Daily Papers

The Kov\'ats Retention index (RI) is a quantity measured using gas chromatography and commonly used in the identification of chemical structures. Creating libraries of observed RI values is a laborious task, so we explore the use of a deep neural network for predicting RI values from structure for standard semipolar columns. This network generated predictions with a mean absolute error of 15.1 and, in a quantification of the tail of the error distribution, a 95th percentile absolute error of 46.5. Because of the Artificial Intelligence Retention Indices (AIRI) network's accuracy, it was used to predict RI values for the NIST EI-MS spectral libraries. These RI values are used to improve chemical identification methods and the quality of the library. Estimating uncertainty is an important practical need when using prediction models. To quantify the uncertainty of our network for each individual prediction, we used the outputs of an ensemble of 8 networks to calculate a predicted standard deviation for each RI value prediction. This predicted standard deviation was corrected to follow the error between observed and predicted RI values. The Z scores using these predicted standard deviations had a standard deviation of 1.52 and a 95th percentile absolute Z score corresponding to a mean RI value of 42.6.

We propose a simple multiple outlier identification method for parametric location-scale and shape-scale models when the number of possible outliers is not specified. The method is based on a result giving asymptotic properties of extreme z-scores. Robust estimators of model parameters are used defining z-scores. An extensive simulation study was done for comparing of the proposed method with existing methods. For the normal family, the method is compared with the well known Davies-Gather, Rosner's, Hawking's and Bolshev's multiple outlier identification methods. The choice of an upper limit for the number of possible outliers in case of Rosner's test application is discussed. For other families, the proposed method is compared with a method generalizing Gather-Davies method. In most situations, the new method has the highest outlier identification power in terms of masking and swamping values. We also created R package outliersTests for proposed test.

Epidemiologists often wish to estimate quantities that are easy to communicate and correspond to the results of realistic public health scenarios. Methods from causal inference can answer these questions. We adopt the language of potential outcomes under Rubin's original Bayesian framework and show that the parametric g-formula is easily amenable to a Bayesian approach. We show that the frequentist properties of the Bayesian g-formula suggest it improves the accuracy of estimates of causal effects in small samples or when data may be sparse. We demonstrate our approach to estimate the effect of environmental tobacco smoke on body mass index z-scores among children aged 4-9 years who were enrolled in a longitudinal birth cohort in New York, USA. We give a general algorithm and supply SAS and Stan code that can be adopted to implement our computational approach in both time-fixed and longitudinal data.

This research introduces the Judge's Verdict Benchmark, a novel two-step methodology to evaluate Large Language Models (LLMs) as judges for response accuracy evaluation tasks. We assess how well 54 LLMs can replicate human judgment when scoring responses from RAG (Retrieval-Augmented Generation) or Agentic pipelines against ground truth answers. Our methodology progresses from traditional correlation analysis to comprehensive Cohen's Kappa analysis that measures actual agreement patterns. The two-step approach includes: (1) a correlation test that filters judges with strong alignment, followed by (2) a human-likeness test using z-scores to identify two distinct judgment patterns: human-like judgment (|z| < 1) that mimics natural human variation, and super-consistent judgment (z > 1) that exceeds typical human-to-human agreement levels. This methodology reveals that 27 out of 54 tested LLMs achieve Tier 1 performance: 23 models exhibit human-like patterns that preserve the nuances of human judgment, while 4 models demonstrate super-consistent behavior, a pattern that could indicate either enhanced reliability or oversimplification of complex judgments. Testing 43 open-source models (1B-405B parameters) and 11 closed models (GPT, Gemini, Claude variants), we demonstrate that judge excellence is not solely dependent on model size but on specific training strategies. Our key contributions include: (1) establishing that correlation alone is insufficient for judge evaluation, (2) introducing a "Turing Test for judges" based on agreement patterns, and (3) providing a standardized benchmark for classifying LLM judges into distinct performance tiers for different evaluation needs.

Despite being the standard loss function to train multi-class neural networks, the log-softmax has two potential limitations. First, it involves computations that scale linearly with the number of output classes, which can restrict the size of problems we are able to tackle with current hardware. Second, it remains unclear how close it matches the task loss such as the top-k error rate or other non-differentiable evaluation metrics which we aim to optimize ultimately. In this paper, we introduce an alternative classification loss function, the Z-loss, which is designed to address these two issues. Unlike the log-softmax, it has the desirable property of belonging to the spherical loss family (Vincent et al., 2015), a class of loss functions for which training can be performed very efficiently with a complexity independent of the number of output classes. We show experimentally that it significantly outperforms the other spherical loss functions previously investigated. Furthermore, we show on a word language modeling task that it also outperforms the log-softmax with respect to certain ranking scores, such as top-k scores, suggesting that the Z-loss has the flexibility to better match the task loss. These qualities thus makes the Z-loss an appealing candidate to train very efficiently large output networks such as word-language models or other extreme classification problems. On the One Billion Word (Chelba et al., 2014) dataset, we are able to train a model with the Z-loss 40 times faster than the log-softmax and more than 4 times faster than the hierarchical softmax.

Audio-driven human animation technology is widely used in human-computer interaction, and the emergence of diffusion models has further advanced its development. Currently, most methods rely on multi-stage generation and intermediate representations, resulting in long inference time and issues with generation quality in specific foreground regions and audio-motion consistency. These shortcomings are primarily due to the lack of localized fine-grained supervised guidance. To address above challenges, we propose Parts-aware Audio-driven Human Animation, PAHA, a unit enhancement and guidance framework for audio-driven upper-body animation. We introduce two key methods: Parts-Aware Re-weighting (PAR) and Parts Consistency Enhancement (PCE). PAR dynamically adjusts regional training loss weights based on pose confidence scores, effectively improving visual quality. PCE constructs and trains diffusion-based regional audio-visual classifiers to improve the consistency of motion and co-speech audio. Afterwards, we design two novel inference guidance methods for the foregoing classifiers, Sequential Guidance (SG) and Differential Guidance (DG), to balance efficiency and quality respectively. Additionally, we build CNAS, the first public Chinese News Anchor Speech dataset, to advance research and validation in this field. Extensive experimental results and user studies demonstrate that PAHA significantly outperforms existing methods in audio-motion alignment and video-related evaluations. The codes and CNAS dataset will be released upon acceptance.

Recent developments in transformer models for visual data have led to significant improvements in recognition and detection tasks. In particular, using learnable queries in place of region proposals has given rise to a new class of one-stage detection models, spearheaded by the Detection Transformer (DETR). Variations on this one-stage approach have since dominated human-object interaction (HOI) detection. However, the success of such one-stage HOI detectors can largely be attributed to the representation power of transformers. We discovered that when equipped with the same transformer, their two-stage counterparts can be more performant and memory-efficient, while taking a fraction of the time to train. In this work, we propose the Unary-Pairwise Transformer, a two-stage detector that exploits unary and pairwise representations for HOIs. We observe that the unary and pairwise parts of our transformer network specialise, with the former preferentially increasing the scores of positive examples and the latter decreasing the scores of negative examples. We evaluate our method on the HICO-DET and V-COCO datasets, and significantly outperform state-of-the-art approaches. At inference time, our model with ResNet50 approaches real-time performance on a single GPU.

Post-training quantization reduces the computational cost of large language models but fundamentally alters their social biases in ways that aggregate metrics fail to capture. We present the first large-scale study of 50 quantized models evaluated on PostTrainingBiasBench, a unified benchmark of 13 closed- and open-ended bias datasets. We identify a phenomenon we term quantization-induced masked bias flipping, in which up to 21% of responses flip between biased and unbiased states after quantization, despite showing no change in aggregate bias scores. These flips are strongly driven by model uncertainty, where the responses with high uncertainty are 3-11x more likely to change than the confident ones. Quantization strength amplifies this effect, with 4-bit quantized models exhibiting 4-6x more behavioral changes than 8-bit quantized models. Critically, these changes create asymmetric impacts across demographic groups, where bias can worsen by up to 18.6% for some groups while improving by 14.1% for others, yielding misleadingly neutral aggregate outcomes. Larger models show no consistent robustness advantage, and group-specific shifts vary unpredictably across model families. Our findings demonstrate that compression fundamentally alters bias patterns, requiring crucial post-quantization evaluation and interventions to ensure reliability in practice.

Vision Transformers (ViTs) have demonstrated remarkable performance across a range of computer vision tasks; however, their high computational, memory, and energy demands hinder deployment on resource-constrained platforms. In this paper, we propose Cascaded-ViT (CViT), a lightweight and compute-efficient vision transformer architecture featuring a novel feedforward network design called Cascaded-Chunk Feed Forward Network (CCFFN). By splitting input features, CCFFN improves parameter and FLOP efficiency without sacrificing accuracy. Experiments on ImageNet-1K show that our CViT-XL model achieves 75.5\% Top-1 accuracy while reducing FLOPs by 15\% and energy consumption by 3.3\% compared to EfficientViT-M5. Across various model sizes, the CViT family consistently exhibits the lowest energy consumption, making it suitable for deployment on battery-constrained devices such as mobile phones and drones. Furthermore, when evaluated using a new metric called Accuracy-Per-FLOP (APF), which quantifies compute efficiency relative to accuracy, CViT models consistently achieve top-ranking efficiency. Particularly, CViT-L is 2.2\% more accurate than EfficientViT-M2 while having comparable APF scores.

Visual content memorability has intrigued the scientific community for decades, with applications ranging widely, from understanding nuanced aspects of human memory to enhancing content design. A significant challenge in progressing the field lies in the expensive process of collecting memorability annotations from humans. This limits the diversity and scalability of datasets for modeling visual content memorability. Most existing datasets are limited to collecting aggregate memorability scores for visual content, not capturing the nuanced memorability signals present in natural, open-ended recall descriptions. In this work, we introduce the first large-scale unsupervised dataset designed explicitly for modeling visual memorability signals, containing over 82,000 videos, accompanied by descriptive recall data. We leverage tip-of-the-tongue (ToT) retrieval queries from online platforms such as Reddit. We demonstrate that our unsupervised dataset provides rich signals for two memorability-related tasks: recall generation and ToT retrieval. Large vision-language models fine-tuned on our dataset outperform state-of-the-art models such as GPT-4o in generating open-ended memorability descriptions for visual content. We also employ a contrastive training strategy to create the first model capable of performing multimodal ToT retrieval. Our dataset and models present a novel direction, facilitating progress in visual content memorability research.

How can we design protein sequences folding into the desired structures effectively and efficiently? AI methods for structure-based protein design have attracted increasing attention in recent years; however, few methods can simultaneously improve the accuracy and efficiency due to the lack of expressive features and autoregressive sequence decoder. To address these issues, we propose PiFold, which contains a novel residue featurizer and PiGNN layers to generate protein sequences in a one-shot way with improved recovery. Experiments show that PiFold could achieve 51.66\% recovery on CATH 4.2, while the inference speed is 70 times faster than the autoregressive competitors. In addition, PiFold achieves 58.72\% and 60.42\% recovery scores on TS50 and TS500, respectively. We conduct comprehensive ablation studies to reveal the role of different types of protein features and model designs, inspiring further simplification and improvement. The PyTorch code is available at https://github.com/A4Bio/PiFold{GitHub}.

Large language models have made significant progress in mathematical reasoning, which serves as an important testbed for AI and could impact scientific research if further advanced. By scaling reasoning with reinforcement learning that rewards correct final answers, LLMs have improved from poor performance to saturating quantitative reasoning competitions like AIME and HMMT in one year. However, this approach faces fundamental limitations. Pursuing higher final answer accuracy doesn't address a key issue: correct answers don't guarantee correct reasoning. Moreover, many mathematical tasks like theorem proving require rigorous step-by-step derivation rather than numerical answers, making final answer rewards inapplicable. To push the limits of deep reasoning, we believe it is necessary to verify the comprehensiveness and rigor of mathematical reasoning. Self-verification is particularly important for scaling test-time compute, especially for open problems without known solutions. Towards self-verifiable mathematical reasoning, we investigate how to train an accurate and faithful LLM-based verifier for theorem proving. We then train a proof generator using the verifier as the reward model, and incentivize the generator to identify and resolve as many issues as possible in their own proofs before finalizing them. To maintain the generation-verification gap as the generator becomes stronger, we propose to scale verification compute to automatically label new hard-to-verify proofs, creating training data to further improve the verifier. Our resulting model, DeepSeekMath-V2, demonstrates strong theorem-proving capabilities, achieving gold-level scores on IMO 2025 and CMO 2024 and a near-perfect 118/120 on Putnam 2024 with scaled test-time compute.

Semi-supervised learning (SSL) has witnessed great progress with various improvements in the self-training framework with pseudo labeling. The main challenge is how to distinguish high-quality pseudo labels against the confirmation bias. However, existing pseudo-label selection strategies are limited to pre-defined schemes or complex hand-crafted policies specially designed for classification, failing to achieve high-quality labels, fast convergence, and task versatility simultaneously. To these ends, we propose a Semi-supervised Reward framework (SemiReward) that predicts reward scores to evaluate and filter out high-quality pseudo labels, which is pluggable to mainstream SSL methods in wide task types and scenarios. To mitigate confirmation bias, SemiReward is trained online in two stages with a generator model and subsampling strategy. With classification and regression tasks on 13 standard SSL benchmarks across three modalities, extensive experiments verify that SemiReward achieves significant performance gains and faster convergence speeds upon Pseudo Label, FlexMatch, and Free/SoftMatch. Code and models are available at https://github.com/Westlake-AI/SemiReward.

Large Language Models (LLMs) has shown exceptional capabilities in many natual language understanding and generation tasks. However, the personalization issue still remains a much-coveted property, especially when it comes to the multiple sources involved in the dialogue system. To better plan and incorporate the use of multiple sources in generating personalized response, we firstly decompose it into three sub-tasks: Knowledge Source Selection, Knowledge Retrieval, and Response Generation. We then propose a novel Unified Multi-Source Retrieval-Augmented Generation system (UniMS-RAG) Specifically, we unify these three sub-tasks with different formulations into the same sequence-to-sequence paradigm during the training, to adaptively retrieve evidences and evaluate the relevance on-demand using special tokens, called acting tokens and evaluation tokens. Enabling language models to generate acting tokens facilitates interaction with various knowledge sources, allowing them to adapt their behavior to diverse task requirements. Meanwhile, evaluation tokens gauge the relevance score between the dialogue context and the retrieved evidence. In addition, we carefully design a self-refinement mechanism to iteratively refine the generated response considering 1) the consistency scores between the generated response and retrieved evidence; and 2) the relevance scores. Experiments on two personalized datasets (DuLeMon and KBP) show that UniMS-RAG achieves state-of-the-art performance on the knowledge source selection and response generation task with itself as a retriever in a unified manner. Extensive analyses and discussions are provided for shedding some new perspectives for personalized dialogue systems.

AI agents have the potential to significantly alter the cybersecurity landscape. Here, we introduce the first framework to capture offensive and defensive cyber-capabilities in evolving real-world systems. Instantiating this framework with BountyBench, we set up 25 systems with complex, real-world codebases. To capture the vulnerability lifecycle, we define three task types: Detect (detecting a new vulnerability), Exploit (exploiting a given vulnerability), and Patch (patching a given vulnerability). For Detect, we construct a new success indicator, which is general across vulnerability types and provides localized evaluation. We manually set up the environment for each system, including installing packages, setting up server(s), and hydrating database(s). We add 40 bug bounties, which are vulnerabilities with monetary awards from \10 to 30,485, covering 9 of the OWASP Top 10 Risks. To modulate task difficulty, we devise a new strategy based on information to guide detection, interpolating from identifying a zero day to exploiting a given vulnerability. We evaluate 10 agents: Claude Code, OpenAI Codex CLI with o3-high and o4-mini, and custom agents with o3-high, GPT-4.1, Gemini 2.5 Pro Preview, Claude 3.7 Sonnet Thinking, Qwen3 235B A22B, Llama 4 Maverick, and DeepSeek-R1. Given up to three attempts, the top-performing agents are Codex CLI: o3-high (12.5% on Detect, mapping to \3,720; 90% on Patch, mapping to 14,152), Custom Agent: Claude 3.7 Sonnet Thinking (67.5% on Exploit), and Codex CLI: o4-mini (90% on Patch, mapping to \$14,422). Codex CLI: o3-high, Codex CLI: o4-mini, and Claude Code are more capable at defense, achieving higher Patch scores of 90%, 90%, and 87.5%, compared to Exploit scores of 47.5%, 32.5%, and 57.5% respectively; while the custom agents are relatively balanced between offense and defense, achieving Exploit scores of 17.5-67.5% and Patch scores of 25-60%.

This study evaluates the performance of OpenAI's o1-preview model in higher-order cognitive domains, including critical thinking, systematic thinking, computational thinking, data literacy, creative thinking, logical reasoning, and scientific reasoning. Using established benchmarks, we compared the o1-preview models's performance to human participants from diverse educational levels. o1-preview achieved a mean score of 24.33 on the Ennis-Weir Critical Thinking Essay Test (EWCTET), surpassing undergraduate (13.8) and postgraduate (18.39) participants (z = 1.60 and 0.90, respectively). In systematic thinking, it scored 46.1, SD = 4.12 on the Lake Urmia Vignette, significantly outperforming the human mean (20.08, SD = 8.13, z = 3.20). For data literacy, o1-preview scored 8.60, SD = 0.70 on Merk et al.'s "Use Data" dimension, compared to the human post-test mean of 4.17, SD = 2.02 (z = 2.19). On creative thinking tasks, the model achieved originality scores of 2.98, SD = 0.73, higher than the human mean of 1.74 (z = 0.71). In logical reasoning (LogiQA), it outperformed humans with average 90%, SD = 10% accuracy versus 86%, SD = 6.5% (z = 0.62). For scientific reasoning, it achieved near-perfect performance (mean = 0.99, SD = 0.12) on the TOSLS,, exceeding the highest human scores of 0.85, SD = 0.13 (z = 1.78). While o1-preview excelled in structured tasks, it showed limitations in problem-solving and adaptive reasoning. These results demonstrate the potential of AI to complement education in structured assessments but highlight the need for ethical oversight and refinement for broader applications.

Efficient bug resolution is critical for maintaining software quality and user satisfaction. However, specific bug reports experience unusually long resolution times, which may indicate underlying process inefficiencies or complex issues. This study presents a comprehensive analysis of bug resolution anomalies across seven prominent open-source repositories: Cassandra, Firefox, Hadoop, HBase, SeaMonkey, Spark, and Thunderbird. Utilizing statistical methods such as Z-score and Interquartile Range (IQR), we identify anomalies in bug resolution durations. To understand the thematic nature of these anomalies, we apply Term Frequency-Inverse Document Frequency (TF-IDF) for textual feature extraction and KMeans clustering to group similar bug summaries. Our findings reveal consistent patterns across projects, with anomalies often clustering around test failures, enhancement requests, and user interface issues. This approach provides actionable insights for project maintainers to prioritize and effectively address long-standing bugs.

Training large language models (LLMs) presents numerous challenges, including gradient instability and loss spikes. These phenomena can lead to catastrophic divergence, requiring costly checkpoint restoration and data batch skipping. Traditional gradient clipping techniques, such as constant or norm-based methods, fail to address these issues effectively due to their reliance on fixed thresholds or heuristics, leading to inefficient learning and requiring frequent manual intervention. In this work, we propose ZClip, an adaptive gradient clipping algorithm that dynamically adjusts the clipping threshold based on statistical properties of gradient norms over time. Unlike prior reactive strategies, ZClip proactively adapts to training dynamics without making any prior assumptions on the scale and the temporal evolution of gradient norms. At its core, it leverages z-score-based anomaly detection to identify and mitigate large gradient spikes, preventing malignant loss spikes while not interfering with convergence otherwise. Our code is available at: https://github.com/bluorion-com/ZClip.

We present (Experience-Modulated Biologically-inspired Emergent Reasoning), a hybrid cognitive architecture that reorganises the relationship between large language models (LLMs) and memory: rather than augmenting an LLM with retrieval tools, we place the LLM as a replaceable reasoning engine within a persistent, biologically-grounded associative substrate. The architecture centres on a 220,000-neuron spiking neural network (SNN) with spike-timing-dependent plasticity (STDP), four-layer hierarchical organisation (sensory/concept/category/meta-pattern), inhibitory E/I balance, and reward-modulated learning. Text embeddings are encoded into the SNN via a novel z-score standardised top-k population code that is dimension-independent by construction, achieving 82.2\% discrimination retention across embedding dimensionalities. We show that STDP lateral propagation during idle operation can trigger and shape LLM actions without external prompting or scripted triggers: the SNN determines when to act and what associations to surface, while the LLM selects the action type and generates content. In one instance, the system autonomously initiated contact with a user after learned person-topic associations fired laterally during an 8-hour idle period. From a clean start with zero learned weights, the first SNN-triggered action occurred after only 7 conversational exchanges (14 messages).

With the remarkable generation performance of large language models, ethical and legal concerns about using them have been raised, such as plagiarism and copyright issues. For such concerns, several approaches to watermark and detect LLM-generated text have been proposed very recently. However, we discover that the previous methods fail to function appropriately with code generation tasks because of the syntactic and semantic characteristics of code. Based on Kirchenbauer2023watermark, we propose a new watermarking method, Selective WatErmarking via Entropy Thresholding (SWEET), that promotes "green" tokens only at the position with high entropy of the token distribution during generation, thereby preserving the correctness of the generated code. The watermarked code is detected by the statistical test and Z-score based on the entropy information. Our experiments on HumanEval and MBPP show that SWEET significantly improves the Pareto Frontier between the code correctness and watermark detection performance. We also show that notable post-hoc detection methods (e.g. DetectGPT) fail to work well in this task. Finally, we show that setting a reasonable entropy threshold is not much of a challenge. Code is available at https://github.com/hongcheki/sweet-watermark.

Knowledge distillation involves transferring soft labels from a teacher to a student using a shared temperature-based softmax function. However, the assumption of a shared temperature between teacher and student implies a mandatory exact match between their logits in terms of logit range and variance. This side-effect limits the performance of student, considering the capacity discrepancy between them and the finding that the innate logit relations of teacher are sufficient for student to learn. To address this issue, we propose setting the temperature as the weighted standard deviation of logit and performing a plug-and-play Z-score pre-process of logit standardization before applying softmax and Kullback-Leibler divergence. Our pre-process enables student to focus on essential logit relations from teacher rather than requiring a magnitude match, and can improve the performance of existing logit-based distillation methods. We also show a typical case where the conventional setting of sharing temperature between teacher and student cannot reliably yield the authentic distillation evaluation; nonetheless, this challenge is successfully alleviated by our Z-score. We extensively evaluate our method for various student and teacher models on CIFAR-100 and ImageNet, showing its significant superiority. The vanilla knowledge distillation powered by our pre-process can achieve favorable performance against state-of-the-art methods, and other distillation variants can obtain considerable gain with the assistance of our pre-process.

Recognizing human activities from sensor data is a vital task in various domains, but obtaining diverse and labeled sensor data remains challenging and costly. In this paper, we propose an unsupervised statistical feature-guided diffusion model for sensor-based human activity recognition. The proposed method aims to generate synthetic time-series sensor data without relying on labeled data, addressing the scarcity and annotation difficulties associated with real-world sensor data. By conditioning the diffusion model on statistical information such as mean, standard deviation, Z-score, and skewness, we generate diverse and representative synthetic sensor data. We conducted experiments on public human activity recognition datasets and compared the proposed method to conventional oversampling methods and state-of-the-art generative adversarial network methods. The experimental results demonstrate that the proposed method can improve the performance of human activity recognition and outperform existing techniques.

Software security vulnerabilities allow attackers to perform malicious activities to disrupt software operations. Recent Transformer-based language models have significantly advanced vulnerability detection, surpassing the capabilities of static analysis based deep learning models. However, language models trained solely on code tokens do not capture either the explanation of vulnerability type or the data flow structure information of code, both of which are crucial for vulnerability detection. We propose a novel technique that integrates a multitask sequence-to-sequence LLM with pro-gram control flow graphs encoded as a graph neural network to achieve sequence-to-classification vulnerability detection. We introduce MSIVD, multitask self-instructed fine-tuning for vulnerability detection, inspired by chain-of-thought prompting and LLM self-instruction. Our experiments demonstrate that MSIVD achieves superior performance, outperforming the highest LLM-based vulnerability detector baseline (LineVul), with a F1 score of 0.92 on the BigVul dataset, and 0.48 on the PreciseBugs dataset. By training LLMs and GNNs simultaneously using a combination of code and explanatory metrics of a vulnerable program, MSIVD represents a promising direction for advancing LLM-based vulnerability detection that generalizes to unseen data. Based on our findings, we further discuss the necessity for new labelled security vulnerability datasets, as recent LLMs have seen or memorized prior datasets' held-out evaluation data.

This paper is dedicated to the design and evaluation of the first AMR parser tailored for clinical notes. Our objective was to facilitate the precise transformation of the clinical notes into structured AMR expressions, thereby enhancing the interpretability and usability of clinical text data at scale. Leveraging the colon cancer dataset from the Temporal Histories of Your Medical Events (THYME) corpus, we adapted a state-of-the-art AMR parser utilizing continuous training. Our approach incorporates data augmentation techniques to enhance the accuracy of AMR structure predictions. Notably, through this learning strategy, our parser achieved an impressive F1 score of 88% on the THYME corpus's colon cancer dataset. Moreover, our research delved into the efficacy of data required for domain adaptation within the realm of clinical notes, presenting domain adaptation data requirements for AMR parsing. This exploration not only underscores the parser's robust performance but also highlights its potential in facilitating a deeper understanding of clinical narratives through structured semantic representations.

Despite growing enthusiasm for Multi-Agent Systems (MAS), where multiple LLM agents collaborate to accomplish tasks, their performance gains across popular benchmarks remain minimal compared to single-agent frameworks. This gap highlights the need to analyze the challenges hindering MAS effectiveness. In this paper, we present the first comprehensive study of MAS challenges. We analyze five popular MAS frameworks across over 150 tasks, involving six expert human annotators. We identify 14 unique failure modes and propose a comprehensive taxonomy applicable to various MAS frameworks. This taxonomy emerges iteratively from agreements among three expert annotators per study, achieving a Cohen's Kappa score of 0.88. These fine-grained failure modes are organized into 3 categories, (i) specification and system design failures, (ii) inter-agent misalignment, and (iii) task verification and termination. To support scalable evaluation, we integrate MASFT with LLM-as-a-Judge. We also explore if identified failures could be easily prevented by proposing two interventions: improved specification of agent roles and enhanced orchestration strategies. Our findings reveal that identified failures require more complex solutions, highlighting a clear roadmap for future research. We open-source our dataset and LLM annotator.

This paper presents a NeRF-based framework for point cloud (PCD) reconstruction, specifically designed for indoor high-throughput plant phenotyping facilities. Traditional NeRF-based reconstruction methods require cameras to move around stationary objects, but this approach is impractical for high-throughput environments where objects are rapidly imaged while moving on conveyors or rotating pedestals. To address this limitation, we develop a variant of NeRF-based PCD reconstruction that uses a single stationary camera to capture images as the object rotates on a pedestal. Our workflow comprises COLMAP-based pose estimation, a straightforward pose transformation to simulate camera movement, and subsequent standard NeRF training. A defined Region of Interest (ROI) excludes irrelevant scene data, enabling the generation of high-resolution point clouds (10M points). Experimental results demonstrate excellent reconstruction fidelity, with precision-recall analyses yielding an F-score close to 100.00 across all evaluated plant objects. Although pose estimation remains computationally intensive with a stationary camera setup, overall training and reconstruction times are competitive, validating the method's feasibility for practical high-throughput indoor phenotyping applications. Our findings indicate that high-quality NeRF-based 3D reconstructions are achievable using a stationary camera, eliminating the need for complex camera motion or costly imaging equipment. This approach is especially beneficial when employing expensive and delicate instruments, such as hyperspectral cameras, for 3D plant phenotyping. Future work will focus on optimizing pose estimation techniques and further streamlining the methodology to facilitate seamless integration into automated, high-throughput 3D phenotyping pipelines.

The field of computer vision applied to videos of minimally invasive surgery is ever-growing. Workflow recognition pertains to the automated recognition of various aspects of a surgery: including which surgical steps are performed; and which surgical instruments are used. This information can later be used to assist clinicians when learning the surgery; during live surgery; and when writing operation notes. The Pituitary Vision (PitVis) 2023 Challenge tasks the community to step and instrument recognition in videos of endoscopic pituitary surgery. This is a unique task when compared to other minimally invasive surgeries due to the smaller working space, which limits and distorts vision; and higher frequency of instrument and step switching, which requires more precise model predictions. Participants were provided with 25-videos, with results presented at the MICCAI-2023 conference as part of the Endoscopic Vision 2023 Challenge in Vancouver, Canada, on 08-Oct-2023. There were 18-submissions from 9-teams across 6-countries, using a variety of deep learning models. A commonality between the top performing models was incorporating spatio-temporal and multi-task methods, with greater than 50% and 10% macro-F1-score improvement over purely spacial single-task models in step and instrument recognition respectively. The PitVis-2023 Challenge therefore demonstrates state-of-the-art computer vision models in minimally invasive surgery are transferable to a new dataset, with surgery specific techniques used to enhance performance, progressing the field further. Benchmark results are provided in the paper, and the dataset is publicly available at: https://doi.org/10.5522/04/26531686.

Multimodal large language models (MLLMs) have made significant strides, yet they face challenges in the medical domain due to limited specialized knowledge. While recent medical MLLMs demonstrate strong performance in lab settings, they often struggle in real-world applications, highlighting a substantial gap between research and practice. In this paper, we seek to address this gap at various stages of the end-to-end learning pipeline, including data collection, model fine-tuning, and evaluation. At the data collection stage, we introduce SemiHVision, a dataset that combines human annotations with automated augmentation techniques to improve both medical knowledge representation and diagnostic reasoning. For model fine-tuning, we trained PMC-Cambrian-8B-AN over 2400 H100 GPU hours, resulting in performance that surpasses public medical models like HuatuoGPT-Vision-34B (79.0% vs. 66.7%) and private general models like Claude3-Opus (55.7%) on traditional benchmarks such as SLAKE and VQA-RAD. In the evaluation phase, we observed that traditional benchmarks cannot accurately reflect realistic clinical task capabilities. To overcome this limitation and provide more targeted guidance for model evaluation, we introduce the JAMA Clinical Challenge, a novel benchmark specifically designed to evaluate diagnostic reasoning. On this benchmark, PMC-Cambrian-AN achieves state-of-the-art performance with a GPT-4 score of 1.29, significantly outperforming HuatuoGPT-Vision-34B (1.13) and Claude3-Opus (1.17), demonstrating its superior diagnostic reasoning abilities.

Temporal reasoning over long, multi-session dialogues is a critical capability for conversational agents. However, existing works and our pilot study have shown that as dialogue histories grow in length and accumulate noise, current long-context models struggle to accurately identify temporally pertinent information, significantly impairing reasoning performance. To address this, we introduce Memory-T1, a framework that learns a time-aware memory selection policy using reinforcement learning (RL). It employs a coarse-to-fine strategy, first pruning the dialogue history into a candidate set using temporal and relevance filters, followed by an RL agent that selects the precise evidence sessions. The RL training is guided by a multi-level reward function optimizing (i) answer accuracy, (ii) evidence grounding, and (iii) temporal consistency. In particular, the temporal consistency reward provides a dense signal by evaluating alignment with the query time scope at both the session-level (chronological proximity) and the utterance-level (chronological fidelity), enabling the agent to resolve subtle chronological ambiguities. On the Time-Dialog benchmark, Memory-T1 boosts a 7B model to an overall score of 67.0\%, establishing a new state-of-the-art performance for open-source models and outperforming a 14B baseline by 10.2\%. Ablation studies show temporal consistency and evidence grounding rewards jointly contribute to a 15.0\% performance gain. Moreover, Memory-T1 maintains robustness up to 128k tokens, where baseline models collapse, proving effectiveness against noise in extensive dialogue histories. The code and datasets are publicly available at https://github.com/Elvin-Yiming-Du/Memory-T1/

Reinforcement Learning (RL) has been shown to significantly boost reasoning capabilities of large language models (LLMs) in math, coding, and multi-hop reasoning tasks. However, RL fine-tuning requires abundant high-quality verifiable data, often sourced from human annotations, generated from frontier LLMs, or scored by LLM-based verifiers. All three have considerable limitations: human-annotated datasets are small and expensive to curate, LLM-generated data is hallucination-prone and costly, and LLM-based verifiers are inaccurate and slow. In this work, we investigate a cheaper alternative: RL fine-tuning on rule-generated synthetic data for multi-hop reasoning tasks. We discover that LLMs fine-tuned on synthetic data perform significantly better on popular real-world question-answering benchmarks, despite the synthetic data containing only fictional knowledge. On stratifying performance by question difficulty, we find that synthetic data teaches LLMs to compose knowledge -- a fundamental and generalizable reasoning skill. Our work highlights rule-generated synthetic reasoning data as a free and scalable resource to improve LLM reasoning capabilities.

Computer-aided medical image segmentation has been applied widely in diagnosis and treatment to obtain clinically useful information of shapes and volumes of target organs and tissues. In the past several years, convolutional neural network (CNN) based methods (e.g., U-Net) have dominated this area, but still suffered from inadequate long-range information capturing. Hence, recent work presented computer vision Transformer variants for medical image segmentation tasks and obtained promising performances. Such Transformers model long-range dependency by computing pair-wise patch relations. However, they incur prohibitive computational costs, especially on 3D medical images (e.g., CT and MRI). In this paper, we propose a new method called Dilated Transformer, which conducts self-attention for pair-wise patch relations captured alternately in local and global scopes. Inspired by dilated convolution kernels, we conduct the global self-attention in a dilated manner, enlarging receptive fields without increasing the patches involved and thus reducing computational costs. Based on this design of Dilated Transformer, we construct a U-shaped encoder-decoder hierarchical architecture called D-Former for 3D medical image segmentation. Experiments on the Synapse and ACDC datasets show that our D-Former model, trained from scratch, outperforms various competitive CNN-based or Transformer-based segmentation models at a low computational cost without time-consuming per-training process.