machine learning methods.

Semantic vectors are learned from data to express semantic relationships between elements of information, for the purpose of solving and informing downstream tasks. Other models exist that learn to map and classify supervised data. However, the two worlds of learning rarely interact to inform one another dynamically, whether across types of data or levels of semantics, in order to form a unified model. We explore the research problem of learning these vectors and propose a framework for learning the semantics of knowledge incrementally and online, across multiple mediums of data, via binary vectors. We discuss the aspects of this framework to spur future research on this approach and problem.

We present ReasonIR-8B, the first retriever specifically trained for general reasoning tasks. Existing retrievers have shown limited gains on reasoning tasks, in part because existing training datasets focus on short factual queries tied to documents that straightforwardly answer them. We develop a synthetic data generation pipeline that, for each document, our pipeline creates a challenging and relevant query, along with a plausibly related but ultimately unhelpful hard negative. By training on a mixture of our synthetic data and existing public data, ReasonIR-8B achieves a new state-of-the-art of 29.9 nDCG@10 without reranker and 36.9 nDCG@10 with reranker on BRIGHT, a widely-used reasoning-intensive information retrieval (IR) benchmark. When applied to RAG tasks, ReasonIR-8B improves MMLU and GPQA performance by 6.4% and 22.6% respectively, relative to the closed-book baseline, outperforming other retrievers and search engines. In addition, ReasonIR-8B uses test-time compute more effectively: on BRIGHT, its performance consistently increases with longer and more information-rich rewritten queries; it continues to outperform other retrievers when combined with an LLM reranker. Our training recipe is general and can be easily extended to future LLMs; to this end, we open-source our code, data, and model.

With advances in foundational and vision-language models, and effective fine-tuning techniques, a large number of both general and special-purpose models have been developed for a variety of visual tasks. Despite the flexibility and accessibility of these models, no single model is able to handle all tasks and/or applications that may be envisioned by potential users. Recent approaches, such as visual programming and multimodal LLMs with integrated tools aim to tackle complex visual tasks, by way of program synthesis. However, such approaches overlook user constraints (e.g., performance / computational needs), produce test-time sample-specific solutions that are difficult to deploy, and, sometimes, require low-level instructions that maybe beyond the abilities of a naive user. To address these limitations, we introduce MMFactory, a universal framework that includes model and metrics routing components, acting like a solution search engine across various available models. Based on a task description and few sample input-output pairs and (optionally) resource and/or performance constraints, MMFactory can suggest a diverse pool of programmatic solutions by instantiating and combining visio-lingual tools from its model repository. In addition to synthesizing these solutions, MMFactory also proposes metrics and benchmarks performance / resource characteristics, allowing users to pick a solution that meets their unique design constraints. From the technical perspective, we also introduced a committee-based solution proposer that leverages multi-agent LLM conversation to generate executable, diverse, universal, and robust solutions for the user. Experimental results show that MMFactory outperforms existing methods by delivering state-of-the-art solutions tailored to user problem specifications. Project page is available at https://davidhalladay.github.io/mmfactory_demo.

Existing Visual-Language-Action (VLA) models have shown promising performance in zero-shot scenarios, demonstrating impressive task execution and reasoning capabilities. However, a significant challenge arises from the limitations of visual encoding, which can result in failures during tasks such as object grasping. Moreover, these models typically suffer from high computational overhead due to their large sizes, often exceeding 7B parameters. While these models excel in reasoning and task planning, the substantial computational overhead they incur makes them impractical for real-time robotic environments, where speed and efficiency are paramount. To address the limitations of existing VLA models, we propose NORA, a 3B-parameter model designed to reduce computational overhead while maintaining strong task performance. NORA adopts the Qwen-2.5-VL-3B multimodal model as its backbone, leveraging its superior visual-semantic understanding to enhance visual reasoning and action grounding. Additionally, our is trained on 970k real-world robot demonstrations and equipped with the FAST+ tokenizer for efficient action sequence generation. Experimental results demonstrate that NORA outperforms existing large-scale VLA models, achieving better task performance with significantly reduced computational overhead, making it a more practical solution for real-time robotic autonomy.

Large Language Models (LLMs) and LLM-based agents show great promise in accelerating scientific research. Existing benchmarks for measuring this potential and guiding future development continue to evolve from pure recall and rote knowledge tasks, towards more practical work such as literature review and experimental planning. Bioinformatics is a domain where fully autonomous AI-driven discovery may be near, but no extensive benchmarks for measuring progress have been introduced to date. We therefore present the Bioinformatics Benchmark (BixBench), a dataset comprising over 50 real-world scenarios of practical biological data analysis with nearly 300 associated open-answer questions designed to measure the ability of LLM-based agents to explore biological datasets, perform long, multi-step analytical trajectories, and interpret the nuanced results of those analyses. We evaluate the performance of two frontier LLMs (GPT-4o and Claude 3.5 Sonnet) using a custom agent framework we open source. We find that even the latest frontier models only achieve 17% accuracy in the open-answer regime, and no better than random in a multiple-choice setting. By exposing the current limitations of frontier models, we hope BixBench can spur the development of agents capable of conducting rigorous bioinformatic analysis and accelerate scientific discovery.

The accelerated adoption of digital pathology and advances in deep learning have enabled the development of powerful models for various pathology tasks across a diverse array of diseases and patient cohorts. However, model training is often difficult due to label scarcity in the medical domain and the model's usage is limited by the specific task and disease for which it is trained. Additionally, most models in histopathology leverage only image data, a stark contrast to how humans teach each other and reason about histopathologic entities. We introduce CONtrastive learning from Captions for Histopathology (CONCH), a visual-language foundation model developed using diverse sources of histopathology images, biomedical text, and notably over 1.17 million image-caption pairs via task-agnostic pretraining. Evaluated on a suite of 13 diverse benchmarks, CONCH can be transferred to a wide range of downstream tasks involving either or both histopathology images and text, achieving state-of-the-art performance on histology image classification, segmentation, captioning, text-to-image and image-to-text retrieval. CONCH represents a substantial leap over concurrent visual-language pretrained systems for histopathology, with the potential to directly facilitate a wide array of machine learning-based workflows requiring minimal or no further supervised fine-tuning.

Deep learning on climatic data holds potential for macroecological applications. However, its adoption remains limited among scientists outside the deep learning community due to storage, compute, and technical expertise barriers. To address this, we introduce Climplicit, a spatio-temporal geolocation encoder pretrained to generate implicit climatic representations anywhere on Earth. By bypassing the need to download raw climatic rasters and train feature extractors, our model uses x3500 less disk space and significantly reduces computational needs for downstream tasks. We evaluate our Climplicit embeddings on biomes classification, species distribution modeling, and plant trait regression. We find that single-layer probing our Climplicit embeddings consistently performs better or on par with training a model from scratch on downstream tasks and overall better than alternative geolocation encoding models.

Recent open-source large reasoning models (LRMs) exhibit strong performance on complex reasoning tasks, but their large parameter count makes them prohibitively expensive for individuals. The compression of large language models (LLMs) offers an effective solution to reduce cost of computational resources. However, systematic studies on the performance of compressed LLMs in complex reasoning tasks, especially for LRMs, are lacking. Most works on quantization and pruning focus on preserving language modeling performance, while existing distillation works do not comprehensively benchmark student models based on reasoning difficulty or compression impact on knowledge and reasoning. In this paper, we benchmark compressed DeepSeek-R1 models on four different reasoning datasets (AIME 2024, FOLIO, Temporal Sequences of BIG-Bench Hard, and MuSiQue), ranging from mathematical to multihop reasoning, using quantization, distillation, and pruning methods. We benchmark 2.51-, 1.73-, and 1.58-bit R1 models that adopt dynamic quantization. We also benchmark distilled R1 models that are based on LLaMA or Qwen and run SparseGPT on them to obtain various sparsity levels. Studying the performance and behavior of compressed LRMs, we report their performance scores and test-time compute (number of tokens spent on each question). Notably, using MuSiQue, we find that parameter count has a much greater impact on LRMs' knowledge memorization than on their reasoning capability, which can inform the choice of compression techniques. Through our empirical analysis of test-time compute, we find that shorter model outputs generally achieve better performance than longer ones across several benchmarks for both R1 and its compressed variants, highlighting the need for more concise reasoning chains.

Large language models (LLMs) are known to struggle with complicated reasoning tasks such as math word problems (MWPs). In this paper, we present how analogy from similarly structured questions can improve LLMs' problem-solving capabilities for MWPs. Specifically, we rely on the retrieval of problems with similar computational graphs to the given question to serve as exemplars in the prompt, providing the correct reasoning path for the generation model to refer to. Empirical results across six math word problem datasets demonstrate the effectiveness of our proposed method, which achieves a significant improvement of up to 6.7 percent on average in absolute value, compared to baseline methods. These results highlight our method's potential in addressing the reasoning challenges in current LLMs.

RNA plays a pivotal role in translating genetic instructions into functional outcomes, underscoring its importance in biological processes and disease mechanisms. Despite the emergence of numerous deep learning approaches for RNA, particularly universal RNA language models, there remains a significant lack of standardized benchmarks to assess the effectiveness of these methods. In this study, we introduce the first comprehensive RNA benchmark BEACON (BEnchmArk for COmprehensive RNA Task and Language Models). First, BEACON comprises 13 distinct tasks derived from extensive previous work covering structural analysis, functional studies, and engineering applications, enabling a comprehensive assessment of the performance of methods on various RNA understanding tasks. Second, we examine a range of models, including traditional approaches like CNNs, as well as advanced RNA foundation models based on language models, offering valuable insights into the task-specific performances of these models. Third, we investigate the vital RNA language model components from the tokenizer and positional encoding aspects. Notably, our findings emphasize the superiority of single nucleotide tokenization and the effectiveness of Attention with Linear Biases (ALiBi) over traditional positional encoding methods. Based on these insights, a simple yet strong baseline called BEACON-B is proposed, which can achieve outstanding performance with limited data and computational resources. The datasets and source code of our benchmark are available at https://github.com/terry-r123/RNABenchmark.

Recent work in mechanistic interpretability has shown that behaviors in language models can be successfully reverse-engineered through circuit analysis. A common criticism, however, is that each circuit is task-specific, and thus such analysis cannot contribute to understanding the models at a higher level. In this work, we present evidence that insights (both low-level findings about specific heads and higher-level findings about general algorithms) can indeed generalize across tasks. Specifically, we study the circuit discovered in Wang et al. (2022) for the Indirect Object Identification (IOI) task and 1.) show that it reproduces on a larger GPT2 model, and 2.) that it is mostly reused to solve a seemingly different task: Colored Objects (Ippolito & Callison-Burch, 2023). We provide evidence that the process underlying both tasks is functionally very similar, and contains about a 78% overlap in in-circuit attention heads. We further present a proof-of-concept intervention experiment, in which we adjust four attention heads in middle layers in order to 'repair' the Colored Objects circuit and make it behave like the IOI circuit. In doing so, we boost accuracy from 49.6% to 93.7% on the Colored Objects task and explain most sources of error. The intervention affects downstream attention heads in specific ways predicted by their interactions in the IOI circuit, indicating that this subcircuit behavior is invariant to the different task inputs. Overall, our results provide evidence that it may yet be possible to explain large language models' behavior in terms of a relatively small number of interpretable task-general algorithmic building blocks and computational components.

Finetuning large language models inflates the costs of NLU applications and remains the bottleneck of development cycles. Recent works in computer vision use data pruning to reduce training time. Pruned data selection with static methods is based on a score calculated for each training example prior to finetuning, which involves important computational overhead. Moreover, the score may not necessarily be representative of sample importance throughout the entire training duration. We propose to address these issues with a refined version of dynamic data pruning, a curriculum which periodically scores and discards unimportant examples during finetuning. Our method leverages an EL2N metric that we extend to the joint intent and slot classification task, and an initial finetuning phase on the full train set. Our results on the GLUE benchmark and four joint NLU datasets show a better time-accuracy trade-off compared to static methods. Our method preserves full accuracy while training on 50% of the data points and reduces computational times by up to 41%. If we tolerate instead a minor drop of accuracy of 1%, we can prune 80% of the training examples for a reduction in finetuning time reaching 66%.

The recent upsurge in pre-trained large models (e.g. GPT-4) has swept across the entire deep learning community. Such powerful large language models (LLMs) demonstrate advanced generative ability and multimodal understanding capability, which quickly achieve new state-of-the-art performances on a variety of benchmarks. The pre-trained LLM usually plays the role as a universal AI model that can conduct various tasks, including context reasoning, article analysis and image content comprehension. However, considering the prohibitively high memory and computational cost for implementing such a large model, the conventional models (such as CNN and ViT), are still essential for many visual perception tasks. In this paper, we propose to enhance the representation ability of ordinary vision models for perception tasks (e.g. image classification) by taking advantage of large pre-trained models. We present a new learning paradigm in which the knowledge extracted from large pre-trained models are utilized to help models like CNN and ViT learn enhanced representations and achieve better performance. Firstly, we curate a high quality description set by prompting a multimodal LLM to generate descriptive text for all training images. Furthermore, we feed these detailed descriptions into a pre-trained encoder to extract text embeddings with rich semantic information that encodes the content of images. During training, text embeddings will serve as extra supervising signals and be aligned with image representations learned by vision models. The alignment process helps vision models learn better and achieve higher accuracy with the assistance of pre-trained LLMs. We conduct extensive experiments to verify that the proposed algorithm consistently improves the performance for various vision models with heterogeneous architectures.

Large transformer models can highly improve Answer Sentence Selection (AS2) tasks, but their high computational costs prevent their use in many real-world applications. In this paper, we explore the following research question: How can we make the AS2 models more accurate without significantly increasing their model complexity? To address the question, we propose a Multiple Heads Student architecture (named CERBERUS), an efficient neural network designed to distill an ensemble of large transformers into a single smaller model. CERBERUS consists of two components: a stack of transformer layers that is used to encode inputs, and a set of ranking heads; unlike traditional distillation technique, each of them is trained by distilling a different large transformer architecture in a way that preserves the diversity of the ensemble members. The resulting model captures the knowledge of heterogeneous transformer models by using just a few extra parameters. We show the effectiveness of CERBERUS on three English datasets for AS2; our proposed approach outperforms all single-model distillations we consider, rivaling the state-of-the-art large AS2 models that have 2.7x more parameters and run 2.5x slower. Code for our model is available at https://github.com/amazon-research/wqa-cerberus

A hallmark of intelligence is the ability to autonomously learn new flexible, cognitive behaviors - that is, behaviors where the appropriate action depends not just on immediate stimuli (as in simple reflexive stimulus-response associations), but on contextual information that must be adequately acquired, stored and processed. While many meta-learning algorithms can design agents that autonomously learn new tasks, cognitive tasks adds another level of learning and memory to typical ``learning-to-learn'' problems. Here we evolve neural networks, endowed with plastic connections and neuromodulation, over a sizable set of simple cognitive tasks adapted from a computational neuroscience framework. The resulting evolved networks can automatically modify their own connectivity to acquire a novel simple cognitive task, never seen during evolution, from stimuli and rewards alone, through the spontaneous operation of their evolved neural organization and plasticity system. Our results emphasize the importance of carefully considering the multiple learning loops involved in the emergence of intelligent behavior.

Neural Architecture Search (NAS) has been widely adopted to design accurate and efficient image classification models. However, applying NAS to a new computer vision task still requires a huge amount of effort. This is because 1) previous NAS research has been over-prioritized on image classification while largely ignoring other tasks; 2) many NAS works focus on optimizing task-specific components that cannot be favorably transferred to other tasks; and 3) existing NAS methods are typically designed to be "proxyless" and require significant effort to be integrated with each new task's training pipelines. To tackle these challenges, we propose FBNetV5, a NAS framework that can search for neural architectures for a variety of vision tasks with much reduced computational cost and human effort. Specifically, we design 1) a search space that is simple yet inclusive and transferable; 2) a multitask search process that is disentangled with target tasks' training pipeline; and 3) an algorithm to simultaneously search for architectures for multiple tasks with a computational cost agnostic to the number of tasks. We evaluate the proposed FBNetV5 targeting three fundamental vision tasks -- image classification, object detection, and semantic segmentation. Models searched by FBNetV5 in a single run of search have outperformed the previous stateof-the-art in all the three tasks: image classification (e.g., +1.3% ImageNet top-1 accuracy under the same FLOPs as compared to FBNetV3), semantic segmentation (e.g., +1.8% higher ADE20K val. mIoU than SegFormer with 3.6x fewer FLOPs), and object detection (e.g., +1.1% COCO val. mAP with 1.2x fewer FLOPs as compared to YOLOX).