Daily Papers

Given the massive cost of language model pre-training, a non-trivial improvement of the optimization algorithm would lead to a material reduction on the time and cost of training. Adam and its variants have been state-of-the-art for years, and more sophisticated second-order (Hessian-based) optimizers often incur too much per-step overhead. In this paper, we propose Sophia, Second-order Clipped Stochastic Optimization, a simple scalable second-order optimizer that uses a light-weight estimate of the diagonal Hessian as the pre-conditioner. The update is the moving average of the gradients divided by the moving average of the estimated Hessian, followed by element-wise clipping. The clipping controls the worst-case update size and tames the negative impact of non-convexity and rapid change of Hessian along the trajectory. Sophia only estimates the diagonal Hessian every handful of iterations, which has negligible average per-step time and memory overhead. On language modeling with GPT-2 models of sizes ranging from 125M to 770M, Sophia achieves a 2x speed-up compared with Adam in the number of steps, total compute, and wall-clock time. Theoretically, we show that Sophia adapts to the curvature in different components of the parameters, which can be highly heterogeneous for language modeling tasks. Our run-time bound does not depend on the condition number of the loss.

Recent advances have shown success in eliciting strong reasoning abilities in multimodal large language models (MLLMs) through rule-based reinforcement learning (RL) with outcome rewards. However, this paradigm typically lacks supervision over the thinking process leading to the final outcome.As a result, the model may learn sub-optimal reasoning strategies, which can hinder its generalization ability. In light of this, we propose SophiaVL-R1, as an attempt to add reward signals for the thinking process in this paradigm. To achieve this, we first train a thinking reward model that evaluates the quality of the entire thinking process. Given that the thinking reward may be unreliable for certain samples due to reward hacking, we propose the Trust-GRPO method, which assigns a trustworthiness weight to the thinking reward during training. This weight is computed based on the thinking reward comparison of responses leading to correct answers versus incorrect answers, helping to mitigate the impact of potentially unreliable thinking rewards. Moreover, we design an annealing training strategy that gradually reduces the thinking reward over time, allowing the model to rely more on the accurate rule-based outcome reward in later training stages. Experiments show that our SophiaVL-R1 surpasses a series of reasoning MLLMs on various benchmarks (e.g., MathVisita, MMMU), demonstrating strong reasoning and generalization capabilities. Notably, our SophiaVL-R1-7B even outperforms LLaVA-OneVision-72B on most benchmarks, despite the latter having 10 times more parameters. All code, models, and datasets are made publicly available at https://github.com/kxfan2002/SophiaVL-R1.

We introduce DIP, a novel unsupervised post-training method designed to enhance dense image representations in large-scale pretrained vision encoders for in-context scene understanding. Unlike prior approaches that rely on complex self-distillation architectures, our method trains the vision encoder using pseudo-tasks that explicitly simulate downstream in-context scenarios, inspired by meta-learning principles. To enable post-training on unlabeled data, we propose an automatic mechanism for generating in-context tasks that combines a pretrained diffusion model and the vision encoder itself. DIP is simple, unsupervised, and computationally efficient, requiring less than 9 hours on a single A100 GPU. By learning dense representations through pseudo in-context tasks, it achieves strong performance across a wide variety of downstream real-world in-context scene understanding tasks. It outperforms both the initial vision encoder and prior methods, offering a practical and effective solution for improving dense representations. Code available here: https://github.com/sirkosophia/DIP

Flow matching in the continuous simplex has emerged as a promising strategy for DNA sequence design, but struggles to scale to higher simplex dimensions required for peptide and protein generation. We introduce Gumbel-Softmax Flow and Score Matching, a generative framework on the simplex based on a novel Gumbel-Softmax interpolant with a time-dependent temperature. Using this interpolant, we introduce Gumbel-Softmax Flow Matching by deriving a parameterized velocity field that transports from smooth categorical distributions to distributions concentrated at a single vertex of the simplex. We alternatively present Gumbel-Softmax Score Matching which learns to regress the gradient of the probability density. Our framework enables high-quality, diverse generation and scales efficiently to higher-dimensional simplices. To enable training-free guidance, we propose Straight-Through Guided Flows (STGFlow), a classifier-based guidance method that leverages straight-through estimators to steer the unconditional velocity field toward optimal vertices of the simplex. STGFlow enables efficient inference-time guidance using classifiers pre-trained on clean sequences, and can be used with any discrete flow method. Together, these components form a robust framework for controllable de novo sequence generation. We demonstrate state-of-the-art performance in conditional DNA promoter design, sequence-only protein generation, and target-binding peptide design for rare disease treatment.

Peptide therapeutics, a major class of medicines, have achieved remarkable success across diseases such as diabetes and cancer, with landmark examples such as GLP-1 receptor agonists revolutionizing the treatment of type-2 diabetes and obesity. Despite their success, designing peptides that satisfy multiple conflicting objectives, such as target binding affinity, solubility, and membrane permeability, remains a major challenge. Classical drug development and structure-based design are ineffective for such tasks, as they fail to optimize global functional properties critical for therapeutic efficacy. Existing generative frameworks are largely limited to continuous spaces, unconditioned outputs, or single-objective guidance, making them unsuitable for discrete sequence optimization across multiple properties. To address this, we present PepTune, a multi-objective discrete diffusion model for the simultaneous generation and optimization of therapeutic peptide SMILES. Built on the Masked Discrete Language Model (MDLM) framework, PepTune ensures valid peptide structures with state-dependent masking schedules and penalty-based objectives. To guide the diffusion process, we propose a Monte Carlo Tree Search (MCTS)-based strategy that balances exploration and exploitation to iteratively refine Pareto-optimal sequences. MCTS integrates classifier-based rewards with search-tree expansion, overcoming gradient estimation challenges and data sparsity inherent to discrete spaces. Using PepTune, we generate diverse, chemically-modified peptides optimized for multiple therapeutic properties, including target binding affinity, membrane permeability, solubility, hemolysis, and non-fouling characteristics on various disease-relevant targets. In total, our results demonstrate that MCTS-guided discrete diffusion is a powerful and modular approach for multi-objective sequence design in discrete state spaces.

The rapid expansion of AI has intensified concerns about its environmental sustainability. Yet, current assessments predominantly focus on operational carbon emissions using secondary data or estimated values, overlooking environmental impacts in other life cycle stages. This study presents the first comprehensive multi-criteria life cycle assessment (LCA) of AI training, examining 16 environmental impact categories based on detailed primary data collection of the Nvidia A100 SXM 40GB GPU. The LCA results for training BLOOM reveal that the use phase dominates 11 of 16 impact categories including climate change (96\%), while manufacturing dominates the remaining 5 impact categories including human toxicity, cancer (99\%) and mineral and metal depletion (85\%). For training GPT-4, the use phase dominates 10 of 16 impact categories, contributing about 96\% to both the climate change and resource use, fossils category. The manufacturing stage dominates 6 of 16 impact categories including human toxicity, cancer (94\%) and eutrophication, freshwater (81\%). Assessing the cradle-to-gate environmental impact distribution across the GPU components reveals that the GPU chip is the largest contributor across 10 of 16 of impact categories and shows particularly pronounced contributions to climate change (81\%) and resource use, fossils (80\%). While primary data collection results in modest changes in carbon estimates compared to database-derived estimates, substantial variations emerge in other categories. Most notably, minerals and metals depletion increases by 33\%, demonstrating the critical importance of primary data for non-carbon accounting. This multi-criteria analysis expands the Sustainable AI discourse beyond operational carbon emissions, challenging current sustainability narratives and highlighting the need for policy frameworks addressing the full spectrum of AI's environmental impact.

The enduring legacy of Euclidean geometry underpins classical machine learning, which, for decades, has been primarily developed for data lying in Euclidean space. Yet, modern machine learning increasingly encounters richly structured data that is inherently nonEuclidean. This data can exhibit intricate geometric, topological and algebraic structure: from the geometry of the curvature of space-time, to topologically complex interactions between neurons in the brain, to the algebraic transformations describing symmetries of physical systems. Extracting knowledge from such non-Euclidean data necessitates a broader mathematical perspective. Echoing the 19th-century revolutions that gave rise to non-Euclidean geometry, an emerging line of research is redefining modern machine learning with non-Euclidean structures. Its goal: generalizing classical methods to unconventional data types with geometry, topology, and algebra. In this review, we provide an accessible gateway to this fast-growing field and propose a graphical taxonomy that integrates recent advances into an intuitive unified framework. We subsequently extract insights into current challenges and highlight exciting opportunities for future development in this field.

As computational demands continue to rise, assessing the environmental footprint of AI requires moving beyond energy and water consumption to include the material demands of specialized hardware. This study quantifies the material footprint of AI training by linking computational workloads to physical hardware needs. The elemental composition of the Nvidia A100 SXM 40 GB graphics processing unit (GPU) was analyzed using inductively coupled plasma optical emission spectroscopy, which identified 32 elements. The results show that AI hardware consists of about 90% heavy metals and only trace amounts of precious metals. The elements copper, iron, tin, silicon, and nickel dominate the GPU composition by mass. In a multi-step methodology, we integrate these measurements with computational throughput per GPU across varying lifespans, accounting for the computational requirements of training specific AI models at different training efficiency regimes. Scenario-based analyses reveal that, depending on Model FLOPs Utilization (MFU) and hardware lifespan, training GPT-4 requires between 1,174 and 8,800 A100 GPUs, corresponding to the extraction and eventual disposal of up to 7 tons of toxic elements. Combined software and hardware optimization strategies can reduce material demands: increasing MFU from 20% to 60% lowers GPU requirements by 67%, while extending lifespan from 1 to 3 years yields comparable savings; implementing both measures together reduces GPU needs by up to 93%. Our findings highlight that incremental performance gains, such as those observed between GPT-3.5 and GPT-4, come at disproportionately high material costs. The study underscores the necessity of incorporating material resource considerations into discussions of AI scalability, emphasizing that future progress in AI must align with principles of resource efficiency and environmental responsibility.

Predicting the intermediate trajectories between an initial and target distribution is a central problem in generative modeling. Existing approaches, such as flow matching and Schr\"odinger Bridge Matching, effectively learn mappings between two distributions by modeling a single stochastic path. However, these methods are inherently limited to unimodal transitions and cannot capture branched or divergent evolution from a common origin to multiple distinct outcomes. To address this, we introduce Branched Schr\"odinger Bridge Matching (BranchSBM), a novel framework that learns branched Schr\"odinger bridges. BranchSBM parameterizes multiple time-dependent velocity fields and growth processes, enabling the representation of population-level divergence into multiple terminal distributions. We show that BranchSBM is not only more expressive but also essential for tasks involving multi-path surface navigation, modeling cell fate bifurcations from homogeneous progenitor states, and simulating diverging cellular responses to perturbations.

Reinforcement learning with stochastic optimal control offers a promising framework for diffusion fine-tuning, where a pre-trained diffusion model is optimized to generate paths that lead to a reward-tilted distribution. While these approaches enable optimization without access to explicit samples from the optimal distribution, they require training on rollouts under the current fine-tuned model, making them susceptible to reinforcing sub-optimal trajectories that yield poor rewards. To overcome this challenge, we introduce TRee Search Guided TRajectory-Aware Fine-Tuning for Discrete Diffusion (TR2-D2), a novel framework that optimizes reward-guided discrete diffusion trajectories with tree search to construct replay buffers for trajectory-aware fine-tuning. These buffers are generated using Monte Carlo Tree Search (MCTS) and subsequently used to fine-tune a pre-trained discrete diffusion model under a stochastic optimal control objective. We validate our framework on single- and multi-objective fine-tuning of biological sequence diffusion models, highlighting the overall effectiveness of TR2-D2 for reliable reward-guided fine-tuning in discrete sequence generation.

Predominant LLMs focus on high-resource languages while leaving low-resource languages, particularly those in Southeast Asia (SEA), underrepresented. In addition, those models are general-purpose and pay limited attention to the e-commerce domain. To overcome these limitations, we introduce Compass-v2, a lightweight Mixture-of-Experts (MoE) model specifically designed for Southeast Asian languages and e-commerce applications. To balance model performance and inference cost, the model is designed with 30B total parameters and 5B active parameters, incorporating both fine-grained and shared expert modules. To enhance multilingual performance, we curated and constructed a high-quality, industry-leading SEA dataset, to the best of our knowledge. To boost performance in the e-commerce domain, we built a dataset comprising hundreds of billions of tokens, sourced through external data mining and internal platform collection. Besides, we pioneered a hybrid reasoning model that supports both fast thinking and deep thinking within a unified framework to enhance the reasoning capabilities, diverging from the conventional industry practice of deploying two separate models. Through extensive experimental evaluations, our model demonstrates state-of-the-art SEA multilingual and e-commerce performance among sub-30B models, while maintaining significantly lower inference cost.

Accurate uncertainty measurement is a key step to building robust and reliable machine learning systems. Conformal prediction is a distribution-free uncertainty quantification algorithm popular for its ease of implementation, statistical coverage guarantees, and versatility for underlying forecasters. However, existing conformal prediction algorithms for time series are limited to single-step prediction without considering the temporal dependency. In this paper, we propose a Copula Conformal Prediction algorithm for multivariate, multi-step Time Series forecasting, CopulaCPTS. We prove that CopulaCPTS has finite sample validity guarantee. On several synthetic and real-world multivariate time series datasets, we show that CopulaCPTS produces more calibrated and sharp confidence intervals for multi-step prediction tasks than existing techniques.

Many high-level skills that are required for computer vision tasks, such as parsing questions, comparing and contrasting semantics, and writing descriptions, are also required in other domains such as natural language processing. In this paper, we ask whether it is possible to learn those skills from text data and then transfer them to vision tasks without ever training on visual training data. Key to our approach is exploiting the joint embedding space of contrastively trained vision and language encoders. In practice, there can be systematic differences between embedding spaces for different modalities in contrastive models, and we analyze how these differences affect our approach and study strategies to mitigate this concern. We produce models using only text training data on four representative tasks: image captioning, visual entailment, visual question answering and visual news captioning, and evaluate them on standard benchmarks using images. We find these models perform close to models trained on images, while surpassing prior work for captioning and visual entailment in this text-only setting by over 9 points, and outperforming all prior work on visual news by over 30 points. We also showcase a variety of stylistic image captioning models that are trained using no image data and no human-curated language data, but instead using readily-available text data from books, the web, or language models.

Computer vision approaches are widely used by autonomous robotic systems to sense the world around them and to guide their decision making as they perform diverse tasks such as collision avoidance, search and rescue, and object manipulation. High accuracy is critical, particularly for Human-on-the-loop (HoTL) systems where decisions are made autonomously by the system, and humans play only a supervisory role. Failures of the vision model can lead to erroneous decisions with potentially life or death consequences. In this paper, we propose a solution based upon adaptive autonomy levels, whereby the system detects loss of reliability of these models and responds by temporarily lowering its own autonomy levels and increasing engagement of the human in the decision-making process. Our solution is applicable for vision-based tasks in which humans have time to react and provide guidance. When implemented, our approach would estimate the reliability of the vision task by considering uncertainty in its model, and by performing covariate analysis to determine when the current operating environment is ill-matched to the model's training data. We provide examples from DroneResponse, in which small Unmanned Aerial Systems are deployed for Emergency Response missions, and show how the vision model's reliability would be used in addition to confidence scores to drive and specify the behavior and adaptation of the system's autonomy. This workshop paper outlines our proposed approach and describes open challenges at the intersection of Computer Vision and Software Engineering for the safe and reliable deployment of vision models in the decision making of autonomous systems.

Large language models (LLMs) have significantly advanced natural language processing, but their progress has yet to be equal across languages. While most LLMs are trained in high-resource languages like English, multilingual models generally underperform monolingual ones. Additionally, aspects of their multilingual foundation sometimes restrict the byproducts they produce, like computational demands and licensing regimes. In this study, we document the development of open-foundation models tailored for use in low-resource settings, their limitations, and their benefits. This is the TeenyTinyLlama pair: two compact models for Brazilian Portuguese text generation. We release them under the permissive Apache 2.0 license on GitHub and Hugging Face for community use and further development. See https://github.com/Nkluge-correa/TeenyTinyLlama

In hematology, computational models offer significant potential to improve diagnostic accuracy, streamline workflows, and reduce the tedious work of analyzing single cells in peripheral blood or bone marrow smears. However, clinical adoption of computational models has been hampered by the lack of generalization due to large batch effects, small dataset sizes, and poor performance in transfer learning from natural images. To address these challenges, we introduce DinoBloom, the first foundation model for single cell images in hematology, utilizing a tailored DINOv2 pipeline. Our model is built upon an extensive collection of 13 diverse, publicly available datasets of peripheral blood and bone marrow smears, the most substantial open-source cohort in hematology so far, comprising over 380,000 white blood cell images. To assess its generalization capability, we evaluate it on an external dataset with a challenging domain shift. We show that our model outperforms existing medical and non-medical vision models in (i) linear probing and k-nearest neighbor evaluations for cell-type classification on blood and bone marrow smears and (ii) weakly supervised multiple instance learning for acute myeloid leukemia subtyping by a large margin. A family of four DinoBloom models (small, base, large, and giant) can be adapted for a wide range of downstream applications, be a strong baseline for classification problems, and facilitate the assessment of batch effects in new datasets. All models are available at github.com/marrlab/DinoBloom.

The natural world is full of complex systems characterized by intricate relations between their components: from social interactions between individuals in a social network to electrostatic interactions between atoms in a protein. Topological Deep Learning (TDL) provides a comprehensive framework to process and extract knowledge from data associated with these systems, such as predicting the social community to which an individual belongs or predicting whether a protein can be a reasonable target for drug development. TDL has demonstrated theoretical and practical advantages that hold the promise of breaking ground in the applied sciences and beyond. However, the rapid growth of the TDL literature has also led to a lack of unification in notation and language across Topological Neural Network (TNN) architectures. This presents a real obstacle for building upon existing works and for deploying TNNs to new real-world problems. To address this issue, we provide an accessible introduction to TDL, and compare the recently published TNNs using a unified mathematical and graphical notation. Through an intuitive and critical review of the emerging field of TDL, we extract valuable insights into current challenges and exciting opportunities for future development.

The field of computational pathology has been transformed with recent advances in foundation models that encode histopathology region-of-interests (ROIs) into versatile and transferable feature representations via self-supervised learning (SSL). However, translating these advancements to address complex clinical challenges at the patient and slide level remains constrained by limited clinical data in disease-specific cohorts, especially for rare clinical conditions. We propose TITAN, a multimodal whole slide foundation model pretrained using 335,645 WSIs via visual self-supervised learning and vision-language alignment with corresponding pathology reports and 423,122 synthetic captions generated from a multimodal generative AI copilot for pathology. Without any finetuning or requiring clinical labels, TITAN can extract general-purpose slide representations and generate pathology reports that generalize to resource-limited clinical scenarios such as rare disease retrieval and cancer prognosis. We evaluate TITAN on diverse clinical tasks and find that TITAN outperforms both ROI and slide foundation models across machine learning settings such as linear probing, few-shot and zero-shot classification, rare cancer retrieval and cross-modal retrieval, and pathology report generation.

As language model agents are applied to real world problems of increasing complexity, they will be expected to formulate plans across large search spaces. If those plans fail for reasons beyond their control, how well do language agents search for alternative ways to achieve their goals? We devise a specialized agentic planning benchmark to study this question. Each planning problem is solved via combinations of function calls. The agent searches for relevant functions from a set of over four thousand possibilities, and observes environmental feedback in the form of function outputs or error messages. Our benchmark confronts the agent with external failures in its workflow, such as functions that suddenly become unavailable. At the same time, even with the introduction of these failures, we guarantee that the task remains solvable. Ideally, an agent's performance on the planning task should not be affected by the presence of external failures. Overall, we find that language agents struggle to formulate and execute backup plans in response to environment feedback. While state-of-the-art models are often able to identify the correct function to use in the right context, they struggle to adapt to feedback from the environment and often fail to pursue alternate courses of action, even when the search space is artificially restricted. We provide a systematic analysis of the failures of both open-source and commercial models, examining the effects of search space size, as well as the benefits of scaling model size in our setting. Our analysis identifies key challenges for current generative models as well as promising directions for future work.

Understanding the mechanisms behind Large Language Models (LLMs) is crucial for designing improved models and strategies. While recent studies have yielded valuable insights into the mechanisms of textual LLMs, the mechanisms of Multi-modal Large Language Models (MLLMs) remain underexplored. In this paper, we apply mechanistic interpretability methods to analyze the visual question answering (VQA) mechanisms in the first MLLM, Llava. We compare the mechanisms between VQA and textual QA (TQA) in color answering tasks and find that: a) VQA exhibits a mechanism similar to the in-context learning mechanism observed in TQA; b) the visual features exhibit significant interpretability when projecting the visual embeddings into the embedding space; and c) Llava enhances the existing capabilities of the corresponding textual LLM Vicuna during visual instruction tuning. Based on these findings, we develop an interpretability tool to help users and researchers identify important visual locations for final predictions, aiding in the understanding of visual hallucination. Our method demonstrates faster and more effective results compared to existing interpretability approaches. Code: https://github.com/zepingyu0512/llava-mechanism

We find arithmetic ability resides within a limited number of attention heads, with each head specializing in distinct operations. To delve into the reason, we introduce the Comparative Neuron Analysis (CNA) method, which identifies an internal logic chain consisting of four distinct stages from input to prediction: feature enhancing with shallow FFN neurons, feature transferring by shallow attention layers, feature predicting by arithmetic heads, and prediction enhancing among deep FFN neurons. Moreover, we identify the human-interpretable FFN neurons within both feature-enhancing and feature-predicting stages. These findings lead us to investigate the mechanism of LoRA, revealing that it enhances prediction probabilities by amplifying the coefficient scores of FFN neurons related to predictions. Finally, we apply our method in model pruning for arithmetic tasks and model editing for reducing gender bias. Code is on https://github.com/zepingyu0512/arithmetic-mechanism.

We study language ideologies in text produced by LLMs through a case study on English gendered language reform (related to role nouns like congressperson/-woman/-man, and singular they). First, we find political bias: when asked to use language that is "correct" or "natural", LLMs use language most similarly to when asked to align with conservative (vs. progressive) values. This shows how LLMs' metalinguistic preferences can implicitly communicate the language ideologies of a particular political group, even in seemingly non-political contexts. Second, we find LLMs exhibit internal inconsistency: LLMs use gender-neutral variants more often when more explicit metalinguistic context is provided. This shows how the language ideologies expressed in text produced by LLMs can vary, which may be unexpected to users. We discuss the broader implications of these findings for value alignment.

We present strong Transformer-based re-ranking and dense retrieval baselines for the recently released TripClick health ad-hoc retrieval collection. We improve the - originally too noisy - training data with a simple negative sampling policy. We achieve large gains over BM25 in the re-ranking task of TripClick, which were not achieved with the original baselines. Furthermore, we study the impact of different domain-specific pre-trained models on TripClick. Finally, we show that dense retrieval outperforms BM25 by considerable margins, even with simple training procedures.

The objectives of this work are cross-modal text-audio and audio-text retrieval, in which the goal is to retrieve the audio content from a pool of candidates that best matches a given written description and vice versa. Text-audio retrieval enables users to search large databases through an intuitive interface: they simply issue free-form natural language descriptions of the sound they would like to hear. To study the tasks of text-audio and audio-text retrieval, which have received limited attention in the existing literature, we introduce three challenging new benchmarks. We first construct text-audio and audio-text retrieval benchmarks from the AudioCaps and Clotho audio captioning datasets. Additionally, we introduce the SoundDescs benchmark, which consists of paired audio and natural language descriptions for a diverse collection of sounds that are complementary to those found in AudioCaps and Clotho. We employ these three benchmarks to establish baselines for cross-modal text-audio and audio-text retrieval, where we demonstrate the benefits of pre-training on diverse audio tasks. We hope that our benchmarks will inspire further research into audio retrieval with free-form text queries. Code, audio features for all datasets used, and the SoundDescs dataset are publicly available at https://github.com/akoepke/audio-retrieval-benchmark.

Retrieval and ranking models are the backbone of many applications such as web search, open domain QA, or text-based recommender systems. The latency of neural ranking models at query time is largely dependent on the architecture and deliberate choices by their designers to trade-off effectiveness for higher efficiency. This focus on low query latency of a rising number of efficient ranking architectures make them feasible for production deployment. In machine learning an increasingly common approach to close the effectiveness gap of more efficient models is to apply knowledge distillation from a large teacher model to a smaller student model. We find that different ranking architectures tend to produce output scores in different magnitudes. Based on this finding, we propose a cross-architecture training procedure with a margin focused loss (Margin-MSE), that adapts knowledge distillation to the varying score output distributions of different BERT and non-BERT passage ranking architectures. We apply the teachable information as additional fine-grained labels to existing training triples of the MSMARCO-Passage collection. We evaluate our procedure of distilling knowledge from state-of-the-art concatenated BERT models to four different efficient architectures (TK, ColBERT, PreTT, and a BERT CLS dot product model). We show that across our evaluated architectures our Margin-MSE knowledge distillation significantly improves re-ranking effectiveness without compromising their efficiency. Additionally, we show our general distillation method to improve nearest neighbor based index retrieval with the BERT dot product model, offering competitive results with specialized and much more costly training methods. To benefit the community, we publish the teacher-score training files in a ready-to-use package.

As Large Language Models (LLMs) have become more advanced, they have outpaced our abilities to accurately evaluate their quality. Not only is finding data to adequately probe particular model properties difficult, but evaluating the correctness of a model's freeform generation alone is a challenge. To address this, many evaluations now rely on using LLMs themselves as judges to score the quality of outputs from other LLMs. Evaluations most commonly use a single large model like GPT4. While this method has grown in popularity, it is costly, has been shown to introduce intramodel bias, and in this work, we find that very large models are often unnecessary. We propose instead to evaluate models using a Panel of LLm evaluators (PoLL). Across three distinct judge settings and spanning six different datasets, we find that using a PoLL composed of a larger number of smaller models outperforms a single large judge, exhibits less intra-model bias due to its composition of disjoint model families, and does so while being over seven times less expensive.

Significant advances have been made in natural language processing in recent years. However, our current deep learning approach to language modeling requires substantial resources in terms of data and computation. One of the side effects of this data-hungry paradigm is the current schism between languages, separating those considered high-resource, where most of the development happens and resources are available, and the low-resource ones, which struggle to attain the same level of performance and autonomy. This study aims to introduce a new set of resources to stimulate the future development of neural text generation in Portuguese. In this work, we document the development of GigaVerbo, a concatenation of deduplicated Portuguese text corpora amounting to 200 billion tokens. Via this corpus, we trained a series of decoder-transformers named Tucano. Our models perform equal or superior to other Portuguese and multilingual language models of similar size in several Portuguese benchmarks. The evaluation of our models also reveals that model performance on many currently available benchmarks used by the Portuguese NLP community has little to no correlation with the scaling of token ingestion during training, highlighting the limitations of such evaluations when it comes to the assessment of Portuguese generative language models. All derivatives of our study are openly released on GitHub and Hugging Face. See https://nkluge-correa.github.io/Tucano/

Training deep networks requires various design decisions regarding for instance their architecture, data augmentation, or optimization. In this work, we find these training variations to result in networks learning unique feature sets from the data. Using public model libraries comprising thousands of models trained on canonical datasets like ImageNet, we observe that for arbitrary pairings of pretrained models, one model extracts significant data context unavailable in the other -- independent of overall performance. Given any arbitrary pairing of pretrained models and no external rankings (such as separate test sets, e.g. due to data privacy), we investigate if it is possible to transfer such "complementary" knowledge from one model to another without performance degradation -- a task made particularly difficult as additional knowledge can be contained in stronger, equiperformant or weaker models. Yet facilitating robust transfer in scenarios agnostic to pretrained model pairings would unlock auxiliary gains and knowledge fusion from any model repository without restrictions on model and problem specifics - including from weaker, lower-performance models. This work therefore provides an initial, in-depth exploration on the viability of such general-purpose knowledge transfer. Across large-scale experiments, we first reveal the shortcomings of standard knowledge distillation techniques, and then propose a much more general extension through data partitioning for successful transfer between nearly all pretrained models, which we show can also be done unsupervised. Finally, we assess both the scalability and impact of fundamental model properties on successful model-agnostic knowledge transfer.

Designing biological sequences that satisfy multiple, often conflicting, functional and biophysical criteria remains a central challenge in biomolecule engineering. While discrete flow matching models have recently shown promise for efficient sampling in high-dimensional sequence spaces, existing approaches address only single objectives or require continuous embeddings that can distort discrete distributions. We present Multi-Objective-Guided Discrete Flow Matching (MOG-DFM), a general framework to steer any pretrained discrete-time flow matching generator toward Pareto-efficient trade-offs across multiple scalar objectives. At each sampling step, MOG-DFM computes a hybrid rank-directional score for candidate transitions and applies an adaptive hypercone filter to enforce consistent multi-objective progression. We also trained two unconditional discrete flow matching models, PepDFM for diverse peptide generation and EnhancerDFM for functional enhancer DNA generation, as base generation models for MOG-DFM. We demonstrate MOG-DFM's effectiveness in generating peptide binders optimized across five properties (hemolysis, non-fouling, solubility, half-life, and binding affinity), and in designing DNA sequences with specific enhancer classes and DNA shapes. In total, MOG-DFM proves to be a powerful tool for multi-property-guided biomolecule sequence design.

We investigate how large language models perform latent multi-hop reasoning in prompts like "Wolfgang Amadeus Mozart's mother's spouse is". To analyze this process, we introduce logit flow, an interpretability method that traces how logits propagate across layers and positions toward the final prediction. Using logit flow, we identify four distinct stages in single-hop knowledge prediction: (A) entity subject enrichment, (B) entity attribute extraction, (C) relation subject enrichment, and (D) relation attribute extraction. Extending this analysis to multi-hop reasoning, we find that failures often stem from the relation attribute extraction stage, where conflicting logits reduce prediction accuracy. To address this, we propose back attention, a novel mechanism that enables lower layers to leverage higher-layer hidden states from different positions during attention computation. With back attention, a 1-layer transformer achieves the performance of a 2-layer transformer. Applied to four LLMs, back attention improves accuracy on five reasoning datasets, demonstrating its effectiveness in enhancing latent multi-hop reasoning ability.

Friendship and rapport play an important role in the formation of constructive social interactions, and have been widely studied in educational settings due to their impact on student outcomes. Given the growing interest in automating the analysis of such phenomena through Machine Learning (ML), access to annotated interaction datasets is highly valuable. However, no dataset on dyadic child-child interactions explicitly capturing rapport currently exists. Moreover, despite advances in the automatic analysis of human behaviour, no previous work has addressed the prediction of rapport in child-child dyadic interactions in educational settings. We present UpStory -- the Uppsala Storytelling dataset: a novel dataset of naturalistic dyadic interactions between primary school aged children, with an experimental manipulation of rapport. Pairs of children aged 8-10 participate in a task-oriented activity: designing a story together, while being allowed free movement within the play area. We promote balanced collection of different levels of rapport by using a within-subjects design: self-reported friendships are used to pair each child twice, either minimizing or maximizing pair separation in the friendship network. The dataset contains data for 35 pairs, totalling 3h 40m of audio and video recordings. It includes two video sources covering the play area, as well as separate voice recordings for each child. An anonymized version of the dataset is made publicly available, containing per-frame head pose, body pose, and face features; as well as per-pair information, including the level of rapport. Finally, we provide ML baselines for the prediction of rapport.

As synthetic media becomes progressively more realistic and barriers to using it continue to lower, the technology has been increasingly utilized for malicious purposes, from financial fraud to nonconsensual pornography. Today, the principal defense against being misled by synthetic media relies on the ability of the human observer to visually and auditorily discern between real and fake. However, it remains unclear just how vulnerable people actually are to deceptive synthetic media in the course of their day to day lives. We conducted a perceptual study with 1276 participants to assess how accurate people were at distinguishing synthetic images, audio only, video only, and audiovisual stimuli from authentic. To reflect the circumstances under which people would likely encounter synthetic media in the wild, testing conditions and stimuli emulated a typical online platform, while all synthetic media used in the survey was sourced from publicly accessible generative AI technology. We find that overall, participants struggled to meaningfully discern between synthetic and authentic content. We also find that detection performance worsens when the stimuli contains synthetic content as compared to authentic content, images featuring human faces as compared to non face objects, a single modality as compared to multimodal stimuli, mixed authenticity as compared to being fully synthetic for audiovisual stimuli, and features foreign languages as compared to languages the observer is fluent in. Finally, we also find that prior knowledge of synthetic media does not meaningfully impact their detection performance. Collectively, these results indicate that people are highly susceptible to being tricked by synthetic media in their daily lives and that human perceptual detection capabilities can no longer be relied upon as an effective counterdefense.

In this paper, we present a novel method for dynamically expanding Convolutional Neural Networks (CNNs) during training, aimed at meeting the increasing demand for efficient and sustainable deep learning models. Our approach, drawing from the seminal work on Self-Expanding Neural Networks (SENN), employs a natural expansion score as an expansion criteria to address the common issue of over-parameterization in deep convolutional neural networks, thereby ensuring that the model's complexity is finely tuned to the task's specific needs. A significant benefit of this method is its eco-friendly nature, as it obviates the necessity of training multiple models of different sizes. We employ a strategy where a single model is dynamically expanded, facilitating the extraction of checkpoints at various complexity levels, effectively reducing computational resource use and energy consumption while also expediting the development cycle by offering diverse model complexities from a single training session. We evaluate our method on the CIFAR-10 dataset and our experimental results validate this approach, demonstrating that dynamically adding layers not only maintains but also improves CNN performance, underscoring the effectiveness of our expansion criteria. This approach marks a considerable advancement in developing adaptive, scalable, and environmentally considerate neural network architectures, addressing key challenges in the field of deep learning.

Prior work in style-controlled text generation has focused on tasks such as emulating the style of prolific literary authors, producing formal or informal text, and the degree of toxicity of generated text. Plentiful demonstrations of these styles are available, and as a result modern language models are often able to emulate them, either via prompting or discriminative control. However, in applications such as writing assistants, it is desirable for language models to produce text in an author-specific style on the basis of a small writing sample. We find that instruction-tuned language models can struggle to reproduce author-specific style demonstrated in a prompt. Instead, we propose to guide a language model to generate text in a target style using contrastively-trained representations that capture stylometric features. A central challenge in doing so is that an author's writing is characterized by surprising token choices under a generic language model. To reconcile this tension, we combine generative re-scoring to achieve an author-specific model, with discriminative control to ensure style consistency at the sequence-level. The combination of these approaches is found to be particularly effective at adhering to an author-specific style in a variety of conditions, including unconditional generation and style transfer, and is applicable to any underlying language model without requiring fine-tuning.

The performance of text summarization has been greatly boosted by pre-trained language models. A main concern of existing methods is that most generated summaries are not factually inconsistent with their source documents. To alleviate the problem, many efforts have focused on developing effective factuality evaluation metrics based on natural language inference, question answering, and syntactic dependency et al. However, these approaches are limited by either their high computational complexity or the uncertainty introduced by multi-component pipelines, resulting in only partial agreement with human judgement. Most recently, large language models(LLMs) have shown excellent performance in not only text generation but also language comprehension. In this paper, we particularly explore ChatGPT's ability to evaluate factual inconsistency under a zero-shot setting by examining it on both coarse-grained and fine-grained evaluation tasks including binary entailment inference, summary ranking, and consistency rating. Experimental results indicate that ChatGPT generally outperforms previous evaluation metrics across the three tasks, indicating its great potential for factual inconsistency evaluation. However, a closer inspection of ChatGPT's output reveals certain limitations including its preference for more lexically similar candidates, false reasoning, and inadequate understanding of instructions.

Recent progress in neural information retrieval has demonstrated large gains in effectiveness, while often sacrificing the efficiency and interpretability of the neural model compared to classical approaches. This paper proposes ColBERTer, a neural retrieval model using contextualized late interaction (ColBERT) with enhanced reduction. Along the effectiveness Pareto frontier, ColBERTer's reductions dramatically lower ColBERT's storage requirements while simultaneously improving the interpretability of its token-matching scores. To this end, ColBERTer fuses single-vector retrieval, multi-vector refinement, and optional lexical matching components into one model. For its multi-vector component, ColBERTer reduces the number of stored vectors per document by learning unique whole-word representations for the terms in each document and learning to identify and remove word representations that are not essential to effective scoring. We employ an explicit multi-task, multi-stage training to facilitate using very small vector dimensions. Results on the MS MARCO and TREC-DL collection show that ColBERTer can reduce the storage footprint by up to 2.5x, while maintaining effectiveness. With just one dimension per token in its smallest setting, ColBERTer achieves index storage parity with the plaintext size, with very strong effectiveness results. Finally, we demonstrate ColBERTer's robustness on seven high-quality out-of-domain collections, yielding statistically significant gains over traditional retrieval baselines.

We consider the task of retrieving audio using free-form natural language queries. To study this problem, which has received limited attention in the existing literature, we introduce challenging new benchmarks for text-based audio retrieval using text annotations sourced from the Audiocaps and Clotho datasets. We then employ these benchmarks to establish baselines for cross-modal audio retrieval, where we demonstrate the benefits of pre-training on diverse audio tasks. We hope that our benchmarks will inspire further research into cross-modal text-based audio retrieval with free-form text queries.

Large language models (LLMs) have substantially advanced machine translation (MT), yet their effectiveness in translating web novels remains unclear. Existing benchmarks rely on surface-level metrics that fail to capture the distinctive traits of this genre. To address these gaps, we introduce DITING, the first comprehensive evaluation framework for web novel translation, assessing narrative and cultural fidelity across six dimensions: idiom translation, lexical ambiguity, terminology localization, tense consistency, zero-pronoun resolution, and cultural safety, supported by over 18K expert-annotated Chinese-English sentence pairs. We further propose AgentEval, a reasoning-driven multi-agent evaluation framework that simulates expert deliberation to assess translation quality beyond lexical overlap, achieving the highest correlation with human judgments among seven tested automatic metrics. To enable metric comparison, we develop MetricAlign, a meta-evaluation dataset of 300 sentence pairs annotated with error labels and scalar quality scores. Comprehensive evaluation of fourteen open, closed, and commercial models reveals that Chinese-trained LLMs surpass larger foreign counterparts, and that DeepSeek-V3 delivers the most faithful and stylistically coherent translations. Our work establishes a new paradigm for exploring LLM-based web novel translation and provides public resources to advance future research.

In this report we describe the development of Command A, a powerful large language model purpose-built to excel at real-world enterprise use cases. Command A is an agent-optimised and multilingual-capable model, with support for 23 languages of global business, and a novel hybrid architecture balancing efficiency with top of the range performance. It offers best-in-class Retrieval Augmented Generation (RAG) capabilities with grounding and tool use to automate sophisticated business processes. These abilities are achieved through a decentralised training approach, including self-refinement algorithms and model merging techniques. We also include results for Command R7B which shares capability and architectural similarities to Command A. Weights for both models have been released for research purposes. This technical report details our original training pipeline and presents an extensive evaluation of our models across a suite of enterprise-relevant tasks and public benchmarks, demonstrating excellent performance and efficiency.

LLMs are seeing growing use for applications such as document analysis and summarization which require large context windows, and with these large context windows KV cache activations surface as the dominant contributor to memory consumption during inference. Quantization is a promising approach for compressing KV cache activations; however, existing solutions fail to represent activations accurately in ultra-low precisions, such as sub-4-bit. In this work, we present KVQuant, which addresses this problem by incorporating novel methods for quantizing cached KV activations, including: (i) Per-Channel Key Quantization, where we adjust the dimension along which we quantize the Key activations to better match the distribution; (ii) Pre-RoPE Key Quantization, where we quantize Key activations before the rotary positional embedding to mitigate its impact on quantization; (iii) Non-Uniform KV Cache Quantization, where we derive per-layer sensitivity-weighted non-uniform datatypes that better represent the distributions; (iv) Per-Vector Dense-and-Sparse Quantization, where we isolate outliers separately for each vector to minimize skews in quantization ranges; and (v) Q-Norm, where we normalize quantization centroids in order to mitigate distribution shift, providing additional benefits for 2-bit quantization. By applying our method to the LLaMA, LLaMA-2, and Mistral models, we achieve <0.1 perplexity degradation with 3-bit quantization on both Wikitext-2 and C4, outperforming existing approaches. Our method enables serving the LLaMA-7B model with a context length of up to 1 million on a single A100-80GB GPU and up to 10 million on an 8-GPU system.

While the progression of Large Language Models (LLMs) has notably propelled financial analysis, their application has largely been confined to singular language realms, leaving untapped the potential of bilingual Chinese-English capacity. To bridge this chasm, we introduce ICE-PIXIU, seamlessly amalgamating the ICE-INTENT model and ICE-FLARE benchmark for bilingual financial analysis. ICE-PIXIU uniquely integrates a spectrum of Chinese tasks, alongside translated and original English datasets, enriching the breadth and depth of bilingual financial modeling. It provides unrestricted access to diverse model variants, a substantial compilation of diverse cross-lingual and multi-modal instruction data, and an evaluation benchmark with expert annotations, comprising 10 NLP tasks, 20 bilingual specific tasks, totaling 1,185k datasets. Our thorough evaluation emphasizes the advantages of incorporating these bilingual datasets, especially in translation tasks and utilizing original English data, enhancing both linguistic flexibility and analytical acuity in financial contexts. Notably, ICE-INTENT distinguishes itself by showcasing significant enhancements over conventional LLMs and existing financial LLMs in bilingual milieus, underscoring the profound impact of robust bilingual data on the accuracy and efficacy of financial NLP.

With the development of web technology, social media texts are becoming a rich source for automatic mental health analysis. As traditional discriminative methods bear the problem of low interpretability, the recent large language models have been explored for interpretable mental health analysis on social media, which aims to provide detailed explanations along with predictions. The results show that ChatGPT can generate approaching-human explanations for its correct classifications. However, LLMs still achieve unsatisfactory classification performance in a zero-shot/few-shot manner. Domain-specific finetuning is an effective solution, but faces 2 challenges: 1) lack of high-quality training data. 2) no open-source LLMs for interpretable mental health analysis were released to lower the finetuning cost. To alleviate these problems, we build the first multi-task and multi-source interpretable mental health instruction (IMHI) dataset on social media, with 105K data samples. The raw social media data are collected from 10 existing sources covering 8 mental health analysis tasks. We use expert-written few-shot prompts and collected labels to prompt ChatGPT and obtain explanations from its responses. To ensure the reliability of the explanations, we perform strict automatic and human evaluations on the correctness, consistency, and quality of generated data. Based on the IMHI dataset and LLaMA2 foundation models, we train MentalLLaMA, the first open-source LLM series for interpretable mental health analysis with instruction-following capability. We also evaluate the performance of MentalLLaMA on the IMHI evaluation benchmark with 10 test sets, where their correctness for making predictions and the quality of explanations are examined. The results show that MentalLLaMA approaches state-of-the-art discriminative methods in correctness and generates high-quality explanations.

Temporal reasoning is a crucial NLP task, providing a nuanced understanding of time-sensitive contexts within textual data. Although recent advancements in LLMs have demonstrated their potential in temporal reasoning, the predominant focus has been on tasks such as temporal expression and temporal relation extraction. These tasks are primarily designed for the extraction of direct and past temporal cues and to engage in simple reasoning processes. A significant gap remains when considering complex reasoning tasks such as event forecasting, which requires multi-step temporal reasoning on events and prediction on the future timestamp. Another notable limitation of existing methods is their incapability to provide an illustration of their reasoning process, hindering explainability. In this paper, we introduce the first task of explainable temporal reasoning, to predict an event's occurrence at a future timestamp based on context which requires multiple reasoning over multiple events, and subsequently provide a clear explanation for their prediction. Our task offers a comprehensive evaluation of both the LLMs' complex temporal reasoning ability, the future event prediction ability, and explainability-a critical attribute for AI applications. To support this task, we present the first multi-source instruction-tuning dataset of explainable temporal reasoning (ExpTime) with 26k derived from the temporal knowledge graph datasets and their temporal reasoning paths, using a novel knowledge-graph-instructed-generation strategy. Based on the dataset, we propose the first open-source LLM series TimeLlaMA based on the foundation LlaMA2, with the ability of instruction following for explainable temporal reasoning. We compare the performance of our method and a variety of LLMs, where our method achieves the state-of-the-art performance of temporal prediction and explanation.

Large language models and vision-language models (which we jointly call LMs) have transformed NLP and CV, demonstrating remarkable potential across various fields. However, their capabilities in affective analysis (i.e. sentiment analysis and emotion detection) remain underexplored. This gap is largely due to the absence of comprehensive evaluation benchmarks, and the inherent complexity of affective analysis tasks. In this paper, we introduce MMAFFBen, the first extensive open-source benchmark for multilingual multimodal affective analysis. MMAFFBen encompasses text, image, and video modalities across 35 languages, covering four key affective analysis tasks: sentiment polarity, sentiment intensity, emotion classification, and emotion intensity. Moreover, we construct the MMAFFIn dataset for fine-tuning LMs on affective analysis tasks, and further develop MMAFFLM-3b and MMAFFLM-7b based on it. We evaluate various representative LMs, including GPT-4o-mini, providing a systematic comparison of their affective understanding capabilities. This project is available at https://github.com/lzw108/MMAFFBen.

Sentiment analysis and emotion detection are important research topics in natural language processing (NLP) and benefit many downstream tasks. With the widespread application of LLMs, researchers have started exploring the application of LLMs based on instruction-tuning in the field of sentiment analysis. However, these models only focus on single aspects of affective classification tasks (e.g. sentimental polarity or categorical emotions), and overlook the regression tasks (e.g. sentiment strength or emotion intensity), which leads to poor performance in downstream tasks. The main reason is the lack of comprehensive affective instruction tuning datasets and evaluation benchmarks, which cover various affective classification and regression tasks. Moreover, although emotional information is useful for downstream tasks, existing downstream datasets lack high-quality and comprehensive affective annotations. In this paper, we propose EmoLLMs, the first series of open-sourced instruction-following LLMs for comprehensive affective analysis based on fine-tuning various LLMs with instruction data, the first multi-task affective analysis instruction dataset (AAID) with 234K data samples based on various classification and regression tasks to support LLM instruction tuning, and a comprehensive affective evaluation benchmark (AEB) with 14 tasks from various sources and domains to test the generalization ability of LLMs. We propose a series of EmoLLMs by fine-tuning LLMs with AAID to solve various affective instruction tasks. We compare our model with a variety of LLMs on AEB, where our models outperform all other open-sourced LLMs, and surpass ChatGPT and GPT-4 in most tasks, which shows that the series of EmoLLMs achieve the ChatGPT-level and GPT-4-level generalization capabilities on affective analysis tasks, and demonstrates our models can be used as affective annotation tools.

Pretrained language models have been used in various natural language processing applications. In the mental health domain, domain-specific language models are pretrained and released, which facilitates the early detection of mental health conditions. Social posts, e.g., on Reddit, are usually long documents. However, there are no domain-specific pretrained models for long-sequence modeling in the mental health domain. This paper conducts domain-specific continued pretraining to capture the long context for mental health. Specifically, we train and release MentalXLNet and MentalLongformer based on XLNet and Longformer. We evaluate the mental health classification performance and the long-range ability of these two domain-specific pretrained models. Our models are released in HuggingFace.

Procedural activities, ranging from routine cooking to complex surgical operations, are highly structured as a set of actions conducted in a specific temporal order. Despite their success on static images and short clips, current self-supervised learning methods often overlook the procedural nature that underpins such activities. We expose the lack of procedural awareness in current SSL methods with a motivating experiment: models pretrained on forward and time-reversed sequences produce highly similar features, confirming that their representations are blind to the underlying procedural order. To address this shortcoming, we propose PL-Stitch, a self-supervised framework that harnesses the inherent temporal order of video frames as a powerful supervisory signal. Our approach integrates two novel probabilistic objectives based on the Plackett-Luce (PL) model. The primary PL objective trains the model to sort sampled frames chronologically, compelling it to learn the global workflow progression. The secondary objective, a spatio-temporal jigsaw loss, complements the learning by capturing fine-grained, cross-frame object correlations. Our approach consistently achieves superior performance across five surgical and cooking benchmarks. Specifically, PL-Stitch yields significant gains in surgical phase recognition (e.g., +11.4 pp k-NN accuracy on Cholec80) and cooking action segmentation (e.g., +5.7 pp linear probing accuracy on Breakfast), demonstrating its effectiveness for procedural video representation learning.

Spatial transcriptomics enables simultaneous measurement of gene expression and tissue morphology, offering unprecedented insights into cellular organization and disease mechanisms. However, the field lacks comprehensive benchmarks for evaluating multimodal learning methods that leverage both histology images and gene expression data. Here, we present HESCAPE, a large-scale benchmark for cross-modal contrastive pretraining in spatial transcriptomics, built on a curated pan-organ dataset spanning 6 different gene panels and 54 donors. We systematically evaluated state-of-the-art image and gene expression encoders across multiple pretraining strategies and assessed their effectiveness on two downstream tasks: gene mutation classification and gene expression prediction. Our benchmark demonstrates that gene expression encoders are the primary determinant of strong representational alignment, and that gene models pretrained on spatial transcriptomics data outperform both those trained without spatial data and simple baseline approaches. However, downstream task evaluation reveals a striking contradiction: while contrastive pretraining consistently improves gene mutation classification performance, it degrades direct gene expression prediction compared to baseline encoders trained without cross-modal objectives. We identify batch effects as a key factor that interferes with effective cross-modal alignment. Our findings highlight the critical need for batch-robust multimodal learning approaches in spatial transcriptomics. To accelerate progress in this direction, we release HESCAPE, providing standardized datasets, evaluation protocols, and benchmarking tools for the community

Advancements in computer-assisted surgical procedures heavily rely on accurate visual data interpretation from camera systems used during surgeries. Traditional open-access datasets focusing on surgical procedures are often limited by their small size, typically consisting of fewer than 100 videos with less than 100K images. To address these constraints, a new dataset called Surg-3M has been compiled using a novel aggregation pipeline that collects high-resolution videos from online sources. Featuring an extensive collection of over 4K surgical videos and more than 3 million high-quality images from multiple procedure types, Surg-3M offers a comprehensive resource surpassing existing alternatives in size and scope, including two novel tasks. To demonstrate the effectiveness of this dataset, we present SurgFM, a self-supervised foundation model pretrained on Surg-3M that achieves impressive results in downstream tasks such as surgical phase recognition, action recognition, and tool presence detection. Combining key components from ConvNeXt, DINO, and an innovative augmented distillation method, SurgFM exhibits exceptional performance compared to specialist architectures across various benchmarks. Our experimental results show that SurgFM outperforms state-of-the-art models in multiple downstream tasks, including significant gains in surgical phase recognition (+8.9pp, +4.7pp, and +3.9pp of Jaccard in AutoLaparo, M2CAI16, and Cholec80), action recognition (+3.1pp of mAP in CholecT50) and tool presence detection (+4.6pp of mAP in Cholec80). Moreover, even when using only half of the data, SurgFM outperforms state-of-the-art models in AutoLaparo and achieves state-of-the-art performance in Cholec80. Both Surg-3M and SurgFM have significant potential to accelerate progress towards developing autonomous robotic surgery systems.

Foundation models are reshaping computational pathology by enabling transfer learning, where models pre-trained on vast datasets can be adapted for downstream diagnostic, prognostic, and therapeutic response tasks. Despite these advances, foundation models are still limited in their ability to encode the entire gigapixel whole-slide images without additional training and often lack complementary multimodal data. Here, we introduce Threads, a slide-level foundation model capable of generating universal representations of whole-slide images of any size. Threads was pre-trained using a multimodal learning approach on a diverse cohort of 47,171 hematoxylin and eosin (H&E)-stained tissue sections, paired with corresponding genomic and transcriptomic profiles - the largest such paired dataset to be used for foundation model development to date. This unique training paradigm enables Threads to capture the tissue's underlying molecular composition, yielding powerful representations applicable to a wide array of downstream tasks. In extensive benchmarking across 54 oncology tasks, including clinical subtyping, grading, mutation prediction, immunohistochemistry status determination, treatment response prediction, and survival prediction, Threads outperformed all baselines while demonstrating remarkable generalizability and label efficiency. It is particularly well suited for predicting rare events, further emphasizing its clinical utility. We intend to make the model publicly available for the broader community.

Reparameterized diffusion models (RDMs) have recently matched autoregressive methods in protein generation, motivating their use for challenging tasks such as designing membrane proteins, which possess interleaved soluble and transmembrane (TM) regions. We introduce the Membrane Diffusion Language Model (MemDLM), a fine-tuned RDM-based protein language model that enables controllable membrane protein sequence design. MemDLM-generated sequences recapitulate the TM residue density and structural features of natural membrane proteins, achieving comparable biological plausibility and outperforming state-of-the-art diffusion baselines in motif scaffolding tasks by producing lower perplexity, higher BLOSUM-62 scores, and improved pLDDT confidence. To enhance controllability, we develop Per-Token Guidance (PET), a novel classifier-guided sampling strategy that selectively solubilizes residues while preserving conserved TM domains, yielding sequences with reduced TM density but intact functional cores. Importantly, MemDLM designs validated in TOXCAT beta-lactamase growth assays demonstrate successful TM insertion, distinguishing high-quality generated sequences from poor ones. Together, our framework establishes the first experimentally-validated diffusion-based model for rational membrane protein generation, integrating de novo design, motif scaffolding, and targeted property optimization.

Spatial transcriptomics (ST) enables interrogating the molecular composition of tissue with ever-increasing resolution, depth, and sensitivity. However, costs, rapidly evolving technology, and lack of standards have constrained computational methods in ST to narrow tasks and small cohorts. In addition, the underlying tissue morphology as reflected by H&E-stained whole slide images (WSIs) encodes rich information often overlooked in ST studies. Here, we introduce HEST-1k, a collection of 1,108 spatial transcriptomic profiles, each linked to a WSI and metadata. HEST-1k was assembled using HEST-Library from 131 public and internal cohorts encompassing 25 organs, two species (Homo Sapiens and Mus Musculus), and 320 cancer samples from 25 cancer types. HEST-1k processing enabled the identification of 1.5 million expression--morphology pairs and 60 million nuclei. HEST-1k is tested on three use cases: (1) benchmarking foundation models for histopathology (HEST-Benchmark), (2) biomarker identification, and (3) multimodal representation learning. HEST-1k, HEST-Library, and HEST-Benchmark can be freely accessed via https://github.com/mahmoodlab/hest.

Recent advancements in Large Language Models (LLMs) have demonstrated their potential in delivering accurate answers to questions about world knowledge. Despite this, existing benchmarks for evaluating LLMs in healthcare predominantly focus on medical doctors, leaving other critical healthcare professions underrepresented. To fill this research gap, we introduce the Examinations for Medical Personnel in Chinese (EMPEC), a pioneering large-scale healthcare knowledge benchmark in traditional Chinese. EMPEC consists of 157,803 exam questions across 124 subjects and 20 healthcare professions, including underrepresented occupations like Optometrists and Audiologists. Each question is tagged with its release time and source, ensuring relevance and authenticity. We conducted extensive experiments on 17 LLMs, including proprietary, open-source models, general domain models and medical specific models, evaluating their performance under various settings. Our findings reveal that while leading models like GPT-4 achieve over 75\% accuracy, they still struggle with specialized fields and alternative medicine. Surprisingly, general-purpose LLMs outperformed medical-specific models, and incorporating EMPEC's training data significantly enhanced performance. Additionally, the results on questions released after the models' training cutoff date were consistent with overall performance trends, suggesting that the models' performance on the test set can predict their effectiveness in addressing unseen healthcare-related queries. The transition from traditional to simplified Chinese characters had a negligible impact on model performance, indicating robust linguistic versatility. Our study underscores the importance of expanding benchmarks to cover a broader range of healthcare professions to better assess the applicability of LLMs in real-world healthcare scenarios.

Standing as one of the most significant barriers to reaching quantum advantage, state-preparation fidelities on noisy intermediate-scale quantum processors suffer from quantum-gate errors, which accumulate over time. A potential remedy is pulse-based state preparation. We numerically investigate the minimal evolution times (METs) attainable by optimizing (microwave and exchange) pulses on silicon hardware. We investigate two state preparation tasks. First, we consider the preparation of molecular ground states and find the METs for H_2, HeH^+, and LiH to be 2.4 ns, 4.4 ns, and 27.2 ns, respectively. Second, we consider transitions between arbitrary states and find the METs for transitions between arbitrary four-qubit states to be below 50 ns. For comparison, connecting arbitrary two-qubit states via one- and two-qubit gates on the same silicon processor requires approximately 200 ns. This comparison indicates that pulse-based state preparation is likely to utilize the coherence times of silicon hardware more efficiently than gate-based state preparation. Finally, we quantify the effect of silicon device parameters on the MET. We show that increasing the maximal exchange amplitude from 10 MHz to 1 GHz accelerates the METs, e.g., for H_2 from 84.3 ns to 2.4 ns. This demonstrates the importance of fast exchange. We also show that increasing the maximal amplitude of the microwave drive from 884 kHz to 56.6 MHz shortens state transitions, e.g., for two-qubit states from 1000 ns to 25 ns. Our results bound both the state-preparation times for general quantum algorithms and the execution times of variational quantum algorithms with silicon spin qubits.

The internet has brought both benefits and harms to society. A prime example of the latter is misinformation, including conspiracy theories, which flood the web. Recent advances in natural language processing, particularly the emergence of large language models (LLMs), have improved the prospects of accurate misinformation detection. However, most LLM-based approaches to conspiracy theory detection focus only on binary classification and fail to account for the important relationship between misinformation and affective features (i.e., sentiment and emotions). Driven by a comprehensive analysis of conspiracy text that reveals its distinctive affective features, we propose ConspEmoLLM, the first open-source LLM that integrates affective information and is able to perform diverse tasks relating to conspiracy theories. These tasks include not only conspiracy theory detection, but also classification of theory type and detection of related discussion (e.g., opinions towards theories). ConspEmoLLM is fine-tuned based on an emotion-oriented LLM using our novel ConDID dataset, which includes five tasks to support LLM instruction tuning and evaluation. We demonstrate that when applied to these tasks, ConspEmoLLM largely outperforms several open-source general domain LLMs and ChatGPT, as well as an LLM that has been fine-tuned using ConDID, but which does not use affective features. This project will be released on https://github.com/lzw108/ConspEmoLLM/.

Target proteins that lack accessible binding pockets and conformational stability have posed increasing challenges for drug development. Induced proximity strategies, such as PROTACs and molecular glues, have thus gained attention as pharmacological alternatives, but still require small molecule docking at binding pockets for targeted protein degradation (TPD). The computational design of protein-based binders presents unique opportunities to access undruggable targets, but have often relied on stable 3D structures or predictions for effective binder generation. Recently, we have leveraged the expressive latent spaces of protein language models (pLMs) for the prioritization of peptide binders from sequence alone, which we have then fused to E3 ubiquitin ligase domains, creating a CRISPR-analogous TPD system for target proteins. However, our methods rely on training discriminator models for ranking heuristically or unconditionally-derived guide peptides for their target binding capability. In this work, we introduce PepMLM, a purely target sequence-conditioned de novo generator of linear peptide binders. By employing a novel masking strategy that uniquely positions cognate peptide sequences at the terminus of target protein sequences, PepMLM tasks the state-of-the-art ESM-2 pLM to fully reconstruct the binder region, achieving low perplexities matching or improving upon previously-validated peptide-protein sequence pairs. After successful in silico benchmarking with AlphaFold-Multimer, we experimentally verify PepMLM's efficacy via fusion of model-derived peptides to E3 ubiquitin ligase domains, demonstrating endogenous degradation of target substrates in cellular models. In total, PepMLM enables the generative design of candidate binders to any target protein, without the requirement of target structure, empowering downstream programmable proteome editing applications.

Retrieving adverbs that describe an action in a video poses a crucial step towards fine-grained video understanding. We propose a framework for video-to-adverb retrieval (and vice versa) that aligns video embeddings with their matching compositional adverb-action text embedding in a joint embedding space. The compositional adverb-action text embedding is learned using a residual gating mechanism, along with a novel training objective consisting of triplet losses and a regression target. Our method achieves state-of-the-art performance on five recent benchmarks for video-adverb retrieval. Furthermore, we introduce dataset splits to benchmark video-adverb retrieval for unseen adverb-action compositions on subsets of the MSR-VTT Adverbs and ActivityNet Adverbs datasets. Our proposed framework outperforms all prior works for the generalisation task of retrieving adverbs from videos for unseen adverb-action compositions. Code and dataset splits are available at https://hummelth.github.io/ReGaDa/.

Training deep learning models for video classification from audio-visual data commonly requires immense amounts of labeled training data collected via a costly process. A challenging and underexplored, yet much cheaper, setup is few-shot learning from video data. In particular, the inherently multi-modal nature of video data with sound and visual information has not been leveraged extensively for the few-shot video classification task. Therefore, we introduce a unified audio-visual few-shot video classification benchmark on three datasets, i.e. the VGGSound-FSL, UCF-FSL, ActivityNet-FSL datasets, where we adapt and compare ten methods. In addition, we propose AV-DIFF, a text-to-feature diffusion framework, which first fuses the temporal and audio-visual features via cross-modal attention and then generates multi-modal features for the novel classes. We show that AV-DIFF obtains state-of-the-art performance on our proposed benchmark for audio-visual (generalised) few-shot learning. Our benchmark paves the way for effective audio-visual classification when only limited labeled data is available. Code and data are available at https://github.com/ExplainableML/AVDIFF-GFSL.

Zero-shot learning models achieve remarkable results on image classification for samples from classes that were not seen during training. However, such models must be trained from scratch with specialised methods: therefore, access to a training dataset is required when the need for zero-shot classification arises. In this paper, we aim to equip pre-trained models with zero-shot classification capabilities without the use of image data. We achieve this with our proposed Image-free Classifier Injection with Semantics (ICIS) that injects classifiers for new, unseen classes into pre-trained classification models in a post-hoc fashion without relying on image data. Instead, the existing classifier weights and simple class-wise descriptors, such as class names or attributes, are used. ICIS has two encoder-decoder networks that learn to reconstruct classifier weights from descriptors (and vice versa), exploiting (cross-)reconstruction and cosine losses to regularise the decoding process. Notably, ICIS can be cheaply trained and applied directly on top of pre-trained classification models. Experiments on benchmark ZSL datasets show that ICIS produces unseen classifier weights that achieve strong (generalised) zero-shot classification performance. Code is available at https://github.com/ExplainableML/ImageFreeZSL .

The visual classification performance of vision-language models such as CLIP has been shown to benefit from additional semantic knowledge from large language models (LLMs) such as GPT-3. In particular, averaging over LLM-generated class descriptors, e.g. "waffle, which has a round shape", can notably improve generalization performance. In this work, we critically study this behavior and propose WaffleCLIP, a framework for zero-shot visual classification which simply replaces LLM-generated descriptors with random character and word descriptors. Without querying external models, we achieve comparable performance gains on a large number of visual classification tasks. This allows WaffleCLIP to both serve as a low-cost alternative, as well as a sanity check for any future LLM-based vision-language model extensions. We conduct an extensive experimental study on the impact and shortcomings of additional semantics introduced with LLM-generated descriptors, and showcase how - if available - semantic context is better leveraged by querying LLMs for high-level concepts, which we show can be done to jointly resolve potential class name ambiguities. Code is available here: https://github.com/ExplainableML/WaffleCLIP.

The latest large language models (LLMs) such as ChatGPT, exhibit strong capabilities in automated mental health analysis. However, existing relevant studies bear several limitations, including inadequate evaluations, lack of prompting strategies, and ignorance of exploring LLMs for explainability. To bridge these gaps, we comprehensively evaluate the mental health analysis and emotional reasoning ability of LLMs on 11 datasets across 5 tasks. We explore the effects of different prompting strategies with unsupervised and distantly supervised emotional information. Based on these prompts, we explore LLMs for interpretable mental health analysis by instructing them to generate explanations for each of their decisions. We convey strict human evaluations to assess the quality of the generated explanations, leading to a novel dataset with 163 human-assessed explanations. We benchmark existing automatic evaluation metrics on this dataset to guide future related works. According to the results, ChatGPT shows strong in-context learning ability but still has a significant gap with advanced task-specific methods. Careful prompt engineering with emotional cues and expert-written few-shot examples can also effectively improve performance on mental health analysis. In addition, ChatGPT generates explanations that approach human performance, showing its great potential in explainable mental health analysis.

Planning an optimal route in a complex environment requires efficient reasoning about the surrounding scene. While human drivers prioritize important objects and ignore details not relevant to the decision, learning-based planners typically extract features from dense, high-dimensional grid representations containing all vehicle and road context information. In this paper, we propose PlanT, a novel approach for planning in the context of self-driving that uses a standard transformer architecture. PlanT is based on imitation learning with a compact object-level input representation. On the Longest6 benchmark for CARLA, PlanT outperforms all prior methods (matching the driving score of the expert) while being 5.3x faster than equivalent pixel-based planning baselines during inference. Combining PlanT with an off-the-shelf perception module provides a sensor-based driving system that is more than 10 points better in terms of driving score than the existing state of the art. Furthermore, we propose an evaluation protocol to quantify the ability of planners to identify relevant objects, providing insights regarding their decision-making. Our results indicate that PlanT can focus on the most relevant object in the scene, even when this object is geometrically distant.

Audio-visual generalised zero-shot learning for video classification requires understanding the relations between the audio and visual information in order to be able to recognise samples from novel, previously unseen classes at test time. The natural semantic and temporal alignment between audio and visual data in video data can be exploited to learn powerful representations that generalise to unseen classes at test time. We propose a multi-modal and Temporal Cross-attention Framework (\modelName) for audio-visual generalised zero-shot learning. Its inputs are temporally aligned audio and visual features that are obtained from pre-trained networks. Encouraging the framework to focus on cross-modal correspondence across time instead of self-attention within the modalities boosts the performance significantly. We show that our proposed framework that ingests temporal features yields state-of-the-art performance on the \ucf, \vgg, and \activity benchmarks for (generalised) zero-shot learning. Code for reproducing all results is available at https://github.com/ExplainableML/TCAF-GZSL.

Peer reviewing is a central process in modern research and essential for ensuring high quality and reliability of published work. At the same time, it is a time-consuming process and increasing interest in emerging fields often results in a high review workload, especially for senior researchers in this area. How to cope with this problem is an open question and it is vividly discussed across all major conferences. In this work, we propose an Argument Mining based approach for the assistance of editors, meta-reviewers, and reviewers. We demonstrate that the decision process in the field of scientific publications is driven by arguments and automatic argument identification is helpful in various use-cases. One of our findings is that arguments used in the peer-review process differ from arguments in other domains making the transfer of pre-trained models difficult. Therefore, we provide the community with a new peer-review dataset from different computer science conferences with annotated arguments. In our extensive empirical evaluation, we show that Argument Mining can be used to efficiently extract the most relevant parts from reviews, which are paramount for the publication decision. The process remains interpretable since the extracted arguments can be highlighted in a review without detaching them from their context.

We introduce Mixtral 8x7B, a Sparse Mixture of Experts (SMoE) language model. Mixtral has the same architecture as Mistral 7B, with the difference that each layer is composed of 8 feedforward blocks (i.e. experts). For every token, at each layer, a router network selects two experts to process the current state and combine their outputs. Even though each token only sees two experts, the selected experts can be different at each timestep. As a result, each token has access to 47B parameters, but only uses 13B active parameters during inference. Mixtral was trained with a context size of 32k tokens and it outperforms or matches Llama 2 70B and GPT-3.5 across all evaluated benchmarks. In particular, Mixtral vastly outperforms Llama 2 70B on mathematics, code generation, and multilingual benchmarks. We also provide a model fine-tuned to follow instructions, Mixtral 8x7B - Instruct, that surpasses GPT-3.5 Turbo, Claude-2.1, Gemini Pro, and Llama 2 70B - chat model on human benchmarks. Both the base and instruct models are released under the Apache 2.0 license.

We develop Polaris, the first safety-focused LLM constellation for real-time patient-AI healthcare conversations. Unlike prior LLM works in healthcare focusing on tasks like question answering, our work specifically focuses on long multi-turn voice conversations. Our one-trillion parameter constellation system is composed of several multibillion parameter LLMs as co-operative agents: a stateful primary agent that focuses on driving an engaging conversation and several specialist support agents focused on healthcare tasks performed by nurses to increase safety and reduce hallucinations. We develop a sophisticated training protocol for iterative co-training of the agents that optimize for diverse objectives. We train our models on proprietary data, clinical care plans, healthcare regulatory documents, medical manuals, and other medical reasoning documents. We align our models to speak like medical professionals, using organic healthcare conversations and simulated ones between patient actors and experienced nurses. This allows our system to express unique capabilities such as rapport building, trust building, empathy and bedside manner. Finally, we present the first comprehensive clinician evaluation of an LLM system for healthcare. We recruited over 1100 U.S. licensed nurses and over 130 U.S. licensed physicians to perform end-to-end conversational evaluations of our system by posing as patients and rating the system on several measures. We demonstrate Polaris performs on par with human nurses on aggregate across dimensions such as medical safety, clinical readiness, conversational quality, and bedside manner. Additionally, we conduct a challenging task-based evaluation of the individual specialist support agents, where we demonstrate our LLM agents significantly outperform a much larger general-purpose LLM (GPT-4) as well as from its own medium-size class (LLaMA-2 70B).