Daily Papers

We present a novel framework for learning on CW-complex structured data points. Recent advances have discussed CW-complexes as ideal learning representations for problems in cheminformatics. However, there is a lack of available machine learning methods suitable for learning on CW-complexes. In this paper we develop notions of convolution and attention that are well defined for CW-complexes. These notions enable us to create the first Hodge informed neural network that can receive a CW-complex as input. We illustrate and interpret this framework in the context of supervised prediction.

We release Code World Model (CWM), a 32-billion-parameter open-weights LLM, to advance research on code generation with world models. To improve code understanding beyond what can be learned from training on static code alone, we mid-train CWM on a large amount of observation-action trajectories from Python interpreter and agentic Docker environments, and perform extensive multi-task reasoning RL in verifiable coding, math, and multi-turn software engineering environments. With CWM, we provide a strong testbed for researchers to explore the opportunities world modeling affords for improving code generation with reasoning and planning in computational environments. We present first steps of how world models can benefit agentic coding, enable step-by-step simulation of Python code execution, and show early results of how reasoning can benefit from the latter. CWM is a dense, decoder-only LLM trained with a context size of up to 131k tokens. Independent of its world modeling capabilities, CWM offers strong performance on general coding and math tasks: it reaches pass@1 scores of 65.8% on SWE-bench Verified (with test-time scaling), 68.6% on LiveCodeBench, 96.6% on Math-500, and 76.0% on AIME 2024. To support further research on code world modeling, we release model checkpoints after mid-training, SFT, and RL.

Large Language Models (LLMs) have significantly aided developers by generating or assisting in code writing, enhancing productivity across various tasks. While identifying incorrect code is often straightforward, detecting vulnerabilities in functionally correct code is more challenging, especially for developers with limited security knowledge, which poses considerable security risks of using LLM-generated code and underscores the need for robust evaluation benchmarks that assess both functional correctness and security. Current benchmarks like CyberSecEval and SecurityEval attempt to solve it but are hindered by unclear and impractical specifications, failing to assess both functionality and security accurately. To tackle these deficiencies, we introduce CWEval, a novel outcome-driven evaluation framework designed to enhance the evaluation of secure code generation by LLMs. This framework not only assesses code functionality but also its security simultaneously with high-quality task specifications and outcome-driven test oracles which provides high accuracy. Coupled with CWEval-bench, a multilingual, security-critical coding benchmark, CWEval provides a rigorous empirical security evaluation on LLM-generated code, overcoming previous benchmarks' shortcomings. Through our evaluations, CWEval reveals a notable portion of functional but insecure code produced by LLMs, and shows a serious inaccuracy of previous evaluations, ultimately contributing significantly to the field of secure code generation. We open-source our artifact at: https://github.com/Co1lin/CWEval .

This paper considers contrastive training for cross-modal 0-shot transfer wherein a pre-trained model in one modality is used for representation learning in another domain using pairwise data. The learnt models in the latter domain can then be used for a diverse set of tasks in a zero-shot way, similar to ``Contrastive Language-Image Pre-training (CLIP)'' and ``Locked-image Tuning (LiT)'' that have recently gained considerable attention. Most existing works for cross-modal representation alignment (including CLIP and LiT) use the standard contrastive training objective, which employs sets of positive and negative examples to align similar and repel dissimilar training data samples. However, similarity amongst training examples has a more continuous nature, thus calling for a more `non-binary' treatment. To address this, we propose a novel loss function called Continuously Weighted Contrastive Loss (CWCL) that employs a continuous measure of similarity. With CWCL, we seek to align the embedding space of one modality with another. Owing to the continuous nature of similarity in the proposed loss function, these models outperform existing methods for 0-shot transfer across multiple models, datasets and modalities. Particularly, we consider the modality pairs of image-text and speech-text and our models achieve 5-8% (absolute) improvement over previous state-of-the-art methods in 0-shot image classification and 20-30% (absolute) improvement in 0-shot speech-to-intent classification and keyword classification.

This paper contributes to the "BraTS 2024 Brain MR Image Synthesis Challenge" and presents a conditional Wavelet Diffusion Model (cWDM) for directly solving a paired image-to-image translation task on high-resolution volumes. While deep learning-based brain tumor segmentation models have demonstrated clear clinical utility, they typically require MR scans from various modalities (T1, T1ce, T2, FLAIR) as input. However, due to time constraints or imaging artifacts, some of these modalities may be missing, hindering the application of well-performing segmentation algorithms in clinical routine. To address this issue, we propose a method that synthesizes one missing modality image conditioned on three available images, enabling the application of downstream segmentation models. We treat this paired image-to-image translation task as a conditional generation problem and solve it by combining a Wavelet Diffusion Model for high-resolution 3D image synthesis with a simple conditioning strategy. This approach allows us to directly apply our model to full-resolution volumes, avoiding artifacts caused by slice- or patch-wise data processing. While this work focuses on a specific application, the presented method can be applied to all kinds of paired image-to-image translation problems, such as CT leftrightarrow MR and MR leftrightarrow PET translation, or mask-conditioned anatomically guided image generation.

The data collected by the current network of gravitational-wave detectors are largely dominated by instrumental noise. Total variation methods based on L1-norm minimization have recently been proposed as a powerful technique for noise removal in gravitational-wave data. In particular, the regularized Rudin-Osher-Fatemi (rROF) model has proven effective to denoise signals embedded in either simulated Gaussian noise or actual detector noise. Importing the rROF model to existing search pipelines seems therefore worth considering. In this paper, we discuss the implementation of two variants of the rROF algorithm as two separate plug-ins of the coherent Wave Burst (cWB) pipeline designed to conduct searches of unmodelled gravitational-wave burst sources. The first approach is based on a single-step rROF method and the second one employs an iterative rROF procedure. Both approaches are calibrated using actual gravitational-wave events from the first three observing runs of the LIGO-Virgo-KAGRA collaboration, namely GW1501914, GW151226, GW170817, and GW190521, encompassing different types of compact binary coalescences. Our analysis shows that the iterative version of the rROF denoising algorithm implemented in the cWB pipeline effectively eliminates noise while preserving the waveform signals intact. Therefore, the combined approach yields higher signal-to-noise values than those computed by the cWB pipeline without the rROF denoising step. The incorporation of the iterative rROF algorithm in the cWB pipeline might hence impact the detectability capabilities of the pipeline along with the inference of source properties.

The online estimation of rhythmic information, such as beat positions, downbeat positions, and meter, is critical for many real-time music applications. Musical rhythm comprises complex hierarchical relationships across time, rendering its analysis intrinsically challenging and at times subjective. Furthermore, systems which attempt to estimate rhythmic information in real-time must be causal and must produce estimates quickly and efficiently. In this work, we introduce an online system for joint beat, downbeat, and meter tracking, which utilizes causal convolutional and recurrent layers, followed by a pair of sequential Monte Carlo particle filters applied during inference. The proposed system does not need to be primed with a time signature in order to perform downbeat tracking, and is instead able to estimate meter and adjust the predictions over time. Additionally, we propose an information gate strategy to significantly decrease the computational cost of particle filtering during the inference step, making the system much faster than previous sampling-based methods. Experiments on the GTZAN dataset, which is unseen during training, show that the system outperforms various online beat and downbeat tracking systems and achieves comparable performance to a baseline offline joint method.

Early tumor detection save lives. Each year, more than 300 million computed tomography (CT) scans are performed worldwide, offering a vast opportunity for effective cancer screening. However, detecting small or early-stage tumors on these CT scans remains challenging, even for experts. Artificial intelligence (AI) models can assist by highlighting suspicious regions, but training such models typically requires extensive tumor masks--detailed, voxel-wise outlines of tumors manually drawn by radiologists. Drawing these masks is costly, requiring years of effort and millions of dollars. In contrast, nearly every CT scan in clinical practice is already accompanied by medical reports describing the tumor's size, number, appearance, and sometimes, pathology results--information that is rich, abundant, and often underutilized for AI training. We introduce R-Super, which trains AI to segment tumors that match their descriptions in medical reports. This approach scales AI training with large collections of readily available medical reports, substantially reducing the need for manually drawn tumor masks. When trained on 101,654 reports, AI models achieved performance comparable to those trained on 723 masks. Combining reports and masks further improved sensitivity by +13% and specificity by +8%, surpassing radiologists in detecting five of the seven tumor types. Notably, R-Super enabled segmentation of tumors in the spleen, gallbladder, prostate, bladder, uterus, and esophagus, for which no public masks or AI models previously existed. This study challenges the long-held belief that large-scale, labor-intensive tumor mask creation is indispensable, establishing a scalable and accessible path toward early detection across diverse tumor types. We plan to release our trained models, code, and dataset at https://github.com/MrGiovanni/R-Super

PanTS is a large-scale, multi-institutional dataset curated to advance research in pancreatic CT analysis. It contains 36,390 CT scans from 145 medical centers, with expert-validated, voxel-wise annotations of over 993,000 anatomical structures, covering pancreatic tumors, pancreas head, body, and tail, and 24 surrounding anatomical structures such as vascular/skeletal structures and abdominal/thoracic organs. Each scan includes metadata such as patient age, sex, diagnosis, contrast phase, in-plane spacing, slice thickness, etc. AI models trained on PanTS achieve significantly better performance in pancreatic tumor detection, localization, and segmentation compared to those trained on existing public datasets. Our analysis indicates that these gains are directly attributable to the 16x larger-scale tumor annotations and indirectly supported by the 24 additional surrounding anatomical structures. As the largest and most comprehensive resource of its kind, PanTS offers a new benchmark for developing and evaluating AI models in pancreatic CT analysis.