Deep Learning
Accelerating scientific discovery with the common task framework
Kutz, J. Nathan, Battaglia, Peter, Brenner, Michael, Carlberg, Kevin, Hagberg, Aric, Ho, Shirley, Hoyer, Stephan, Lange, Henning, Lipson, Hod, Mahoney, Michael W., Noe, Frank, Welling, Max, Zanna, Laure, Zhu, Francis, Brunton, Steven L.
Machine learning (ML) and artificial intelligence (AI) algorithms are transforming and empowering the characterization and control of dynamic systems in the engineering, physical, and biological sciences. These emerging modeling paradigms require comparative metrics to evaluate a diverse set of scientific objectives, including forecasting, state reconstruction, generalization, and control, while also considering limited data scenarios and noisy measurements. We introduce a common task framework (CTF) for science and engineering, which features a growing collection of challenge data sets with a diverse set of practical and common objectives. The CTF is a critically enabling technology that has contributed to the rapid advance of ML/AI algorithms in traditional applications such as speech recognition, language processing, and computer vision. There is a critical need for the objective metrics of a CTF to compare the diverse algorithms being rapidly developed and deployed in practice today across science and engineering.
Hybrid Fuzzing with LLM-Guided Input Mutation and Semantic Feedback
Software fuzzing has become a cornerstone in automated vulnerability discovery, yet existing mutation strategies often lack semantic awareness, leading to redundant test cases and slow exploration of deep program states. In this work, I present a hybrid fuzzing framework that integrates static and dynamic analysis with Large Language Model (LLM)-guided input mutation and semantic feedback. Static analysis extracts control-flow and data-flow information, which is transformed into structured prompts for the LLM to generate syntactically valid and semantically diverse inputs. During execution, I augment traditional coverage-based feedback with semantic feedback signals-derived from program state changes, exception types, and output semantics-allowing the fuzzer to prioritize inputs that trigger novel program behaviors beyond mere code coverage. I implement our approach atop AFL++, combining program instrumentation with embedding-based semantic similarity metrics to guide seed selection. Evaluation on real-world open-source targets, including libpng, tcpdump, and sqlite, demonstrates that our method achieves faster time-to-first-bug, higher semantic diversity, and a competitive number of unique bugs compared to state-of-the-art fuzzers. This work highlights the potential of combining LLM reasoning with semantic-aware feedback to accelerate and deepen vulnerability discovery.
Multiscale Astrocyte Network Calcium Dynamics for Biologically Plausible Intelligence in Anomaly Detection
Iskar, Berk, Barros, Michael Taynnan
Network anomaly detection systems encounter several challenges with traditional detectors trained offline. They become susceptible to concept drift and new threats such as zero-day or polymorphic attacks. To address this limitation, we propose a Ca$^{2+}$-modulated learning framework that draws inspiration from astrocytic Ca$^{2+}$ signaling in the brain, where rapid, context-sensitive adaptation enables robust information processing. Our approach couples a multicellular astrocyte dynamics simulator with a deep neural network (DNN). The simulator models astrocytic Ca$^{2+}$ dynamics through three key mechanisms: IP$_3$-mediated Ca$^{2+}$ release, SERCA pump uptake, and conductance-aware diffusion through gap junctions between cells. Evaluation of our proposed network on CTU-13 (Neris) network traffic data demonstrates the effectiveness of our biologically plausible approach. The Ca$^{2+}$-gated model outperforms a matched baseline DNN, achieving up to $\sim$98\% accuracy with reduced false positives and negatives across multiple train/test splits. Importantly, this improved performance comes with negligible runtime overhead once Ca$^{2+}$ trajectories are precomputed. While demonstrated here for cybersecurity applications, this Ca$^{2+}$-modulated learning framework offers a generic solution for streaming detection tasks that require rapid, biologically grounded adaptation to evolving data patterns.
TwIST: Rigging the Lottery in Transformers with Independent Subnetwork Training
Menezes, Michael, Su, Barbara, Feng, Xinze, Farhat, Yehya, Shili, Hamza, Kyrillidis, Anastasios
We introduce TwIST, a distributed training framework for efficient large language model (LLM) sparsification. TwIST trains multiple subnetworks in parallel, periodically aggregates their parameters, and resamples new subnetworks during training. This process identifies high-quality subnetworks ("golden tickets") without requiring post-training procedures such as calibration or Hessian-based recovery. As a result, TwIST enables zero-cost pruning at deployment time while achieving perplexity competitive with state-of-the-art post-training sparsification methods. The benefits are most pronounced under aggressive sparsity (e.g., 50%+), where TwIST significantly outperforms baseline methods; for example, reaching 23.14 PPL compared to 31.64 for the closest prior approach. Unlike unstructured pruning, TwIST produces structured, dense matrices that offer practical inference speedups and memory reductions on commodity hardware (e.g., CPUs) that do not support efficient sparse computation. TwIST provides an efficient training-time path to deployable sparse LLMs without additional fine-tuning or recovery overhead.
CareMedEval dataset: Evaluating Critical Appraisal and Reasoning in the Biomedical Field
Bonzi, Doria, Guiggi, Alexandre, Bรฉchet, Frรฉdรฉric, Ramisch, Carlos, Favre, Benoit
Critical appraisal of scientific literature is an essential skill in the biomedical field. While large language models (LLMs) can offer promising support in this task, their reliability remains limited, particularly for critical reasoning in specialized domains. We introduce CareMedEval, an original dataset designed to evaluate LLMs on biomedical critical appraisal and reasoning tasks. Derived from authentic exams taken by French medical students, the dataset contains 534 questions based on 37 scientific articles. Unlike existing benchmarks, CareMedEval explicitly evaluates critical reading and reasoning grounded in scientific papers. Benchmarking state-of-the-art generalist and biomedical-specialized LLMs under various context conditions reveals the difficulty of the task: open and commercial models fail to exceed an Exact Match Rate of 0.5 even though generating intermediate reasoning tokens considerably improves the results. Yet, models remain challenged especially on questions about study limitations and statistical analysis. CareMedEval provides a challenging benchmark for grounded reasoning, exposing current LLM limitations and paving the way for future development of automated support for critical appraisal.
Node-Based Editing for Multimodal Generation of Text, Audio, Image, and Video
Kyaw, Alexander Htet, Sivalingam, Lenin Ravindranath
We present a node-based storytelling system for multimodal content generation. The system represents stories as graphs of nodes that can be expanded, edited, and iteratively refined through direct user edits and natural-language prompts. Each node can integrate text, images, audio, and video, allowing creators to compose multimodal narratives. A task selection agent routes between specialized generative tasks that handle story generation, node structure reasoning, node diagram formatting, and context generation. The interface supports targeted editing of individual nodes, automatic branching for parallel storylines, and node-based iterative refinement. Our results demonstrate that node-based editing supports control over narrative structure and iterative generation of text, images, audio, and video. We report quantitative outcomes on automatic story outline generation and qualitative observations of editing workflows. Finally, we discuss current limitations such as scalability to longer narratives and consistency across multiple nodes, and outline future work toward human-in-the-loop and user-centered creative AI tools.
Control Barrier Function for Aligning Large Language Models
Abstract--This paper proposes a control-based framework for aligning large language models (LLMs) by leveraging a control barrier function (CBF) to ensure user-desirable text generation. The presented framework applies the CBF safety filter to the predicted token generated from the baseline LLM, to intervene in the generated text. The safety filter includes two significant advantages: this safety filter is an add-on type, allowing it to be used for alignment purposes without fine-tuning the baseline LLM, and if there is an evaluation model regarding the desired alignment, it can be directly applied to the filter design. The overall text-generation system is implemented with open-source language models, aiming to generate positive text. I. Introduction While large language models (LLMs) are known to have strong language understanding, reasoning and writing abilities, they can also generate harmful, biased, toxic, or unethical content [1], [2]. Alignment of LLMs ensures that they generate content that is "desirable" for user, meaning that the content is ethical and safe. Various approaches for LLM alignment have been presented (see the literature [1], [2], [3] and reference therein). The major approach to LLM alignment is reinforcement learning from human feedback (RLHF, [4]), where a reward model is constructed by human feedback and then used for the training of LLMs. Variants of RLHF methods are also proposed, such as Safe-RLHF by [5], SENSEI by [6], and f-DPG by [7], and their implementations are presented, such as training pre-trained LLMs [8], [9]. Collecting human feedback with data is time-consuming and expensive.
A Criminology of Machines
While the possibility of reaching human-like Artificial Intelligence (AI) remains controversial, the likelihood that the future will be characterized by a society with a growing presence of autonomous machines is high. Autonomous AI agents are already deployed and active across several industries and digital environments and alongside human-human and human-machine interactions, machine-machine interactions are poised to become increasingly prevalent. Given these developments, I argue that criminology must begin to address the implications of this transition for crime and social control. Drawing on Actor-Network Theory and Woolgar's decades-old call for a sociology of machines -- frameworks that acquire renewed relevance with the rise of generative AI agents -- I contend that criminologists should move beyond conceiving AI solely as a tool. Instead, AI agents should be recognized as entities with agency encompassing computational, social, and legal dimensions. Building on the literature on AI safety, I thus examine the risks associated with the rise of multi-agent AI systems, proposing a dual taxonomy to characterize the channels through which interactions among AI agents may generate deviant, unlawful, or criminal outcomes. I then advance and discuss four key questions that warrant theoretical and empirical attention: (1) Can we assume that machines will simply mimic humans? (2) Will crime theories developed for humans suffice to explain deviant or criminal behaviors emerging from interactions between autonomous AI agents? (3) What types of criminal behaviors will be affected first? (4) How might this unprecedented societal shift impact policing? These questions underscore the urgent need for criminologists to theoretically and empirically engage with the implications of multi-agent AI systems for the study of crime and play a more active role in debates on AI safety and governance.
NEF-NET+: Adapting Electrocardio panorama in the wild
Zhan, Zehui, Hu, Yaojun, Zhan, Jiajing, Lian, Wanchen, Wu, Wanqing, Chen, Jintai
Conventional multi-lead electrocardiogram (ECG) systems capture cardiac signals from a fixed set of anatomical viewpoints defined by lead placement. However, certain cardiac conditions (e.g., Brugada syndrome) require additional, non-standard viewpoints to reveal diagnostically critical patterns that may be absent in standard leads. To systematically overcome this limitation, Nef-Net was recently introduced to reconstruct a continuous electrocardiac field, enabling virtual observation of ECG signals from arbitrary views (termed Electrocardio Panorama). Despite its promise, Nef-Net operates under idealized assumptions and faces in-the-wild challenges, such as long-duration ECG modeling, robustness to device-specific signal artifacts, and suboptimal lead placement calibration. This paper presents NEF-NET+, an enhanced framework for realistic panoramic ECG synthesis that supports arbitrary-length signal synthesis from any desired view, generalizes across ECG devices, and compensates for operator-induced deviations in electrode placement. These capabilities are enabled by a newly designed model architecture that performs direct view transformation, incorporating a workflow comprising offline pretraining, device calibration tuning steps as well as an on-the-fly calibration step for patient-specific adaptation. To rigorously evaluate panoramic ECG synthesis, we construct a new Electrocardio Panorama benchmark, called Panobench, comprising 5367 recordings with 48-view per subject, capturing the full spatial variability of cardiac electrical activity. Experimental results show that NEF-NET+ delivers substantial improvements over Nef-Net, yielding an increase of around 6 dB in PSNR in real-world setting. The code and Panobench will be released in a subsequent publication.
FATE: A Formal Benchmark Series for Frontier Algebra of Multiple Difficulty Levels
Jiang, Jiedong, He, Wanyi, Wang, Yuefeng, Gao, Guoxiong, Hu, Yongle, Wang, Jingting, Guan, Nailing, Wu, Peihao, Dai, Chunbo, Xiao, Liang, Dong, Bin
Recent advances in large language models (LLMs) have demonstrated impressive capabilities in formal theorem proving, particularly on contest-based mathematical benchmarks like the IMO. However, these contests do not reflect the depth, breadth, and abstraction of modern mathematical research. To bridge this gap, we introduce FATE (Formal Algebra Theorem Evaluation), a new benchmark series in formal algebra designed to chart a course toward advanced mathematical reasoning. We present two new components, FATE-H and FATE-X, each with 100 problems in abstract and commutative algebra. The FATE series spans a difficulty spectrum from undergraduate exercises to problems exceeding PhD qualifying exams. Notably, FATE-X is the first formal benchmark to surpass both PhD-level exam difficulty and the coverage of the Mathlib library. Our evaluations of state-of-the-art LLM provers on this new benchmark reveal a stark performance gap compared to contest math: the best model achieves only 3% (pass@64) accuracy on FATE-H and 0% on FATE-X. Our two-stage evaluation reveals that models' natural-language reasoning is notably more accurate than their ability to formalize this reasoning. We systematically classify the common errors that arise during this formalization process. Furthermore, a comparative study shows that a specialized prover can exhibit less effective reflection than general-purpose models, reducing its accuracy at the natural-language stage. We believe FATE provides a robust and challenging benchmark that establishes essential checkpoints on the path toward research-level formal mathematical reasoning.