Daily Papers

Dense 3D reconstruction from RGB images traditionally assumes static camera pose estimates. This assumption has endured, even as recent works have increasingly focused on real-time methods for mobile devices. However, the assumption of a fixed pose for each image does not hold for online execution: poses from real-time SLAM are dynamic and may be updated following events such as bundle adjustment and loop closure. This has been addressed in the RGB-D setting, by de-integrating past views and re-integrating them with updated poses, but it remains largely untreated in the RGB-only setting. We formalize this problem to define the new task of dense online reconstruction from dynamically-posed images. To support further research, we introduce a dataset called LivePose containing the dynamic poses from a SLAM system running on ScanNet. We select three recent reconstruction systems and apply a framework based on de-integration to adapt each one to the dynamic-pose setting. In addition, we propose a novel, non-linear de-integration module that learns to remove stale scene content. We show that responding to pose updates is critical for high-quality reconstruction, and that our de-integration framework is an effective solution.

This paper discusses the methods that we used for our submissions to the WMT 2023 Terminology Shared Task for German-to-English (DE-EN), English-to-Czech (EN-CS), and Chinese-to-English (ZH-EN) language pairs. The task aims to advance machine translation (MT) by challenging participants to develop systems that accurately translate technical terms, ultimately enhancing communication and understanding in specialised domains. To this end, we conduct experiments that utilise large language models (LLMs) for two purposes: generating synthetic bilingual terminology-based data, and post-editing translations generated by an MT model through incorporating pre-approved terms. Our system employs a four-step process: (i) using an LLM to generate bilingual synthetic data based on the provided terminology, (ii) fine-tuning a generic encoder-decoder MT model, with a mix of the terminology-based synthetic data generated in the first step and a randomly sampled portion of the original generic training data, (iii) generating translations with the fine-tuned MT model, and (iv) finally, leveraging an LLM for terminology-constrained automatic post-editing of the translations that do not include the required terms. The results demonstrate the effectiveness of our proposed approach in improving the integration of pre-approved terms into translations. The number of terms incorporated into the translations of the blind dataset increases from an average of 36.67% with the generic model to an average of 72.88% by the end of the process. In other words, successful utilisation of terms nearly doubles across the three language pairs.

Cell instance segmentation in cytology images has significant importance for biology analysis and cancer screening, while remains challenging due to 1) the extensive overlapping translucent cell clusters that cause the ambiguous boundaries, and 2) the confusion of mimics and debris as nuclei. In this work, we proposed a De-overlapping Network (DoNet) in a decompose-and-recombined strategy. A Dual-path Region Segmentation Module (DRM) explicitly decomposes the cell clusters into intersection and complement regions, followed by a Semantic Consistency-guided Recombination Module (CRM) for integration. To further introduce the containment relationship of the nucleus in the cytoplasm, we design a Mask-guided Region Proposal Strategy (MRP) that integrates the cell attention maps for inner-cell instance prediction. We validate the proposed approach on ISBI2014 and CPS datasets. Experiments show that our proposed DoNet significantly outperforms other state-of-the-art (SOTA) cell instance segmentation methods. The code is available at https://github.com/DeepDoNet/DoNet.

Benchmarks are essential for consistent evaluation and reproducibility. The integration of Artificial Intelligence into Software Engineering (AI4SE) has given rise to numerous benchmarks for tasks such as code generation and bug fixing. However, this surge presents challenges: (1) scattered benchmark knowledge across tasks, (2) difficulty in selecting relevant benchmarks, (3) the absence of a uniform standard for benchmark development, and (4) limitations of existing benchmarks. In this paper, we review 173 studies and identify 204 AI4SE benchmarks. We classify these benchmarks, analyze their limitations, and expose gaps in practices. Based on our review, we created BenchScout, a semantic search tool to find relevant benchmarks, using automated clustering of the contexts from associated studies. We conducted a user study with 22 participants to evaluate BenchScout's usability, effectiveness, and intuitiveness which resulted in average scores of 4.5, 4.0, and 4.1 out of 5. To advance benchmarking standards, we propose BenchFrame, a unified method to enhance benchmark quality. As a case study, we applied BenchFrame to the HumanEval benchmark and addressed its main limitations. This led to HumanEvalNext, featuring (1) corrected errors, (2) improved language conversion, (3) expanded test coverage, and (4) increased difficulty. We then evaluated ten state-of-the-art code language models on HumanEval, HumanEvalPlus, and HumanEvalNext. On HumanEvalNext, models showed a pass@1 score reduction of 31.22% and 19.94% compared to HumanEval and HumanEvalPlus, respectively.

Zero-Input AI (ZIA) introduces a novel framework for human-computer interaction by enabling proactive intent prediction without explicit user commands. It integrates gaze tracking, bio-signals (EEG, heart rate), and contextual data (time, location, usage history) into a multi-modal model for real-time inference, targeting <100 ms latency. The proposed architecture employs a transformer-based model with cross-modal attention, variational Bayesian inference for uncertainty estimation, and reinforcement learning for adaptive optimization. To support deployment on edge devices (CPUs, TPUs, NPUs), ZIA utilizes quantization, weight pruning, and linear attention to reduce complexity from quadratic to linear with sequence length. Theoretical analysis establishes an information-theoretic bound on prediction error and demonstrates how multi-modal fusion improves accuracy over single-modal approaches. Expected performance suggests 85-90% accuracy with EEG integration and 60-100 ms inference latency. ZIA provides a scalable, privacy-preserving framework for accessibility, healthcare, and consumer applications, advancing AI toward anticipatory intelligence.

Automatic speech recognition systems have undoubtedly advanced with the integration of multilingual and multitask models such as Whisper, which have shown a promising ability to understand and process speech across a wide range of languages. Despite their robustness, these models often fall short in handling the linguistic distinctions of minority languages. This study addresses this gap by integrating traditional and novel language models with fine-tuned Whisper models to raise their performance in less commonly studied languages. Through rigorous fine-tuning and evaluation across multiple datasets, we demonstrate substantial improvements in word error rate, particularly in low-resource scenarios. Our approach not only does take advantage of the extensive data Whisper was pre-trained on, but also complements its linguistic adaptability by incorporating language models. We obtained improvements up to 51\% for in-distribution datasets and up to 34\% for out-of-distribution sentences using statistical language models, while large language models provided moderate but consistently robust improvement across diverse linguistic contexts. The findings reveal that, while the integration reliably benefits all model sizes, the extent of improvement varies, highlighting the importance of optimized language model parameters. Finally, we emphasize the importance of selecting appropriate evaluation parameters when reporting the results using transformer-based ASR models. In summary, this research clears the way for more inclusive ASR technologies that perform better across languages by enriching their linguistic knowledge. For further implementation details of this study, the technical documentation and source code are available at http://www.github.com/hitz-zentroa/whisper-lm.

The Internet of Things (IoT) triggers new types of cyber risks. Therefore, the integration of new IoT devices and services requires a self-assessment of IoT cyber security posture. By security posture this article refers to the cybersecurity strength of an organisation to predict, prevent and respond to cyberthreats. At present, there is a gap in the state of the art, because there are no self-assessment methods for quantifying IoT cyber risk posture. To address this gap, an empirical analysis is performed of 12 cyber risk assessment approaches. The results and the main findings from the analysis is presented as the current and a target risk state for IoT systems, followed by conclusions and recommendations on a transformation roadmap, describing how IoT systems can achieve the target state with a new goal-oriented dependency model. By target state, we refer to the cyber security target that matches the generic security requirements of an organisation. The research paper studies and adapts four alternatives for IoT risk assessment and identifies the goal-oriented dependency modelling as a dominant approach among the risk assessment models studied. The new goal-oriented dependency model in this article enables the assessment of uncontrollable risk states in complex IoT systems and can be used for a quantitative self-assessment of IoT cyber risk posture.

The ubiquity of camera-enabled devices has led to large amounts of unlabeled image data being produced at the edge. The integration of self-supervised learning (SSL) and federated learning (FL) into one coherent system can potentially offer data privacy guarantees while also advancing the quality and robustness of the learned visual representations without needing to move data around. However, client bias and divergence during FL aggregation caused by data heterogeneity limits the performance of learned visual representations on downstream tasks. In this paper, we propose a new aggregation strategy termed Layer-wise Divergence Aware Weight Aggregation (L-DAWA) to mitigate the influence of client bias and divergence during FL aggregation. The proposed method aggregates weights at the layer-level according to the measure of angular divergence between the clients' model and the global model. Extensive experiments with cross-silo and cross-device settings on CIFAR-10/100 and Tiny ImageNet datasets demonstrate that our methods are effective and obtain new SOTA performance on both contrastive and non-contrastive SSL approaches.

Large Language Models (LLMs) excel at generating fluent text but struggle to enforce external constraints because they generate tokens sequentially without explicit control mechanisms. GenCP addresses this limitation by combining LLM predictions with Constraint Programming (CP) reasoning, formulating text generation as a Constraint Satisfaction Problem (CSP). In this paper, we improve GenCP by integrating Masked Language Models (MLMs) for domain generation, which allows bidirectional constraint propagation that leverages both past and future tokens. This integration bridges the gap between token-level prediction and structured constraint enforcement, leading to more reliable and constraint-aware text generation. Our evaluation on COLLIE benchmarks demonstrates that incorporating domain preview via MLM calls significantly improves GenCP's performance. Although this approach incurs additional MLM calls and, in some cases, increased backtracking, the overall effect is a more efficient use of LLM inferences and an enhanced ability to generate feasible and meaningful solutions, particularly in tasks with strict content constraints.

We present BricksRL, a platform designed to democratize access to robotics for reinforcement learning research and education. BricksRL facilitates the creation, design, and training of custom LEGO robots in the real world by interfacing them with the TorchRL library for reinforcement learning agents. The integration of TorchRL with the LEGO hubs, via Bluetooth bidirectional communication, enables state-of-the-art reinforcement learning training on GPUs for a wide variety of LEGO builds. This offers a flexible and cost-efficient approach for scaling and also provides a robust infrastructure for robot-environment-algorithm communication. We present various experiments across tasks and robot configurations, providing built plans and training results. Furthermore, we demonstrate that inexpensive LEGO robots can be trained end-to-end in the real world to achieve simple tasks, with training times typically under 120 minutes on a normal laptop. Moreover, we show how users can extend the capabilities, exemplified by the successful integration of non-LEGO sensors. By enhancing accessibility to both robotics and reinforcement learning, BricksRL establishes a strong foundation for democratized robotic learning in research and educational settings.

Vision language models (VLMs) have experienced rapid advancements through the integration of large language models (LLMs) with image-text pairs, yet they struggle with detailed regional visual understanding due to limited spatial awareness of the vision encoder, and the use of coarse-grained training data that lacks detailed, region-specific captions. To address this, we introduce RegionGPT (short as RGPT), a novel framework designed for complex region-level captioning and understanding. RGPT enhances the spatial awareness of regional representation with simple yet effective modifications to existing visual encoders in VLMs. We further improve performance on tasks requiring a specific output scope by integrating task-guided instruction prompts during both training and inference phases, while maintaining the model's versatility for general-purpose tasks. Additionally, we develop an automated region caption data generation pipeline, enriching the training set with detailed region-level captions. We demonstrate that a universal RGPT model can be effectively applied and significantly enhancing performance across a range of region-level tasks, including but not limited to complex region descriptions, reasoning, object classification, and referring expressions comprehension.

Diffusion priors have been used for blind face restoration (BFR) by fine-tuning diffusion models (DMs) on restoration datasets to recover low-quality images. However, the naive application of DMs presents several key limitations. (i) The diffusion prior has inferior semantic consistency (e.g., ID, structure and color.), increasing the difficulty of optimizing the BFR model; (ii) reliance on hundreds of denoising iterations, preventing the effective cooperation with perceptual losses, which is crucial for faithful restoration. Observing that the latent consistency model (LCM) learns consistency noise-to-data mappings on the ODE-trajectory and therefore shows more semantic consistency in the subject identity, structural information and color preservation, we propose InterLCM to leverage the LCM for its superior semantic consistency and efficiency to counter the above issues. Treating low-quality images as the intermediate state of LCM, InterLCM achieves a balance between fidelity and quality by starting from earlier LCM steps. LCM also allows the integration of perceptual loss during training, leading to improved restoration quality, particularly in real-world scenarios. To mitigate structural and semantic uncertainties, InterLCM incorporates a Visual Module to extract visual features and a Spatial Encoder to capture spatial details, enhancing the fidelity of restored images. Extensive experiments demonstrate that InterLCM outperforms existing approaches in both synthetic and real-world datasets while also achieving faster inference speed.

Conventional recommender systems (RSs) face challenges in precisely capturing users' fine-grained preferences. Large language models (LLMs) have shown capabilities in commonsense reasoning and leveraging external tools that may help address these challenges. However, existing LLM-based RSs suffer from hallucinations, misalignment between the semantic space of items and the behavior space of users, or overly simplistic control strategies (e.g., whether to rank or directly present existing results). To bridge these gap, we introduce ToolRec, a framework for LLM-empowered recommendations via tool learning that uses LLMs as surrogate users, thereby guiding the recommendation process and invoking external tools to generate a recommendation list that aligns closely with users' nuanced preferences. We formulate the recommendation process as a process aimed at exploring user interests in attribute granularity. The process factors in the nuances of the context and user preferences. The LLM then invokes external tools based on a user's attribute instructions and probes different segments of the item pool. We consider two types of attribute-oriented tools: rank tools and retrieval tools. Through the integration of LLMs, ToolRec enables conventional recommender systems to become external tools with a natural language interface. Extensive experiments verify the effectiveness of ToolRec, particularly in scenarios that are rich in semantic content.

Federated learning (FL) is a privacy-friendly type of machine learning where devices locally train a model on their private data and typically communicate model updates with a server. In decentralized FL (DFL), peers communicate model updates with each other instead. However, DFL is challenging since (1) the training data possessed by different peers is often non-i.i.d. (i.e., distributed differently between the peers) and (2) malicious, or Byzantine, attackers can share arbitrary model updates with other peers to subvert the training process. We address these two challenges and present Bristle, middleware between the learning application and the decentralized network layer. Bristle leverages transfer learning to predetermine and freeze the non-output layers of a neural network, significantly speeding up model training and lowering communication costs. To securely update the output layer with model updates from other peers, we design a fast distance-based prioritizer and a novel performance-based integrator. Their combined effect results in high resilience to Byzantine attackers and the ability to handle non-i.i.d. classes. We empirically show that Bristle converges to a consistent 95% accuracy in Byzantine environments, outperforming all evaluated baselines. In non-Byzantine environments, Bristle requires 83% fewer iterations to achieve 90% accuracy compared to state-of-the-art methods. We show that when the training classes are non-i.i.d., Bristle significantly outperforms the accuracy of the most Byzantine-resilient baselines by 2.3x while reducing communication costs by 90%.

The energy levels of hydrogen-like atoms are obtained from the phase-space quantization, one of the pillars of the old quantum theory, by three different methods - (i) direct integration, (ii) Sommerfeld's original method, and (iii) complex integration. The difficulties come from the imposition of elliptical orbits to the electron, resulting in a variable radial component of the linear momentum. Details of the calculation, which constitute a recurrent gap in textbooks that deal with phase-space quantization, are shown in depth in an accessible fashion for students of introductory quantum mechanics courses.

This article conducts a literature review of current and future challenges in the use of artificial intelligence (AI) in cyber physical systems. The literature review is focused on identifying a conceptual framework for increasing resilience with AI through automation supporting both, a technical and human level. The methodology applied resembled a literature review and taxonomic analysis of complex internet of things (IoT) interconnected and coupled cyber physical systems. There is an increased attention on propositions on models, infrastructures and frameworks of IoT in both academic and technical papers. These reports and publications frequently represent a juxtaposition of other related systems and technologies (e.g. Industrial Internet of Things, Cyber Physical Systems, Industry 4.0 etc.). We review academic and industry papers published between 2010 and 2020. The results determine a new hierarchical cascading conceptual framework for analysing the evolution of AI decision-making in cyber physical systems. We argue that such evolution is inevitable and autonomous because of the increased integration of connected devices (IoT) in cyber physical systems. To support this argument, taxonomic methodology is adapted and applied for transparency and justifications of concepts selection decisions through building summary maps that are applied for designing the hierarchical cascading conceptual framework.

Digital technologies have changed the way supply chain operations are structured. In this article, we conduct systematic syntheses of literature on the impact of new technologies on supply chains and the related cyber risks. A taxonomic/cladistic approach is used for the evaluations of progress in the area of supply chain integration in the Industrial Internet of Things and Industry 4.0, with a specific focus on the mitigation of cyber risks. An analytical framework is presented, based on a critical assessment with respect to issues related to new types of cyber risk and the integration of supply chains with new technologies. This paper identifies a dynamic and self-adapting supply chain system supported with Artificial Intelligence and Machine Learning (AI/ML) and real-time intelligence for predictive cyber risk analytics. The system is integrated into a cognition engine that enables predictive cyber risk analytics with real-time intelligence from IoT networks at the edge. This enhances capacities and assist in the creation of a comprehensive understanding of the opportunities and threats that arise when edge computing nodes are deployed, and when AI/ML technologies are migrated to the periphery of IoT networks.

We introduce REAL, a benchmark and framework for multi-turn agent evaluations on deterministic simulations of real-world websites. REAL comprises high-fidelity, deterministic replicas of 11 widely-used websites across domains such as e-commerce, travel, communication, and professional networking. We also release a benchmark consisting of 112 practical tasks that mirror everyday complex user interactions requiring both accurate information retrieval and state-changing actions. All interactions occur within this fully controlled setting, eliminating safety risks and enabling robust, reproducible evaluation of agent capability and reliability. Our novel evaluation framework combines programmatic checks of website state for action-based tasks with rubric-guided LLM-based judgments for information retrieval. The framework supports both open-source and proprietary agent systems through a flexible evaluation harness that accommodates black-box commands within browser environments, allowing research labs to test agentic systems without modification. Our empirical results show that frontier language models achieve at most a 41% success rate on REAL, highlighting critical gaps in autonomous web navigation and task completion capabilities. Our framework supports easy integration of new tasks, reproducible evaluation, and scalable post-training data generation, marking a significant step forward in evaluating and advancing agent capabilities.

Continuous latent variables (LVs) are a key ingredient of many generative models, as they allow modelling expressive mixtures with an uncountable number of components. In contrast, probabilistic circuits (PCs) are hierarchical discrete mixtures represented as computational graphs composed of input, sum and product units. Unlike continuous LV models, PCs provide tractable inference but are limited to discrete LVs with categorical (i.e. unordered) states. We bridge these model classes by introducing probabilistic integral circuits (PICs), a new language of computational graphs that extends PCs with integral units representing continuous LVs. In the first place, PICs are symbolic computational graphs and are fully tractable in simple cases where analytical integration is possible. In practice, we parameterise PICs with light-weight neural nets delivering an intractable hierarchical continuous mixture that can be approximated arbitrarily well with large PCs using numerical quadrature. On several distribution estimation benchmarks, we show that such PIC-approximating PCs systematically outperform PCs commonly learned via expectation-maximization or SGD.

Online multi-object tracking has been recently dominated by tracking-by-detection (TbD) methods, where recent advances rely on increasingly sophisticated heuristics for tracklet representation, feature fusion, and multi-stage matching. The key strength of TbD lies in its modular design, enabling the integration of specialized off-the-shelf models like motion predictors and re-identification. However, the extensive usage of human-crafted rules for temporal associations makes these methods inherently limited in their ability to capture the complex interplay between various tracking cues. In this work, we introduce CAMEL, a novel association module for Context-Aware Multi-Cue ExpLoitation, that learns resilient association strategies directly from data, breaking free from hand-crafted heuristics while maintaining TbD's valuable modularity. At its core, CAMEL employs two transformer-based modules and relies on a novel association-centric training scheme to effectively model the complex interactions between tracked targets and their various association cues. Unlike end-to-end detection-by-tracking approaches, our method remains lightweight and fast to train while being able to leverage external off-the-shelf models. Our proposed online tracking pipeline, CAMELTrack, achieves state-of-the-art performance on multiple tracking benchmarks. Our code is available at https://github.com/TrackingLaboratory/CAMELTrack.

Balancing cost and performance is crucial when choosing high- versus low-resolution point-cloud roadside sensors. For example, LiDAR delivers dense point cloud, while 4D millimeter-wave radar, though spatially sparser, embeds velocity cues that help distinguish objects and come at a lower price. Unfortunately, the sensor placement strategies will influence point cloud density and distribution across the coverage area. Compounding the first challenge is the fact that different sensor mixtures often demand distinct neural network architectures to maximize their complementary strengths. Without an evaluation framework that establishes a benchmark for comparison, it is imprudent to make claims regarding whether marginal gains result from higher resolution and new sensing modalities or from the algorithms. We present an ex-ante evaluation that addresses the two challenges. First, we realized a simulation tool that builds on integer programming to automatically compare different sensor placement strategies against coverage and cost jointly. Additionally, inspired by human multi-sensory integration, we propose a modular framework to assess whether reductions in spatial resolution can be compensated by informational richness in detecting traffic participants. Extensive experimental testing on the proposed framework shows that fusing velocity-encoded radar with low-resolution LiDAR yields marked gains (14 percent AP for pedestrians and an overall mAP improvement of 1.5 percent across six categories) at lower cost than high-resolution LiDAR alone. Notably, these marked gains hold regardless of the specific deep neural modules employed in our frame. The result challenges the prevailing assumption that high resolution are always superior to low-resolution alternatives.

We present LaMDA: Language Models for Dialog Applications. LaMDA is a family of Transformer-based neural language models specialized for dialog, which have up to 137B parameters and are pre-trained on 1.56T words of public dialog data and web text. While model scaling alone can improve quality, it shows less improvements on safety and factual grounding. We demonstrate that fine-tuning with annotated data and enabling the model to consult external knowledge sources can lead to significant improvements towards the two key challenges of safety and factual grounding. The first challenge, safety, involves ensuring that the model's responses are consistent with a set of human values, such as preventing harmful suggestions and unfair bias. We quantify safety using a metric based on an illustrative set of human values, and we find that filtering candidate responses using a LaMDA classifier fine-tuned with a small amount of crowdworker-annotated data offers a promising approach to improving model safety. The second challenge, factual grounding, involves enabling the model to consult external knowledge sources, such as an information retrieval system, a language translator, and a calculator. We quantify factuality using a groundedness metric, and we find that our approach enables the model to generate responses grounded in known sources, rather than responses that merely sound plausible. Finally, we explore the use of LaMDA in the domains of education and content recommendations, and analyze their helpfulness and role consistency.

Vector search has emerged as the foundation for large-scale information retrieval and machine learning systems, with search engines like Google and Bing processing tens of thousands of queries per second on petabyte-scale document datasets by evaluating vector similarities between encoded query texts and web documents. As performance demands for vector search systems surge, accelerated hardware offers a promising solution in the post-Moore's Law era. We introduce FANNS, an end-to-end and scalable vector search framework on FPGAs. Given a user-provided recall requirement on a dataset and a hardware resource budget, FANNS automatically co-designs hardware and algorithm, subsequently generating the corresponding accelerator. The framework also supports scale-out by incorporating a hardware TCP/IP stack in the accelerator. FANNS attains up to 23.0times and 37.2times speedup compared to FPGA and CPU baselines, respectively, and demonstrates superior scalability to GPUs, achieving 5.5times and 7.6times speedup in median and 95th percentile (P95) latency within an eight-accelerator configuration. The remarkable performance of FANNS lays a robust groundwork for future FPGA integration in data centers and AI supercomputers.

Current tools for machine learning fairness only admit a limited range of fairness definitions and have seen little integration with automatic differentiation libraries, despite the central role these libraries play in modern machine learning pipelines. We introduce a framework of fairness regularization terms (fairrets) which quantify bias as modular objectives that are easily integrated in automatic differentiation pipelines. By employing a general definition of fairness in terms of linear-fractional statistics, a wide class of fairrets can be computed efficiently. Experiments show the behavior of their gradients and their utility in enforcing fairness with minimal loss of predictive power compared to baselines. Our contribution includes a PyTorch implementation of the fairret framework.

Antimicrobial resistance (AMR) is escalating and outpacing current antibiotic development. Thus, discovering antibiotics effective against emerging pathogens is becoming increasingly critical. However, existing approaches cannot rapidly identify effective molecules against novel pathogens or emerging drug-resistant strains. Here, we introduce ApexOracle, an artificial intelligence (AI) model that both predicts the antibacterial potency of existing compounds and designs de novo molecules active against strains it has never encountered. Departing from models that rely solely on molecular features, ApexOracle incorporates pathogen-specific context through the integration of molecular features captured via a foundational discrete diffusion language model and a dual-embedding framework that combines genomic- and literature-derived strain representations. Across diverse bacterial species and chemical modalities, ApexOracle consistently outperformed state-of-the-art approaches in activity prediction and demonstrated reliable transferability to novel pathogens with little or no antimicrobial data. Its unified representation-generation architecture further enables the in silico creation of "new-to-nature" molecules with high predicted efficacy against priority threats. By pairing rapid activity prediction with targeted molecular generation, ApexOracle offers a scalable strategy for countering AMR and preparing for future infectious-disease outbreaks.

In an experiment on a turbulent jet, we detect interfacial turbulent layers in a frame that moves, on average, along with the \tnti. This significantly prolongs the observation time of scalar and velocity structures and enables the measurement of two types of Lagrangian coherent structures. One structure, the finite-time Lyapunov field (FTLE), quantifies advective transport barriers of fluid parcels while the other structure highlights barriers of diffusive momentum transport. These two complementary structures depend on large-scale and small-scale motion and are therefore associated with the growth of the turbulent region through engulfment or nibbling, respectively. We detect the \tnti\ from cluster analysis, where we divide the measured scalar field into four clusters. Not only the \tnti\ can be found this way, but also the next, internal, turbulent-turbulent interface. Conditional averages show that these interfaces are correlated with barriers of advective and diffusive transport when the Lagrangian integration time is smaller than the integral time scale. Diffusive structures decorrelate faster since they have a smaller timescale. Conditional averages of these structures at internal turbulent-turbulent interfaces show the same pattern with a more pronounced jump at the interface indicative of a shear layer. This is quite an unexpected outcome, as the internal interface is now defined not by the presence or absence of vorticity, but by conditional vorticity corresponding to two uniform concentration zones. The long-time diffusive momentum flux along Lagrangian paths represents the growth of the turbulent flow into the irrotational domain, a direct demonstration of nibbling. The diffusive flux parallel to the \tnti\ appears to be concentrated in a diffusive superlayer whose width is comparable with the Taylor microscale, which is relatively invariant in time.

The widespread enthusiasm for deep learning has recently expanded into the domain of tabular data. Recognizing that the advancement in deep tabular methods is often inspired by classical methods, e.g., integration of nearest neighbors into neural networks, we investigate whether these classical methods can be revitalized with modern techniques. We revisit a differentiable version of K-nearest neighbors (KNN) -- Neighbourhood Components Analysis (NCA) -- originally designed to learn a linear projection to capture semantic similarities between instances, and seek to gradually add modern deep learning techniques on top. Surprisingly, our implementation of NCA using SGD and without dimensionality reduction already achieves decent performance on tabular data, in contrast to the results of using existing toolboxes like scikit-learn. Further equipping NCA with deep representations and additional training stochasticity significantly enhances its capability, being on par with the leading tree-based method CatBoost and outperforming existing deep tabular models in both classification and regression tasks on 300 datasets. We conclude our paper by analyzing the factors behind these improvements, including loss functions, prediction strategies, and deep architectures. The code is available at https://github.com/qile2000/LAMDA-TALENT.

SpeechBrain is an open-source Conversational AI toolkit based on PyTorch, focused particularly on speech processing tasks such as speech recognition, speech enhancement, speaker recognition, text-to-speech, and much more. It promotes transparency and replicability by releasing both the pre-trained models and the complete "recipes" of code and algorithms required for training them. This paper presents SpeechBrain 1.0, a significant milestone in the evolution of the toolkit, which now has over 200 recipes for speech, audio, and language processing tasks, and more than 100 models available on Hugging Face. SpeechBrain 1.0 introduces new technologies to support diverse learning modalities, Large Language Model (LLM) integration, and advanced decoding strategies, along with novel models, tasks, and modalities. It also includes a new benchmark repository, offering researchers a unified platform for evaluating models across diverse tasks.

There are two common ways in which developers are incorporating proprietary and domain-specific data when building applications of Large Language Models (LLMs): Retrieval-Augmented Generation (RAG) and Fine-Tuning. RAG augments the prompt with the external data, while fine-Tuning incorporates the additional knowledge into the model itself. However, the pros and cons of both approaches are not well understood. In this paper, we propose a pipeline for fine-tuning and RAG, and present the tradeoffs of both for multiple popular LLMs, including Llama2-13B, GPT-3.5, and GPT-4. Our pipeline consists of multiple stages, including extracting information from PDFs, generating questions and answers, using them for fine-tuning, and leveraging GPT-4 for evaluating the results. We propose metrics to assess the performance of different stages of the RAG and fine-Tuning pipeline. We conduct an in-depth study on an agricultural dataset. Agriculture as an industry has not seen much penetration of AI, and we study a potentially disruptive application - what if we could provide location-specific insights to a farmer? Our results show the effectiveness of our dataset generation pipeline in capturing geographic-specific knowledge, and the quantitative and qualitative benefits of RAG and fine-tuning. We see an accuracy increase of over 6 p.p. when fine-tuning the model and this is cumulative with RAG, which increases accuracy by 5 p.p. further. In one particular experiment, we also demonstrate that the fine-tuned model leverages information from across geographies to answer specific questions, increasing answer similarity from 47% to 72%. Overall, the results point to how systems built using LLMs can be adapted to respond and incorporate knowledge across a dimension that is critical for a specific industry, paving the way for further applications of LLMs in other industrial domains.

The ability to accurately interpret complex visual information is a crucial topic of multimodal large language models (MLLMs). Recent work indicates that enhanced visual perception significantly reduces hallucinations and improves performance on resolution-sensitive tasks, such as optical character recognition and document analysis. A number of recent MLLMs achieve this goal using a mixture of vision encoders. Despite their success, there is a lack of systematic comparisons and detailed ablation studies addressing critical aspects, such as expert selection and the integration of multiple vision experts. This study provides an extensive exploration of the design space for MLLMs using a mixture of vision encoders and resolutions. Our findings reveal several underlying principles common to various existing strategies, leading to a streamlined yet effective design approach. We discover that simply concatenating visual tokens from a set of complementary vision encoders is as effective as more complex mixing architectures or strategies. We additionally introduce Pre-Alignment to bridge the gap between vision-focused encoders and language tokens, enhancing model coherence. The resulting family of MLLMs, Eagle, surpasses other leading open-source models on major MLLM benchmarks. Models and code: https://github.com/NVlabs/Eagle

Achieving a balance between computational speed, prediction accuracy, and universal applicability in molecular simulations has been a persistent challenge. This paper presents substantial advancements in the TorchMD-Net software, a pivotal step forward in the shift from conventional force fields to neural network-based potentials. The evolution of TorchMD-Net into a more comprehensive and versatile framework is highlighted, incorporating cutting-edge architectures such as TensorNet. This transformation is achieved through a modular design approach, encouraging customized applications within the scientific community. The most notable enhancement is a significant improvement in computational efficiency, achieving a very remarkable acceleration in the computation of energy and forces for TensorNet models, with performance gains ranging from 2-fold to 10-fold over previous iterations. Other enhancements include highly optimized neighbor search algorithms that support periodic boundary conditions and the smooth integration with existing molecular dynamics frameworks. Additionally, the updated version introduces the capability to integrate physical priors, further enriching its application spectrum and utility in research. The software is available at https://github.com/torchmd/torchmd-net.

Despite their success at many natural language processing (NLP) tasks, large language models (LLMs) still struggle to effectively leverage knowledge for knowledge-intensive tasks, manifesting limitations such as generating incomplete, non-factual, or illogical answers. These limitations stem from inadequate knowledge awareness of LLMs during vanilla fine-tuning. To address these problems, we propose a knowledge-aware fine-tuning (KnowTuning) method to explicitly and implicitly improve the knowledge awareness of LLMs. We devise an explicit knowledge-aware generation stage to train LLMs to explicitly identify knowledge triples in answers. We also propose an implicit knowledge-aware comparison stage to train LLMs to implicitly distinguish between reliable and unreliable knowledge, in three aspects: completeness, factuality, and logicality. Extensive experiments on both generic and medical question answering (QA) datasets confirm the effectiveness of KnowTuning, through automatic and human evaluations, across various sizes of LLMs. Finally, we demonstrate that the improvements of KnowTuning generalize to unseen QA datasets.

The paper introduces D-CODE, a new framework blending Data Colony Optimization (DCO) algorithms inspired by biological colonies' collective behaviours with Dynamic Efficiency (DE) models for real-time adaptation. DCO utilizes metaheuristic strategies from ant colonies, bee swarms, and fungal networks to efficiently explore complex data landscapes, while DE enables continuous resource recalibration and process adjustments for optimal performance amidst changing conditions. Through a mixed-methods approach involving simulations and case studies, D-CODE outperforms traditional techniques, showing improvements of 3-4% in solution quality, 2-3 times faster convergence rates, and up to 25% higher computational efficiency. The integration of DCO's robust optimization and DE's dynamic responsiveness positions D-CODE as a transformative paradigm for intelligent systems design, with potential applications in operational efficiency, decision support, and computational intelligence, supported by empirical validation and promising outcomes.

Geo-localization is an essential component of Unmanned Aerial Vehicle (UAV) navigation systems to ensure precise absolute self-localization in outdoor environments. To address the challenges of GPS signal interruptions or low illumination, Thermal Geo-localization (TG) employs aerial thermal imagery to align with reference satellite maps to accurately determine the UAV's location. However, existing TG methods lack uncertainty measurement in their outputs, compromising system robustness in the presence of textureless or corrupted thermal images, self-similar or outdated satellite maps, geometric noises, or thermal images exceeding satellite maps. To overcome these limitations, this paper presents UASTHN, a novel approach for Uncertainty Estimation (UE) in Deep Homography Estimation (DHE) tasks for TG applications. Specifically, we introduce a novel Crop-based Test-Time Augmentation (CropTTA) strategy, which leverages the homography consensus of cropped image views to effectively measure data uncertainty. This approach is complemented by Deep Ensembles (DE) employed for model uncertainty, offering comparable performance with improved efficiency and seamless integration with any DHE model. Extensive experiments across multiple DHE models demonstrate the effectiveness and efficiency of CropTTA in TG applications. Analysis of detected failure cases underscores the improved reliability of CropTTA under challenging conditions. Finally, we demonstrate the capability of combining CropTTA and DE for a comprehensive assessment of both data and model uncertainty. Our research provides profound insights into the broader intersection of localization and uncertainty estimation. The code and models are publicly available.

We demonstrate text as a strong cross-modal interface. Rather than relying on deep embeddings to connect image and language as the interface representation, our approach represents an image as text, from which we enjoy the interpretability and flexibility inherent to natural language. We employ an autoencoder that uses a pre-trained text-to-image diffusion model for decoding. The encoder is trained to transform an input image into text, which is then fed into the fixed text-to-image diffusion decoder to reconstruct the original input -- a process we term De-Diffusion. Experiments validate both the precision and comprehensiveness of De-Diffusion text representing images, such that it can be readily ingested by off-the-shelf text-to-image tools and LLMs for diverse multi-modal tasks. For example, a single De-Diffusion model can generalize to provide transferable prompts for different text-to-image tools, and also achieves a new state of the art on open-ended vision-language tasks by simply prompting large language models with few-shot examples.

The rapid advancement of speech generation models has heightened privacy and security concerns related to voice cloning (VC). Recent studies have investigated disrupting unauthorized voice cloning by introducing adversarial perturbations. However, determined attackers can mitigate these protective perturbations and successfully execute VC. In this study, we conduct the first systematic evaluation of these protective perturbations against VC under realistic threat models that include perturbation purification. Our findings reveal that while existing purification methods can neutralize a considerable portion of the protective perturbations, they still lead to distortions in the feature space of VC models, which degrades the performance of VC. From this perspective, we propose a novel two-stage purification method: (1) Purify the perturbed speech; (2) Refine it using phoneme guidance to align it with the clean speech distribution. Experimental results demonstrate that our method outperforms state-of-the-art purification methods in disrupting VC defenses. Our study reveals the limitations of adversarial perturbation-based VC defenses and underscores the urgent need for more robust solutions to mitigate the security and privacy risks posed by VC. The code and audio samples are available at https://de-antifake.github.io.

This study introduces De-DSI, a novel framework that fuses large language models (LLMs) with genuine decentralization for information retrieval, particularly employing the differentiable search index (DSI) concept in a decentralized setting. Focused on efficiently connecting novel user queries with document identifiers without direct document access, De-DSI operates solely on query-docid pairs. To enhance scalability, an ensemble of DSI models is introduced, where the dataset is partitioned into smaller shards for individual model training. This approach not only maintains accuracy by reducing the number of data each model needs to handle but also facilitates scalability by aggregating outcomes from multiple models. This aggregation uses a beam search to identify top docids and applies a softmax function for score normalization, selecting documents with the highest scores for retrieval. The decentralized implementation demonstrates that retrieval success is comparable to centralized methods, with the added benefit of the possibility of distributing computational complexity across the network. This setup also allows for the retrieval of multimedia items through magnet links, eliminating the need for platforms or intermediaries.

Documents often exhibit various forms of degradation, which make it hard to be read and substantially deteriorate the performance of an OCR system. In this paper, we propose an effective end-to-end framework named Document Enhancement Generative Adversarial Networks (DE-GAN) that uses the conditional GANs (cGANs) to restore severely degraded document images. To the best of our knowledge, this practice has not been studied within the context of generative adversarial deep networks. We demonstrate that, in different tasks (document clean up, binarization, deblurring and watermark removal), DE-GAN can produce an enhanced version of the degraded document with a high quality. In addition, our approach provides consistent improvements compared to state-of-the-art methods over the widely used DIBCO 2013, DIBCO 2017 and H-DIBCO 2018 datasets, proving its ability to restore a degraded document image to its ideal condition. The obtained results on a wide variety of degradation reveal the flexibility of the proposed model to be exploited in other document enhancement problems.

Objective: Patient notes in electronic health records (EHRs) may contain critical information for medical investigations. However, the vast majority of medical investigators can only access de-identified notes, in order to protect the confidentiality of patients. In the United States, the Health Insurance Portability and Accountability Act (HIPAA) defines 18 types of protected health information (PHI) that needs to be removed to de-identify patient notes. Manual de-identification is impractical given the size of EHR databases, the limited number of researchers with access to the non-de-identified notes, and the frequent mistakes of human annotators. A reliable automated de-identification system would consequently be of high value. Materials and Methods: We introduce the first de-identification system based on artificial neural networks (ANNs), which requires no handcrafted features or rules, unlike existing systems. We compare the performance of the system with state-of-the-art systems on two datasets: the i2b2 2014 de-identification challenge dataset, which is the largest publicly available de-identification dataset, and the MIMIC de-identification dataset, which we assembled and is twice as large as the i2b2 2014 dataset. Results: Our ANN model outperforms the state-of-the-art systems. It yields an F1-score of 97.85 on the i2b2 2014 dataset, with a recall 97.38 and a precision of 97.32, and an F1-score of 99.23 on the MIMIC de-identification dataset, with a recall 99.25 and a precision of 99.06. Conclusion: Our findings support the use of ANNs for de-identification of patient notes, as they show better performance than previously published systems while requiring no feature engineering.

De novo peptide sequencing is a critical task in proteomics. However, the performance of current deep learning-based methods is limited by the inherent complexity of mass spectrometry data and the heterogeneous distribution of noise signals, leading to data-specific biases. We present RankNovo, the first deep reranking framework that enhances de novo peptide sequencing by leveraging the complementary strengths of multiple sequencing models. RankNovo employs a list-wise reranking approach, modeling candidate peptides as multiple sequence alignments and utilizing axial attention to extract informative features across candidates. Additionally, we introduce two new metrics, PMD (Peptide Mass Deviation) and RMD (residual Mass Deviation), which offer delicate supervision by quantifying mass differences between peptides at both the sequence and residue levels. Extensive experiments demonstrate that RankNovo not only surpasses its base models used to generate training candidates for reranking pre-training, but also sets a new state-of-the-art benchmark. Moreover, RankNovo exhibits strong zero-shot generalization to unseen models whose generations were not exposed during training, highlighting its robustness and potential as a universal reranking framework for peptide sequencing. Our work presents a novel reranking strategy that fundamentally challenges existing single-model paradigms and advances the frontier of accurate de novo sequencing. Our source code is provided on GitHub.

Computational design of protein-binding proteins is a fundamental capability with broad utility in biomedical research and biotechnology. Recent methods have made strides against some target proteins, but on-demand creation of high-affinity binders without multiple rounds of experimental testing remains an unsolved challenge. This technical report introduces AlphaProteo, a family of machine learning models for protein design, and details its performance on the de novo binder design problem. With AlphaProteo, we achieve 3- to 300-fold better binding affinities and higher experimental success rates than the best existing methods on seven target proteins. Our results suggest that AlphaProteo can generate binders "ready-to-use" for many research applications using only one round of medium-throughput screening and no further optimization.

How can we detect if copyrighted content was used in the training process of a language model, considering that the training data is typically undisclosed? We are motivated by the premise that a language model is likely to identify verbatim excerpts from its training text. We propose DE-COP, a method to determine whether a piece of copyrighted content was included in training. DE-COP's core approach is to probe an LLM with multiple-choice questions, whose options include both verbatim text and their paraphrases. We construct BookTection, a benchmark with excerpts from 165 books published prior and subsequent to a model's training cutoff, along with their paraphrases. Our experiments show that DE-COP surpasses the prior best method by 9.6% in detection performance (AUC) on models with logits available. Moreover, DE-COP also achieves an average accuracy of 72% for detecting suspect books on fully black-box models where prior methods give approx 4% accuracy. Our code and datasets are available at https://github.com/avduarte333/DE-COP_Method

Innovations like protein diffusion have enabled significant progress in de novo protein design, which is a vital topic in life science. These methods typically depend on protein structure encoders to model residue backbone frames, where atoms do not exist. Most prior encoders rely on atom-wise features, such as angles and distances between atoms, which are not available in this context. Thus far, only several simple encoders, such as IPA, have been proposed for this scenario, exposing the frame modeling as a bottleneck. In this work, we proffer the Vector Field Network (VFN), which enables network layers to perform learnable vector computations between coordinates of frame-anchored virtual atoms, thus achieving a higher capability for modeling frames. The vector computation operates in a manner similar to a linear layer, with each input channel receiving 3D virtual atom coordinates instead of scalar values. The multiple feature vectors output by the vector computation are then used to update the residue representations and virtual atom coordinates via attention aggregation. Remarkably, VFN also excels in modeling both frames and atoms, as the real atoms can be treated as the virtual atoms for modeling, positioning VFN as a potential universal encoder. In protein diffusion (frame modeling), VFN exhibits an impressive performance advantage over IPA, excelling in terms of both designability (67.04% vs. 53.58%) and diversity (66.54% vs. 51.98%). In inverse folding (frame and atom modeling), VFN outperforms the previous SoTA model, PiFold (54.7% vs. 51.66%), on sequence recovery rate. We also propose a method of equipping VFN with the ESM model, which significantly surpasses the previous ESM-based SoTA (62.67% vs. 55.65%), LM-Design, by a substantial margin.

De novo drug design requires simultaneously generating novel molecules outside of training data and predicting their target properties, making it a hard task for generative models. To address this, we propose Joint Transformer that combines a Transformer decoder, Transformer encoder, and a predictor in a joint generative model with shared weights. We formulate a probabilistic black-box optimization algorithm that employs Joint Transformer to generate novel molecules with improved target properties and outperforms other SMILES-based optimization methods in de novo drug design.

This paper reformulates a classical result in probability theory from the 1930s in modern categorical terms: de Finetti's representation theorem is redescribed as limit statement for a chain of finite spaces in the Kleisli category of the Giry monad. This new limit is used to identify among exchangeable coalgebras the final one.

De-identification of electronic health records (EHR) is a vital step towards advancing health informatics research and maximising the use of available data. It is a two-step process where step one is the identification of protected health information (PHI), and step two is replacing such PHI with surrogates. Despite the recent advances in automatic de-identification of EHR, significant obstacles remain if the abundant health data available are to be used to the full potential. Accuracy in de-identification could be considered a necessary, but not sufficient condition for the use of EHR without individual patient consent. We present here a comprehensive review of the progress to date, both the impressive successes in achieving high accuracy and the significant risks and challenges that remain. To best of our knowledge, this is the first paper to present a complete picture of end-to-end automatic de-identification. We review 18 recently published automatic de-identification systems -designed to de-identify EHR in the form of free text- to show the advancements made in improving the overall accuracy of the system, and in identifying individual PHI. We argue that despite the improvements in accuracy there remain challenges in surrogate generation and replacements of identified PHIs, and the risks posed to patient protection and privacy.

De novo design seeks to generate molecules with required property profiles by virtual design-make-test cycles. With the emergence of deep learning and neural generative models in many application areas, models for molecular design based on neural networks appeared recently and show promising results. However, the new models have not been profiled on consistent tasks, and comparative studies to well-established algorithms have only seldom been performed. To standardize the assessment of both classical and neural models for de novo molecular design, we propose an evaluation framework, GuacaMol, based on a suite of standardized benchmarks. The benchmark tasks encompass measuring the fidelity of the models to reproduce the property distribution of the training sets, the ability to generate novel molecules, the exploration and exploitation of chemical space, and a variety of single and multi-objective optimization tasks. The benchmarking open-source Python code, and a leaderboard can be found on https://benevolent.ai/guacamol

This article presents the Cogni-CISMeF project, which aims at improving medical information search in the CISMeF system (Catalog and Index of French-language health resources) by including a conversational agent to interact with the user in natural language. To study the cognitive processes involved during the information search, a bottom-up methodology was adopted. Experimentation has been set up to obtain human dialogs between a user (playing the role of patient) dealing with medical information search and a CISMeF expert refining the request. The analysis of these dialogs underlined the use of discursive evidence: vocabulary, reformulation, implicit or explicit expression of user intentions, conversational sequences, etc. A model of artificial agent is proposed. It leads the user in its information search by proposing to him examples, assistance and choices. This model was implemented and integrated in the CISMeF system. ---- Cet article d\'ecrit le projet Cogni-CISMeF qui propose un module de dialogue Homme-Machine \`a int\'egrer dans le syst\`eme d'indexation de connaissances m\'edicales CISMeF (Catalogue et Index des Sites M\'edicaux Francophones). Nous avons adopt\'e une d\'emarche de mod\'elisation cognitive en proc\'edant \`a un recueil de corpus de dialogues entre un utilisateur (jouant le r\^ole d'un patient) d\'esirant une information m\'edicale et un expert CISMeF af inant cette demande pour construire la requ\^ete. Nous avons analys\'e la structure des dialogues ainsi obtenus et avons \'etudi\'e un certain nombre d'indices discursifs : vocabulaire employ\'e, marques de reformulation, commentaires m\'eta et \'epilinguistiques, expression implicite ou explicite des intentions de l'utilisateur, encha\^inement conversationnel, etc. De cette analyse, nous avons construit un mod\`ele d'agent artificiel dot\'e de capacit\'es cognitives capables d'aider l'utilisateur dans sa t\^ache de recherche d'information. Ce mod\`ele a \'et\'e impl\'ement\'e et int\'egr\'e dans le syst\`eme CISMeF.

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.

Recent works have successfully demonstrated that sparse deep reinforcement learning agents can be competitive against their dense counterparts. This opens up opportunities for reinforcement learning applications in fields where inference time and memory requirements are cost-sensitive or limited by hardware. Until now, dense-to-sparse methods have relied on hand-designed sparsity schedules that are not synchronized with the agent's learning pace. Crucially, the final sparsity level is chosen as a hyperparameter, which requires careful tuning as setting it too high might lead to poor performances. In this work, we address these shortcomings by crafting a dense-to-sparse algorithm that we name Eau De Q-Network (EauDeQN). To increase sparsity at the agent's learning pace, we consider multiple online networks with different sparsity levels, where each online network is trained from a shared target network. At each target update, the online network with the smallest loss is chosen as the next target network, while the other networks are replaced by a pruned version of the chosen network. We evaluate the proposed approach on the Atari 2600 benchmark and the MuJoCo physics simulator, showing that EauDeQN reaches high sparsity levels while keeping performances high.

Legal tasks and datasets are often used as benchmarks for the capabilities of language models. However, openly available annotated datasets are rare. In this paper, we introduce AGB-DE, a corpus of 3,764 clauses from German consumer contracts that have been annotated and legally assessed by legal experts. Together with the data, we present a first baseline for the task of detecting potentially void clauses, comparing the performance of an SVM baseline with three fine-tuned open language models and the performance of GPT-3.5. Our results show the challenging nature of the task, with no approach exceeding an F1-score of 0.54. While the fine-tuned models often performed better with regard to precision, GPT-3.5 outperformed the other approaches with regard to recall. An analysis of the errors indicates that one of the main challenges could be the correct interpretation of complex clauses, rather than the decision boundaries of what is permissible and what is not.

Machine Learning (ML) models have been utilized for malware detection for over two decades. Consequently, this ignited an ongoing arms race between malware authors and antivirus systems, compelling researchers to propose defenses for malware-detection models against evasion attacks. However, most if not all existing defenses against evasion attacks suffer from sizable performance degradation and/or can defend against only specific attacks, which makes them less practical in real-world settings. In this work, we develop a certified defense, DRSM (De-Randomized Smoothed MalConv), by redesigning the de-randomized smoothing technique for the domain of malware detection. Specifically, we propose a window ablation scheme to provably limit the impact of adversarial bytes while maximally preserving local structures of the executables. After showing how DRSM is theoretically robust against attacks with contiguous adversarial bytes, we verify its performance and certified robustness experimentally, where we observe only marginal accuracy drops as the cost of robustness. To our knowledge, we are the first to offer certified robustness in the realm of static detection of malware executables. More surprisingly, through evaluating DRSM against 9 empirical attacks of different types, we observe that the proposed defense is empirically robust to some extent against a diverse set of attacks, some of which even fall out of the scope of its original threat model. In addition, we collected 15.5K recent benign raw executables from diverse sources, which will be made public as a dataset called PACE (Publicly Accessible Collection(s) of Executables) to alleviate the scarcity of publicly available benign datasets for studying malware detection and provide future research with more representative data of the time.

To ensure a balance between open access to justice and personal data protection, the South Korean judiciary mandates the de-identification of court judgments before they can be publicly disclosed. However, the current de-identification process is inadequate for handling court judgments at scale while adhering to strict legal requirements. Additionally, the legal definitions and categorizations of personal identifiers are vague and not well-suited for technical solutions. To tackle these challenges, we propose a de-identification framework called Thunder-DeID, which aligns with relevant laws and practices. Specifically, we (i) construct and release the first Korean legal dataset containing annotated judgments along with corresponding lists of entity mentions, (ii) introduce a systematic categorization of Personally Identifiable Information (PII), and (iii) develop an end-to-end deep neural network (DNN)-based de-identification pipeline. Our experimental results demonstrate that our model achieves state-of-the-art performance in the de-identification of court judgments.

High magnetic field and low temperature transport is carried out in order to characterize the charge carriers of PtSe_2. In particular, the Shubnikov-de Haas oscillations arising at applied magnetic field strengths gtrsim 4.5,T are found to occur exclusively in plane and emerge at a layer thickness of approx 18,nm, increasing in amplitude and decreasing in frequency for thinner PtSe_2 flakes. Moreover, the quantum transport time, Berry phase, Dingle temperature and cyclotron mass of the charge carriers are ascertained. The emergence of weak antilocalization (WAL) lies in contrast to the presence of magnetic moments from Pt vacancies. An explanation is provided on how WAL and the Kondo effect can be observed within the same material. Detailed information about the charge carriers and transport phenomena in PtSe_2 is obtained, which is relevant for the design of prospective spintronic and orbitronic devices and for the realization of orbital Hall effect-based architectures.

The rise of chronic diseases and pandemics like COVID-19 has emphasized the need for effective patient data processing while ensuring privacy through anonymization and de-identification of protected health information (PHI). Anonymized data facilitates research without compromising patient confidentiality. This paper introduces expert small AI models developed using the LLM-in-the-loop methodology to meet the demand for domain-specific de-identification NER models. These models overcome the privacy risks associated with large language models (LLMs) used via APIs by eliminating the need to transmit or store sensitive data. More importantly, they consistently outperform LLMs in de-identification tasks, offering superior performance and reliability. Our de-identification NER models, developed in eight languages (English, German, Italian, French, Romanian, Turkish, Spanish, and Arabic) achieved f1-micro score averages of 0.966, 0.975, 0.976, 0.970, 0.964, 0.974, 0.978, and 0.953 respectively. These results establish them as the most accurate healthcare anonymization solutions, surpassing existing small models and even general-purpose LLMs such as GPT-4o. While Part-1 of this series introduced the LLM-in-the-loop methodology for bio-medical document translation, this second paper showcases its success in developing cost-effective expert small NER models in de-identification tasks. Our findings lay the groundwork for future healthcare AI innovations, including biomedical entity and relation extraction, demonstrating the value of specialized models for domain-specific challenges.

Data de-identification makes it possible to glean insights from data while preserving user privacy. The use of Trusted Execution Environments (TEEs) allow for the execution of de-identification applications on the cloud without the need for a user to trust the third-party application provider. In this paper, we present SPIDEr - Secure Pipeline for Information De-Identification with End-to-End Encryption, our implementation of an end-to-end encrypted data de-identification pipeline. SPIDEr supports classical anonymisation techniques such as suppression, pseudonymisation, generalisation, and aggregation, as well as techniques that offer a formal privacy guarantee such as k-anonymisation and differential privacy. To enable scalability and improve performance on constrained TEE hardware, we enable batch processing of data for differential privacy computations. We present our design of the control flows for end-to-end secure execution of de-identification operations within a TEE. As part of the control flow for running SPIDEr within the TEE, we perform attestation, a process that verifies that the software binaries were properly instantiated on a known, trusted platform.

The loudness war, an ongoing phenomenon in the music industry characterized by the increasing final loudness of music while reducing its dynamic range, has been a controversial topic for decades. Music mastering engineers have used limiters to heavily compress and make music louder, which can induce ear fatigue and hearing loss in listeners. In this paper, we introduce music de-limiter networks that estimate uncompressed music from heavily compressed signals. Inspired by the principle of a limiter, which performs sample-wise gain reduction of a given signal, we propose the framework of sample-wise gain inversion (SGI). We also present the musdb-XL-train dataset, consisting of 300k segments created by applying a commercial limiter plug-in for training real-world friendly de-limiter networks. Our proposed de-limiter network achieves excellent performance with a scale-invariant source-to-distortion ratio (SI-SDR) of 23.8 dB in reconstructing musdb-HQ from musdb- XL data, a limiter-applied version of musdb-HQ. The training data, codes, and model weights are available in our repository (https://github.com/jeonchangbin49/De-limiter).

Pre-trained language models have achieved great success in various large-scale information retrieval tasks. However, most of pretraining tasks are based on counterfeit retrieval data where the query produced by the tailored rule is assumed as the user's issued query on the given document or passage. Therefore, we explore to use large-scale click logs to pretrain a language model instead of replying on the simulated queries. Specifically, we propose to use user behavior features to pretrain a debiased language model for document ranking. Extensive experiments on Baidu desensitization click logs validate the effectiveness of our method. Our team on WSDM Cup 2023 Pre-training for Web Search won the 1st place with a Discounted Cumulative Gain @ 10 (DCG@10) score of 12.16525 on the final leaderboard.

In the field of antibody engineering, an essential task is to design a novel antibody whose paratopes bind to a specific antigen with correct epitopes. Understanding antibody structure and its paratope can facilitate a mechanistic understanding of its function. Therefore, antibody structure prediction from its sequence alone has always been a highly valuable problem for de novo antibody design. AlphaFold2, a breakthrough in the field of structural biology, provides a solution to predict protein structure based on protein sequences and computationally expensive coevolutionary multiple sequence alignments (MSAs). However, the computational efficiency and undesirable prediction accuracy of antibodies, especially on the complementarity-determining regions (CDRs) of antibodies limit their applications in the industrially high-throughput drug design. To learn an informative representation of antibodies, we employed a deep antibody language model (ALM) on curated sequences from the observed antibody space database via a transformer model. We also developed a novel model named xTrimoABFold to predict antibody structure from antibody sequence based on the pretrained ALM as well as efficient evoformers and structural modules. The model was trained end-to-end on the antibody structures in PDB by minimizing the ensemble loss of domain-specific focal loss on CDR and the frame-aligned point loss. xTrimoABFold outperforms AlphaFold2 and other protein language model based SOTAs, e.g., OmegaFold, HelixFold-Single, and IgFold with a large significant margin (30+\% improvement on RMSD) while performing 151 times faster than AlphaFold2. To the best of our knowledge, xTrimoABFold achieved state-of-the-art antibody structure prediction. Its improvement in both accuracy and efficiency makes it a valuable tool for de novo antibody design and could make further improvements in immuno-theory.

In Novel Class Discovery (NCD), the goal is to find new classes in an unlabeled set given a labeled set of known but different classes. While NCD has recently gained attention from the community, no framework has yet been proposed for heterogeneous tabular data, despite being a very common representation of data. In this paper, we propose TabularNCD, a new method for discovering novel classes in tabular data. We show a way to extract knowledge from already known classes to guide the discovery process of novel classes in the context of tabular data which contains heterogeneous variables. A part of this process is done by a new method for defining pseudo labels, and we follow recent findings in Multi-Task Learning to optimize a joint objective function. Our method demonstrates that NCD is not only applicable to images but also to heterogeneous tabular data.

Learning causal structure from observational data often assumes that we observe independent and identically distributed (i.\,i.\,d) data. The traditional approach aims to find a graphical representation that encodes the same set of conditional independence relationships as those present in the observed distribution. It is known that under i.\,i.\,d assumption, even with infinite data, there is a limit to how fine-grained a causal structure we can identify. To overcome this limitation, recent work has explored using data originating from different, related environments to learn richer causal structure. These approaches implicitly rely on the independent causal mechanisms (ICM) principle, which postulates that the mechanism giving rise to an effect given its causes and the mechanism which generates the causes do not inform or influence each other. Thus, components of the causal model can independently change from environment to environment. Despite its wide application in machine learning and causal inference, there is a lack of statistical formalization of the ICM principle and how it enables identification of richer causal structures from grouped data. Here we present new causal de Finetti theorems which offer a first statistical formalization of ICM principle and show how causal structure identification is possible from exchangeable data. Our work provides theoretical justification for a broad range of techniques leveraging multi-environment data to learn causal structure.

This paper proposes a method for the automatic creation of variables (in the case of regression) that complement the information contained in the initial input vector. The method works as a pre-processing step in which the continuous values of the variable to be regressed are discretized into a set of intervals which are then used to define value thresholds. Then classifiers are trained to predict whether the value to be regressed is less than or equal to each of these thresholds. The different outputs of the classifiers are then concatenated in the form of an additional vector of variables that enriches the initial vector of the regression problem. The implemented system can thus be considered as a generic pre-processing tool. We tested the proposed enrichment method with 5 types of regressors and evaluated it in 33 regression datasets. Our experimental results confirm the interest of the approach.

Many machine learning algorithms are trained and evaluated by splitting data from a single source into training and test sets. While such focus on in-distribution learning scenarios has led to interesting advancement, it has not been able to tell if models are relying on dataset biases as shortcuts for successful prediction (e.g., using snow cues for recognising snowmobiles), resulting in biased models that fail to generalise when the bias shifts to a different class. The cross-bias generalisation problem has been addressed by de-biasing training data through augmentation or re-sampling, which are often prohibitive due to the data collection cost (e.g., collecting images of a snowmobile on a desert) and the difficulty of quantifying or expressing biases in the first place. In this work, we propose a novel framework to train a de-biased representation by encouraging it to be different from a set of representations that are biased by design. This tactic is feasible in many scenarios where it is much easier to define a set of biased representations than to define and quantify bias. We demonstrate the efficacy of our method across a variety of synthetic and real-world biases; our experiments show that the method discourages models from taking bias shortcuts, resulting in improved generalisation. Source code is available at https://github.com/clovaai/rebias.

These handouts are designed for people who is just starting involved with the topic artificial neural networks. We show how it works a single artificial neuron (McCulloch & Pitt model), mathematically and graphically. We do explain the delta rule, a learning algorithm to find the neuron weights. We also present some examples in MATLAB/Octave. There are examples for classification task for lineal and non-lineal problems. At the end, we present an artificial neural network, a feed-forward neural network along its learning algorithm backpropagation. ----- Estos apuntes est\'an dise\~nados para personas que por primera vez se introducen en el tema de las redes neuronales artificiales. Se muestra el funcionamiento b\'asico de una neurona, matem\'aticamente y gr\'aficamente. Se explica la Regla Delta, algoritmo deaprendizaje para encontrar los pesos de una neurona. Tambi\'en se muestran ejemplos en MATLAB/Octave. Hay ejemplos para problemas de clasificaci\'on, para problemas lineales y no-lineales. En la parte final se muestra la arquitectura de red neuronal artificial conocida como backpropagation.

Proteins are dynamic molecular machines whose biological functions, spanning enzymatic catalysis, signal transduction, and structural adaptation, are intrinsically linked to their motions. Designing proteins with targeted dynamic properties, however, remains a challenge due to the complex, degenerate relationships between sequence, structure, and molecular motion. Here, we introduce VibeGen, a generative AI framework that enables end-to-end de novo protein design conditioned on normal mode vibrations. VibeGen employs an agentic dual-model architecture, comprising a protein designer that generates sequence candidates based on specified vibrational modes and a protein predictor that evaluates their dynamic accuracy. This approach synergizes diversity, accuracy, and novelty during the design process. Via full-atom molecular simulations as direct validation, we demonstrate that the designed proteins accurately reproduce the prescribed normal mode amplitudes across the backbone while adopting various stable, functionally relevant structures. Notably, generated sequences are de novo, exhibiting no significant similarity to natural proteins, thereby expanding the accessible protein space beyond evolutionary constraints. Our work integrates protein dynamics into generative protein design, and establishes a direct, bidirectional link between sequence and vibrational behavior, unlocking new pathways for engineering biomolecules with tailored dynamical and functional properties. This framework holds broad implications for the rational design of flexible enzymes, dynamic scaffolds, and biomaterials, paving the way toward dynamics-informed AI-driven protein engineering.

Generative models, particularly text-to-image (T2I) diffusion models, play a crucial role in medical image analysis. However, these models are prone to training data memorization, posing significant risks to patient privacy. Synthetic chest X-ray generation is one of the most common applications in medical image analysis with the MIMIC-CXR dataset serving as the primary data repository for this task. This study adopts a data-driven approach and presents the first systematic attempt to identify prompts and text tokens in MIMIC-CXR that contribute the most to training data memorization. Our analysis reveals an unexpected finding: prompts containing traces of de-identification procedures are among the most memorized, with de-identification markers contributing the most. Furthermore, we also find existing inference-time memorization mitigation strategies are ineffective and fail to sufficiently reduce the model's reliance on memorized text tokens highlighting a broader issue in T2I synthesis with MIMIC-CXR. On this front, we propose actionable strategies to enhance privacy and improve the reliability of generative models in medical imaging. Finally, our results provide a foundation for future work on developing and benchmarking memorization mitigation techniques for synthetic chest X-ray generation using the MIMIC-CXR dataset.

The modern surge in camera usage alongside widespread computer vision technology applications poses significant privacy and security concerns. Current artificial intelligence (AI) technologies aid in recognizing relevant events and assisting in daily tasks in homes, offices, hospitals, etc. The need to access or process personal information for these purposes raises privacy concerns. While software-level solutions like face de-identification provide a good privacy/utility trade-off, they present vulnerabilities to sniffing attacks. In this paper, we propose a hardware-level face de-identification method to solve this vulnerability. Specifically, our approach first learns an optical encoder along with a regression model to obtain a face heatmap while hiding the face identity from the source image. We also propose an anonymization framework that generates a new face using the privacy-preserving image, face heatmap, and a reference face image from a public dataset as input. We validate our approach with extensive simulations and hardware experiments.

Artificial intelligence (AI)-driven methods can vastly improve the historically costly drug design process, with various generative models already in widespread use. Generative models for de novo drug design, in particular, focus on the creation of novel biological compounds entirely from scratch, representing a promising future direction. Rapid development in the field, combined with the inherent complexity of the drug design process, creates a difficult landscape for new researchers to enter. In this survey, we organize de novo drug design into two overarching themes: small molecule and protein generation. Within each theme, we identify a variety of subtasks and applications, highlighting important datasets, benchmarks, and model architectures and comparing the performance of top models. We take a broad approach to AI-driven drug design, allowing for both micro-level comparisons of various methods within each subtask and macro-level observations across different fields. We discuss parallel challenges and approaches between the two applications and highlight future directions for AI-driven de novo drug design as a whole. An organized repository of all covered sources is available at https://github.com/gersteinlab/GenAI4Drug.

Through evolution, nature has presented a set of remarkable protein materials, including elastins, silks, keratins and collagens with superior mechanical performances that play crucial roles in mechanobiology. However, going beyond natural designs to discover proteins that meet specified mechanical properties remains challenging. Here we report a generative model that predicts protein designs to meet complex nonlinear mechanical property-design objectives. Our model leverages deep knowledge on protein sequences from a pre-trained protein language model and maps mechanical unfolding responses to create novel proteins. Via full-atom molecular simulations for direct validation, we demonstrate that the designed proteins are novel, and fulfill the targeted mechanical properties, including unfolding energy and mechanical strength, as well as the detailed unfolding force-separation curves. Our model offers rapid pathways to explore the enormous mechanobiological protein sequence space unconstrained by biological synthesis, using mechanical features as target to enable the discovery of protein materials with superior mechanical properties.

We derive a minimalist but powerful deterministic denoising-diffusion model. While denoising diffusion has shown great success in many domains, its underlying theory remains largely inaccessible to non-expert users. Indeed, an understanding of graduate-level concepts such as Langevin dynamics or score matching appears to be required to grasp how it works. We propose an alternative approach that requires no more than undergrad calculus and probability. We consider two densities and observe what happens when random samples from these densities are blended (linearly interpolated). We show that iteratively blending and deblending samples produces random paths between the two densities that converge toward a deterministic mapping. This mapping can be evaluated with a neural network trained to deblend samples. We obtain a model that behaves like deterministic denoising diffusion: it iteratively maps samples from one density (e.g., Gaussian noise) to another (e.g., cat images). However, compared to the state-of-the-art alternative, our model is simpler to derive, simpler to implement, more numerically stable, achieves higher quality results in our experiments, and has interesting connections to computer graphics.

Generative models, such as DALL-E, Midjourney, and Stable Diffusion, have societal implications that extend beyond the field of computer science. These models require large image databases like LAION-2B, which contain two billion images. At this scale, manual inspection is difficult and automated analysis is challenging. In addition, recent studies show that duplicated images pose copyright problems for models trained on LAION2B, which hinders its usability. This paper proposes an algorithmic chain that runs with modest compute, that compresses CLIP features to enable efficient duplicate detection, even for vast image volumes. Our approach demonstrates that roughly 700 million images, or about 30\%, of LAION-2B's images are likely duplicated. Our method also provides the histograms of duplication on this dataset, which we use to reveal more examples of verbatim copies by Stable Diffusion and further justify the approach. The current version of the de-duplicated set will be distributed online.

Discovering novel drug candidate molecules is one of the most fundamental and critical steps in drug development. Generative deep learning models, which create synthetic data given a probability distribution, have been developed with the purpose of picking completely new samples from a partially known space. Generative models offer high potential for designing de novo molecules; however, in order for them to be useful in real-life drug development pipelines, these models should be able to design target-specific molecules, which is the next step in this field. In this study, we propose DrugGEN, for the de novo design of drug candidate molecules that interact with selected target proteins. The proposed system represents compounds and protein structures as graphs and processes them via serially connected two generative adversarial networks comprising graph transformers. DrugGEN is trained using a large dataset of compounds from ChEMBL and target-specific bioactive molecules, to design effective and specific inhibitory molecules against the AKT1 protein, which has critical importance for developing treatments against various types of cancer. On fundamental benchmarks, DrugGEN models have either competitive or better performance against other methods. To assess the target-specific generation performance, we conducted further in silico analysis with molecular docking and deep learning-based bioactivity prediction. Results indicate that de novo molecules have high potential for interacting with the AKT1 protein structure in the level of its native ligand. DrugGEN can be used to design completely novel and effective target-specific drug candidate molecules for any druggable protein, given target features and a dataset of experimental bioactivities. Code base, datasets, results and trained models of DrugGEN are available at https://github.com/HUBioDataLab/DrugGEN

The rectified linear unit (ReLU) is a highly successful activation function in neural networks as it allows networks to easily obtain sparse representations, which reduces overfitting in overparameterized networks. However, in network pruning, we find that the sparsity introduced by ReLU, which we quantify by a term called dynamic dead neuron rate (DNR), is not beneficial for the pruned network. Interestingly, the more the network is pruned, the smaller the dynamic DNR becomes during optimization. This motivates us to propose a method to explicitly reduce the dynamic DNR for the pruned network, i.e., de-sparsify the network. We refer to our method as Activating-while-Pruning (AP). We note that AP does not function as a stand-alone method, as it does not evaluate the importance of weights. Instead, it works in tandem with existing pruning methods and aims to improve their performance by selective activation of nodes to reduce the dynamic DNR. We conduct extensive experiments using popular networks (e.g., ResNet, VGG) via two classical and three state-of-the-art pruning methods. The experimental results on public datasets (e.g., CIFAR-10/100) suggest that AP works well with existing pruning methods and improves the performance by 3% - 4%. For larger scale datasets (e.g., ImageNet) and state-of-the-art networks (e.g., vision transformer), we observe an improvement of 2% - 3% with AP as opposed to without. Lastly, we conduct an ablation study to examine the effectiveness of the components comprising AP.

Tandem mass spectrometry has played a pivotal role in advancing proteomics, enabling the analysis of protein composition in biological samples. Despite the development of various deep learning methods for identifying amino acid sequences (peptides) responsible for observed spectra, challenges persist in de novo peptide sequencing. Firstly, prior methods struggle to identify amino acids with post-translational modifications (PTMs) due to their lower frequency in training data compared to canonical amino acids, further resulting in decreased peptide-level identification precision. Secondly, diverse types of noise and missing peaks in mass spectra reduce the reliability of training data (peptide-spectrum matches, PSMs). To address these challenges, we propose AdaNovo, a novel framework that calculates conditional mutual information (CMI) between the spectrum and each amino acid/peptide, using CMI for adaptive model training. Extensive experiments demonstrate AdaNovo's state-of-the-art performance on a 9-species benchmark, where the peptides in the training set are almost completely disjoint from the peptides of the test sets. Moreover, AdaNovo excels in identifying amino acids with PTMs and exhibits robustness against data noise. The supplementary materials contain the official code.

Recent research advances achieve human-level accuracy for de-identifying free-text clinical notes on research datasets, but gaps remain in reproducing this in large real-world settings. This paper summarizes lessons learned from building a system used to de-identify over one billion real clinical notes, in a fully automated way, that was independently certified by multiple organizations for production use. A fully automated solution requires a very high level of accuracy that does not require manual review. A hybrid context-based model architecture is described, which outperforms a Named Entity Recogniton (NER) - only model by 10% on the i2b2-2014 benchmark. The proposed system makes 50%, 475%, and 575% fewer errors than the comparable AWS, Azure, and GCP services respectively while also outperforming ChatGPT by 33%. It exceeds 98% coverage of sensitive data across 7 European languages, without a need for fine tuning. A second set of described models enable data obfuscation -- replacing sensitive data with random surrogates -- while retaining name, date, gender, clinical, and format consistency. Both the practical need and the solution architecture that provides for reliable & linked anonymized documents are described.

The digitization of healthcare has facilitated the sharing and re-using of medical data but has also raised concerns about confidentiality and privacy. HIPAA (Health Insurance Portability and Accountability Act) mandates removing re-identifying information before the dissemination of medical records. Thus, effective and efficient solutions for de-identifying medical data, especially those in free-text forms, are highly needed. While various computer-assisted de-identification methods, including both rule-based and learning-based, have been developed and used in prior practice, such solutions still lack generalizability or need to be fine-tuned according to different scenarios, significantly imposing restrictions in wider use. The advancement of large language models (LLM), such as ChatGPT and GPT-4, have shown great potential in processing text data in the medical domain with zero-shot in-context learning, especially in the task of privacy protection, as these models can identify confidential information by their powerful named entity recognition (NER) capability. In this work, we developed a novel GPT4-enabled de-identification framework (``DeID-GPT") to automatically identify and remove the identifying information. Compared to existing commonly used medical text data de-identification methods, our developed DeID-GPT showed the highest accuracy and remarkable reliability in masking private information from the unstructured medical text while preserving the original structure and meaning of the text. This study is one of the earliest to utilize ChatGPT and GPT-4 for medical text data processing and de-identification, which provides insights for further research and solution development on the use of LLMs such as ChatGPT/GPT-4 in healthcare. Codes and benchmarking data information are available at https://github.com/yhydhx/ChatGPT-API.

Patient notes contain a wealth of information of potentially great interest to medical investigators. However, to protect patients' privacy, Protected Health Information (PHI) must be removed from the patient notes before they can be legally released, a process known as patient note de-identification. The main objective for a de-identification system is to have the highest possible recall. Recently, the first neural-network-based de-identification system has been proposed, yielding state-of-the-art results. Unlike other systems, it does not rely on human-engineered features, which allows it to be quickly deployed, but does not leverage knowledge from human experts or from electronic health records (EHRs). In this work, we explore a method to incorporate human-engineered features as well as features derived from EHRs to a neural-network-based de-identification system. Our results show that the addition of features, especially the EHR-derived features, further improves the state-of-the-art in patient note de-identification, including for some of the most sensitive PHI types such as patient names. Since in a real-life setting patient notes typically come with EHRs, we recommend developers of de-identification systems to leverage the information EHRs contain.

Reconstructing 3D objects from a single image remains challenging, especially under real-world occlusions. While recent diffusion-based view synthesis models can generate consistent novel views from a single RGB image, they typically assume fully visible inputs and fail when parts of the object are occluded, resulting in degraded 3D reconstruction quality. We propose DeOcc-1-to-3, an end-to-end framework for occlusion-aware multi-view generation that synthesizes six structurally consistent novel views directly from a single occluded image, enabling reliable 3D reconstruction without prior inpainting or manual annotations. Our self-supervised training pipeline leverages occluded-unoccluded image pairs and pseudo-ground-truth views to teach the model structure-aware completion and view consistency. Without modifying the original architecture, we fully fine-tune the view synthesis model to jointly learn completion and multi-view generation. Additionally, we introduce the first benchmark for occlusion-aware reconstruction, covering diverse occlusion levels, object categories, and masking patterns, providing a standardized protocol for future evaluation.

Tandem mass spectrometry has played a pivotal role in advancing proteomics, enabling the high-throughput analysis of protein composition in biological tissues. Many deep learning methods have been developed for de novo peptide sequencing task, i.e., predicting the peptide sequence for the observed mass spectrum. However, two key challenges seriously hinder the further advancement of this important task. Firstly, since there is no consensus for the evaluation datasets, the empirical results in different research papers are often not comparable, leading to unfair comparison. Secondly, the current methods are usually limited to amino acid-level or peptide-level precision and recall metrics. In this work, we present the first unified benchmark NovoBench for de novo peptide sequencing, which comprises diverse mass spectrum data, integrated models, and comprehensive evaluation metrics. Recent impressive methods, including DeepNovo, PointNovo, Casanovo, InstaNovo, AdaNovo and pi-HelixNovo are integrated into our framework. In addition to amino acid-level and peptide-level precision and recall, we evaluate the models' performance in terms of identifying post-tranlational modifications (PTMs), efficiency and robustness to peptide length, noise peaks and missing fragment ratio, which are important influencing factors while seldom be considered. Leveraging this benchmark, we conduct a large-scale study of current methods, report many insightful findings that open up new possibilities for future development.

Over recent years, an increasing amount of compute and data has been poured into training large language models (LLMs), usually by doing one-pass learning on as many tokens as possible randomly selected from large-scale web corpora. While training on ever-larger portions of the internet leads to consistent performance improvements, the size of these improvements diminishes with scale, and there has been little work exploring the effect of data selection on pre-training and downstream performance beyond simple de-duplication methods such as MinHash. Here, we show that careful data selection (on top of de-duplicated data) via pre-trained model embeddings can speed up training (20% efficiency gains) and improves average downstream accuracy on 16 NLP tasks (up to 2%) at the 6.7B model scale. Furthermore, we show that repeating data intelligently consistently outperforms baseline training (while repeating random data performs worse than baseline training). Our results indicate that clever data selection can significantly improve LLM pre-training, calls into question the common practice of training for a single epoch on as much data as possible, and demonstrates a path to keep improving our models past the limits of randomly sampling web data.

Fairness in visual recognition is becoming a prominent and critical topic of discussion as recognition systems are deployed at scale in the real world. Models trained from data in which target labels are correlated with protected attributes (e.g., gender, race) are known to learn and exploit those correlations. In this work, we introduce a method for training accurate target classifiers while mitigating biases that stem from these correlations. We use GANs to generate realistic-looking images, and perturb these images in the underlying latent space to generate training data that is balanced for each protected attribute. We augment the original dataset with this perturbed generated data, and empirically demonstrate that target classifiers trained on the augmented dataset exhibit a number of both quantitative and qualitative benefits. We conduct a thorough evaluation across multiple target labels and protected attributes in the CelebA dataset, and provide an in-depth analysis and comparison to existing literature in the space.

We propose a self-consistent explanation of Rieger-type periodicities, the Schwabe cycle, and the Suess-de Vries cycle of the solar dynamo in terms of resonances of various wave phenomena with gravitational forces exerted by the orbiting planets. Starting on the high-frequency side, we show that the two-planet spring tides of Venus, Earth and Jupiter are able to excite magneto-Rossby waves which can be linked with typical Rieger-type periods. We argue then that the 11.07-year beat period of those magneto-Rossby waves synchronizes an underlying conventional alpha-Omega-dynamo, by periodically changing either the field storage capacity in the tachocline or some portion of the alpha-effect therein. We also strengthen the argument that the Suess-de Vries cycle appears as an 193-year beat period between the 22.14-year Hale cycle and a spin-orbit coupling effect related with the 19.86-year rosette-like motion of the Sun around the barycenter.

The rapid expansion of genomic sequence data calls for new methods to achieve robust sequence representations. Existing techniques often neglect intricate structural details, emphasizing mainly contextual information. To address this, we developed k-mer embeddings that merge contextual and structural string information by enhancing De Bruijn graphs with structural similarity connections. Subsequently, we crafted a self-supervised method based on Contrastive Learning that employs a heterogeneous Graph Convolutional Network encoder and constructs positive pairs based on node similarities. Our embeddings consistently outperform prior techniques for Edit Distance Approximation and Closest String Retrieval tasks.

Generative models have demonstrated substantial promise in Natural Language Processing (NLP) and have found application in designing molecules, as seen in General Pretrained Transformer (GPT) models. In our efforts to develop such a tool for exploring the organic chemical space in search of potentially electro-active compounds, we present "LLamol", a single novel generative transformer model based on the LLama 2 architecture, which was trained on a 13M superset of organic compounds drawn from diverse public sources. To allow for a maximum flexibility in usage and robustness in view of potentially incomplete data, we introduce "Stochastic Context Learning" as a new training procedure. We demonstrate that the resulting model adeptly handles single- and multi-conditional organic molecule generation with up to four conditions, yet more are possible. The model generates valid molecular structures in SMILES notation while flexibly incorporating three numerical and/or one token sequence into the generative process, just as requested. The generated compounds are very satisfactory in all scenarios tested. In detail, we showcase the model's capability to utilize token sequences for conditioning, either individually or in combination with numerical properties, making LLamol a potent tool for de novo molecule design, easily expandable with new properties.

Deep generative diffusion models are a promising avenue for 3D de novo molecular design in materials science and drug discovery. However, their utility is still limited by suboptimal performance on large molecular structures and limited training data. To address this gap, we explore the design space of E(3)-equivariant diffusion models, focusing on previously unexplored areas. Our extensive comparative analysis evaluates the interplay between continuous and discrete state spaces. From this investigation, we present the EQGAT-diff model, which consistently outperforms established models for the QM9 and GEOM-Drugs datasets. Significantly, EQGAT-diff takes continuous atom positions, while chemical elements and bond types are categorical and uses time-dependent loss weighting, substantially increasing training convergence, the quality of generated samples, and inference time. We also showcase that including chemically motivated additional features like hybridization states in the diffusion process enhances the validity of generated molecules. To further strengthen the applicability of diffusion models to limited training data, we investigate the transferability of EQGAT-diff trained on the large PubChem3D dataset with implicit hydrogen atoms to target different data distributions. Fine-tuning EQGAT-diff for just a few iterations shows an efficient distribution shift, further improving performance throughout data sets. Finally, we test our model on the Crossdocked data set for structure-based de novo ligand generation, underlining the importance of our findings showing state-of-the-art performance on Vina docking scores.

Conformal prediction is a widely used method to quantify the uncertainty of a classifier under the assumption of exchangeability (e.g., IID data). We generalize conformal prediction to the Hidden Markov Model (HMM) framework where the assumption of exchangeability is not valid. The key idea of the proposed method is to partition the non-exchangeable Markovian data from the HMM into exchangeable blocks by exploiting the de Finetti's Theorem for Markov Chains discovered by Diaconis and Freedman (1980). The permutations of the exchangeable blocks are viewed as randomizations of the observed Markovian data from the HMM. The proposed method provably retains all desirable theoretical guarantees offered by the classical conformal prediction framework in both exchangeable and Markovian settings. In particular, while the lack of exchangeability introduced by Markovian samples constitutes a violation of a crucial assumption for classical conformal prediction, the proposed method views it as an advantage that can be exploited to improve the performance further. Detailed numerical and empirical results that complement the theoretical conclusions are provided to illustrate the practical feasibility of the proposed method.

We present BlenderBot 3x, an update on the conversational model BlenderBot 3, which is now trained using organic conversation and feedback data from participating users of the system in order to improve both its skills and safety. We are publicly releasing the participating de-identified interaction data for use by the research community, in order to spur further progress. Training models with organic data is challenging because interactions with people "in the wild" include both high quality conversations and feedback, as well as adversarial and toxic behavior. We study techniques that enable learning from helpful teachers while avoiding learning from people who are trying to trick the model into unhelpful or toxic responses. BlenderBot 3x is both preferred in conversation to BlenderBot 3, and is shown to produce safer responses in challenging situations. While our current models are still far from perfect, we believe further improvement can be achieved by continued use of the techniques explored in this work.

There has been tremendous progress in multimodal Large Language Models (LLMs). Recent works have extended these models to video input with promising instruction following capabilities. However, an important missing piece is temporal localization. These models cannot accurately answer the "When?" questions. We identify three key aspects that limit their temporal localization capabilities: (i) time representation, (ii) architecture, and (iii) data. We address these shortcomings by proposing Language Instructed Temporal-Localization Assistant (LITA) with the following features: (1) We introduce time tokens that encode timestamps relative to the video length to better represent time in videos. (2) We introduce SlowFast tokens in the architecture to capture temporal information at fine temporal resolution. (3) We emphasize temporal localization data for LITA. In addition to leveraging existing video datasets with timestamps, we propose a new task, Reasoning Temporal Localization (RTL), along with the dataset, ActivityNet-RTL, for learning and evaluating this task. Reasoning temporal localization requires both the reasoning and temporal localization of Video LLMs. LITA demonstrates strong performance on this challenging task, nearly doubling the temporal mean intersection-over-union (mIoU) of baselines. In addition, we show that our emphasis on temporal localization also substantially improves video-based text generation compared to existing Video LLMs, including a 36% relative improvement of Temporal Understanding. Code is available at: https://github.com/NVlabs/LITA

The pre-training of large language models usually requires massive amounts of resources, both in terms of computation and data. Frequently used web sources such as Common Crawl might contain enough noise to make this pre-training sub-optimal. In this work, we experiment with different sampling methods from the Spanish version of mC4, and present a novel data-centric technique which we name perplexity sampling that enables the pre-training of language models in roughly half the amount of steps and using one fifth of the data. The resulting models are comparable to the current state-of-the-art, and even achieve better results for certain tasks. Our work is proof of the versatility of Transformers, and paves the way for small teams to train their models on a limited budget. Our models are available at this https://huggingface.co/bertin-project{URL}.

Entities are at the center of how we represent and aggregate knowledge. For instance, Encyclopedias such as Wikipedia are structured by entities (e.g., one per Wikipedia article). The ability to retrieve such entities given a query is fundamental for knowledge-intensive tasks such as entity linking and open-domain question answering. Current approaches can be understood as classifiers among atomic labels, one for each entity. Their weight vectors are dense entity representations produced by encoding entity meta information such as their descriptions. This approach has several shortcomings: (i) context and entity affinity is mainly captured through a vector dot product, potentially missing fine-grained interactions; (ii) a large memory footprint is needed to store dense representations when considering large entity sets; (iii) an appropriately hard set of negative data has to be subsampled at training time. In this work, we propose GENRE, the first system that retrieves entities by generating their unique names, left to right, token-by-token in an autoregressive fashion. This mitigates the aforementioned technical issues since: (i) the autoregressive formulation directly captures relations between context and entity name, effectively cross encoding both; (ii) the memory footprint is greatly reduced because the parameters of our encoder-decoder architecture scale with vocabulary size, not entity count; (iii) the softmax loss is computed without subsampling negative data. We experiment with more than 20 datasets on entity disambiguation, end-to-end entity linking and document retrieval tasks, achieving new state-of-the-art or very competitive results while using a tiny fraction of the memory footprint of competing systems. Finally, we demonstrate that new entities can be added by simply specifying their names. Code and pre-trained models at https://github.com/facebookresearch/GENRE.

In this work, we explore whether the recently demonstrated zero-shot abilities of the T0 model extend to Named Entity Recognition for out-of-distribution languages and time periods. Using a historical newspaper corpus in 3 languages as test-bed, we use prompts to extract possible named entities. Our results show that a naive approach for prompt-based zero-shot multilingual Named Entity Recognition is error-prone, but highlights the potential of such an approach for historical languages lacking labeled datasets. Moreover, we also find that T0-like models can be probed to predict the publication date and language of a document, which could be very relevant for the study of historical texts.

In this work, we introduce sequence-to-sequence language resources for Catalan, a moderately under-resourced language, towards two tasks, namely: Summarization and Machine Translation (MT). We present two new abstractive summarization datasets in the domain of newswire. We also introduce a parallel Catalan-English corpus, paired with three different brand new test sets. Finally, we evaluate the data presented with competing state of the art models, and we develop baselines for these tasks using a newly created Catalan BART. We release the resulting resources of this work under open license to encourage the development of language technology in Catalan.

In this paper, we present the first multilingual FAQ dataset publicly available. We collected around 6M FAQ pairs from the web, in 21 different languages. Although this is significantly larger than existing FAQ retrieval datasets, it comes with its own challenges: duplication of content and uneven distribution of topics. We adopt a similar setup as Dense Passage Retrieval (DPR) and test various bi-encoders on this dataset. Our experiments reveal that a multilingual model based on XLM-RoBERTa achieves the best results, except for English. Lower resources languages seem to learn from one another as a multilingual model achieves a higher MRR than language-specific ones. Our qualitative analysis reveals the brittleness of the model on simple word changes. We publicly release our dataset, model and training script.

For many (minority) languages, the resources needed to train large models are not available. We investigate the performance of zero-shot transfer learning with as little data as possible, and the influence of language similarity in this process. We retrain the lexical layers of four BERT-based models using data from two low-resource target language varieties, while the Transformer layers are independently fine-tuned on a POS-tagging task in the model's source language. By combining the new lexical layers and fine-tuned Transformer layers, we achieve high task performance for both target languages. With high language similarity, 10MB of data appears sufficient to achieve substantial monolingual transfer performance. Monolingual BERT-based models generally achieve higher downstream task performance after retraining the lexical layer than multilingual BERT, even when the target language is included in the multilingual model.

We present mGENRE, a sequence-to-sequence system for the Multilingual Entity Linking (MEL) problem -- the task of resolving language-specific mentions to a multilingual Knowledge Base (KB). For a mention in a given language, mGENRE predicts the name of the target entity left-to-right, token-by-token in an autoregressive fashion. The autoregressive formulation allows us to effectively cross-encode mention string and entity names to capture more interactions than the standard dot product between mention and entity vectors. It also enables fast search within a large KB even for mentions that do not appear in mention tables and with no need for large-scale vector indices. While prior MEL works use a single representation for each entity, we match against entity names of as many languages as possible, which allows exploiting language connections between source input and target name. Moreover, in a zero-shot setting on languages with no training data at all, mGENRE treats the target language as a latent variable that is marginalized at prediction time. This leads to over 50% improvements in average accuracy. We show the efficacy of our approach through extensive evaluation including experiments on three popular MEL benchmarks where mGENRE establishes new state-of-the-art results. Code and pre-trained models at https://github.com/facebookresearch/GENRE.

Large generative language models have been very successful for English, but other languages lag behind, in part due to data and computational limitations. We propose a method that may overcome these problems by adapting existing pre-trained models to new languages. Specifically, we describe the adaptation of English GPT-2 to Italian and Dutch by retraining lexical embeddings without tuning the Transformer layers. As a result, we obtain lexical embeddings for Italian and Dutch that are aligned with the original English lexical embeddings. Additionally, we scale up complexity by transforming relearned lexical embeddings of GPT-2 small to the GPT-2 medium embedding space. This method minimises the amount of training and prevents losing information during adaptation that was learned by GPT-2. English GPT-2 models with relearned lexical embeddings can generate realistic sentences in Italian and Dutch. Though on average these sentences are still identifiable as artificial by humans, they are assessed on par with sentences generated by a GPT-2 model fully trained from scratch.

We extract an optimal subset of architectural parameters for the BERT architecture from Devlin et al. (2018) by applying recent breakthroughs in algorithms for neural architecture search. This optimal subset, which we refer to as "Bort", is demonstrably smaller, having an effective (that is, not counting the embedding layer) size of 5.5% the original BERT-large architecture, and 16% of the net size. Bort is also able to be pretrained in 288 GPU hours, which is 1.2% of the time required to pretrain the highest-performing BERT parametric architectural variant, RoBERTa-large (Liu et al., 2019), and about 33% of that of the world-record, in GPU hours, required to train BERT-large on the same hardware. It is also 7.9x faster on a CPU, as well as being better performing than other compressed variants of the architecture, and some of the non-compressed variants: it obtains performance improvements of between 0.3% and 31%, absolute, with respect to BERT-large, on multiple public natural language understanding (NLU) benchmarks.

In the last few years, pre-trained neural architectures have provided impressive improvements across several NLP tasks. Still, generative language models are available mainly for English. We develop GePpeTto, the first generative language model for Italian, built using the GPT-2 architecture. We provide a thorough analysis of GePpeTto's quality by means of both an automatic and a human-based evaluation. The automatic assessment consists in (i) calculating perplexity across different genres and (ii) a profiling analysis over GePpeTto's writing characteristics. We find that GePpeTto's production is a sort of bonsai version of human production, with shorter but yet complex sentences. Human evaluation is performed over a sentence completion task, where GePpeTto's output is judged as natural more often than not, and much closer to the original human texts than to a simpler language model which we take as baseline.

The transformer-based pre-trained language model BERT has helped to improve state-of-the-art performance on many natural language processing (NLP) tasks. Using the same architecture and parameters, we developed and evaluated a monolingual Dutch BERT model called BERTje. Compared to the multilingual BERT model, which includes Dutch but is only based on Wikipedia text, BERTje is based on a large and diverse dataset of 2.4 billion tokens. BERTje consistently outperforms the equally-sized multilingual BERT model on downstream NLP tasks (part-of-speech tagging, named-entity recognition, semantic role labeling, and sentiment analysis). Our pre-trained Dutch BERT model is made available at https://github.com/wietsedv/bertje.

We present a large-scale study of gender bias in occupation classification, a task where the use of machine learning may lead to negative outcomes on peoples' lives. We analyze the potential allocation harms that can result from semantic representation bias. To do so, we study the impact on occupation classification of including explicit gender indicators---such as first names and pronouns---in different semantic representations of online biographies. Additionally, we quantify the bias that remains when these indicators are "scrubbed," and describe proxy behavior that occurs in the absence of explicit gender indicators. As we demonstrate, differences in true positive rates between genders are correlated with existing gender imbalances in occupations, which may compound these imbalances.

Capturing complex temporal relationships between video and audio modalities is vital for Audio-Visual Emotion Recognition (AVER). However, existing methods lack attention to local details, such as facial state changes between video frames, which can reduce the discriminability of features and thus lower recognition accuracy. In this paper, we propose a Detail-Enhanced Intra- and Inter-modal Interaction network(DE-III) for AVER, incorporating several novel aspects. We introduce optical flow information to enrich video representations with texture details that better capture facial state changes. A fusion module integrates the optical flow estimation with the corresponding video frames to enhance the representation of facial texture variations. We also design attentive intra- and inter-modal feature enhancement modules to further improve the richness and discriminability of video and audio representations. A detailed quantitative evaluation shows that our proposed model outperforms all existing methods on three benchmark datasets for both concrete and continuous emotion recognition. To encourage further research and ensure replicability, we will release our full code upon acceptance.