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Aug 12

Leveraging Online Olympiad-Level Math Problems for LLMs Training and Contamination-Resistant Evaluation

Advances in Large Language Models (LLMs) have sparked interest in their ability to solve Olympiad-level math problems. However, the training and evaluation of these models are constrained by the limited size and quality of available datasets, as creating large-scale data for such advanced problems requires extensive effort from human experts. In addition, current benchmarks are prone to contamination, leading to unreliable evaluations. In this paper, we present an automated pipeline that leverages the rich resources of the Art of Problem Solving (AoPS) forum, which predominantly features Olympiad-level problems and community-driven solutions. Using open-source LLMs, we develop a method to extract question-answer pairs from the forum, resulting in AoPS-Instruct, a dataset of more than 600,000 high-quality QA pairs. Our experiments demonstrate that fine-tuning LLMs on AoPS-Instruct improves their reasoning abilities across various benchmarks. Moreover, we build an automatic pipeline that introduces LiveAoPSBench, an evolving evaluation set with timestamps, derived from the latest forum data, providing a contamination-resistant benchmark for assessing LLM performance. Notably, we observe a significant decline in LLM performance over time, suggesting their success on older examples may stem from pre-training exposure rather than true reasoning ability. Our work presents a scalable approach to creating and maintaining large-scale, high-quality datasets for advanced math reasoning, offering valuable insights into the capabilities and limitations of LLMs in this domain. Our benchmark and code is available at https://github.com/DSL-Lab/aops

  • 6 authors
·
Jan 24, 2025

POIROT: Aligning Attack Behavior with Kernel Audit Records for Cyber Threat Hunting

Cyber threat intelligence (CTI) is being used to search for indicators of attacks that might have compromised an enterprise network for a long time without being discovered. To have a more effective analysis, CTI open standards have incorporated descriptive relationships showing how the indicators or observables are related to each other. However, these relationships are either completely overlooked in information gathering or not used for threat hunting. In this paper, we propose a system, called POIROT, which uses these correlations to uncover the steps of a successful attack campaign. We use kernel audits as a reliable source that covers all causal relations and information flows among system entities and model threat hunting as an inexact graph pattern matching problem. Our technical approach is based on a novel similarity metric which assesses an alignment between a query graph constructed out of CTI correlations and a provenance graph constructed out of kernel audit log records. We evaluate POIROT on publicly released real-world incident reports as well as reports of an adversarial engagement designed by DARPA, including ten distinct attack campaigns against different OS platforms such as Linux, FreeBSD, and Windows. Our evaluation results show that POIROT is capable of searching inside graphs containing millions of nodes and pinpoint the attacks in a few minutes, and the results serve to illustrate that CTI correlations could be used as robust and reliable artifacts for threat hunting.

  • 4 authors
·
Sep 30, 2019

Robust Collaborative Learning with Linear Gradient Overhead

Collaborative learning algorithms, such as distributed SGD (or D-SGD), are prone to faulty machines that may deviate from their prescribed algorithm because of software or hardware bugs, poisoned data or malicious behaviors. While many solutions have been proposed to enhance the robustness of D-SGD to such machines, previous works either resort to strong assumptions (trusted server, homogeneous data, specific noise model) or impose a gradient computational cost that is several orders of magnitude higher than that of D-SGD. We present MoNNA, a new algorithm that (a) is provably robust under standard assumptions and (b) has a gradient computation overhead that is linear in the fraction of faulty machines, which is conjectured to be tight. Essentially, MoNNA uses Polyak's momentum of local gradients for local updates and nearest-neighbor averaging (NNA) for global mixing, respectively. While MoNNA is rather simple to implement, its analysis has been more challenging and relies on two key elements that may be of independent interest. Specifically, we introduce the mixing criterion of (alpha, lambda)-reduction to analyze the non-linear mixing of non-faulty machines, and present a way to control the tension between the momentum and the model drifts. We validate our theory by experiments on image classification and make our code available at https://github.com/LPD-EPFL/robust-collaborative-learning.

  • 6 authors
·
Sep 22, 2022

AmaraSpatial-10K: A Spatially and Semantically Aligned 3D Dataset for Spatial Computing and Embodied AI

Web-scale 3D asset collections are abundant, but rarely deployment-ready. Assets ship with arbitrary metric scale, incorrect pivots and forward axes, brittle geometry, and textures that do not support relighting, which limits their utility for embodied AI, robotics simulation, game development, and AR/VR. We present AmaraSpatial-10K, a dataset of over 10,000 synthetic 3D assets designed for downstream use rather than volume alone. Each asset is released as a metric-scaled, semantically anchored .glb with separated PBR material maps, a convex collision hull, a paired reference image, and rich multi-sentence text metadata. The dataset spans indoor objects, vehicles, architecture, creatures, and props under a unified spatial convention. Alongside the dataset, we introduce an evaluation suite for 3D asset banks. The suite comprises a continuous Scale Plausibility Score (SPS) with an LLM-as-Judge interval protocol, an LLM Concept Density score for metadata, an anchor-error metric, and a cross-modal CLIP coherence protocol, and we use it to audit AmaraSpatial-10K alongside matched subsets from Objaverse, HSSD, ABO, and GSO. Compared with Objaverse-sourced assets, we demonstrate that AmaraSpatial-10K substantially improves text-based retrieval precision (CLIP Recall@5 of 0.612 vs 0.181, a 3.4x improvement with median rank falling from 267 to 3), and we establish that it satisfies the spatial and semantic prerequisites for physics-aware scene composition and embodied-AI asset banks, leaving those downstream evaluations to future work. AmaraSpatial-10K is publicly available on Hugging Face.

  • 5 authors
·
Apr 23

PeerPrism: Peer Evaluation Expertise vs Review-writing AI

Large Language Models (LLMs) are increasingly used in scientific peer review, assisting with drafting, rewriting, expansion, and refinement. However, existing peer-review LLM detection methods largely treat authorship as a binary problem-human vs. AI-without accounting for the hybrid nature of modern review workflows. In practice, evaluative ideas and surface realization may originate from different sources, creating a spectrum of human-AI collaboration. In this work, we introduce PeerPrism, a large-scale benchmark of 20,690 peer reviews explicitly designed to disentangle idea provenance from text provenance. We construct controlled generation regimes spanning fully human, fully synthetic, and multiple hybrid transformations. This design enables systematic evaluation of whether detectors identify the origin of the surface text or the origin of the evaluative reasoning. We benchmark state-of-the-art LLM text detection methods on PeerPrism. While several methods achieve high accuracy on the standard binary task (human vs. fully synthetic), their predictions diverge sharply under hybrid regimes. In particular, when ideas originate from humans but the surface text is AI-generated, detectors frequently disagree and produce contradictory classifications. Accompanied by stylometric and semantic analyses, our results show that current detection methods conflate surface realization with intellectual contribution. Overall, we demonstrate that LLM detection in peer review cannot be reduced to a binary attribution problem. Instead, authorship must be modeled as a multidimensional construct spanning semantic reasoning and stylistic realization. PeerPrism is the first benchmark evaluating human-AI collaboration in these settings. We release all code, data, prompts, and evaluation scripts to facilitate reproducible research at https://github.com/Reviewerly-Inc/PeerPrism.

  • 6 authors
·
Apr 15

Interpretable graph-based models on multimodal biomedical data integration: A technical review and benchmarking

Integrating heterogeneous biomedical data including imaging, omics, and clinical records supports accurate diagnosis and personalised care. Graph-based models fuse such non-Euclidean data by capturing spatial and relational structure, yet clinical uptake requires regulator-ready interpretability. We present the first technical survey of interpretable graph based models for multimodal biomedical data, covering 26 studies published between Jan 2019 and Sep 2024. Most target disease classification, notably cancer and rely on static graphs from simple similarity measures, while graph-native explainers are rare; post-hoc methods adapted from non-graph domains such as gradient saliency, and SHAP predominate. We group existing approaches into four interpretability families, outline trends such as graph-in-graph hierarchies, knowledge-graph edges, and dynamic topology learning, and perform a practical benchmark. Using an Alzheimer disease cohort, we compare Sensitivity Analysis, Gradient Saliency, SHAP and Graph Masking. SHAP and Sensitivity Analysis recover the broadest set of known AD pathways and Gene-Ontology terms, whereas Gradient Saliency and Graph Masking surface complementary metabolic and transport signatures. Permutation tests show all four beat random gene sets, but with distinct trade-offs: SHAP and Graph Masking offer deeper biology at higher compute cost, while Gradient Saliency and Sensitivity Analysis are quicker though coarser. We also provide a step-by-step flowchart covering graph construction, explainer choice and resource budgeting to help researchers balance transparency and performance. This review synthesises the state of interpretable graph learning for multimodal medicine, benchmarks leading techniques, and charts future directions, from advanced XAI tools to under-studied diseases, serving as a concise reference for method developers and translational scientists.

  • 6 authors
·
May 3, 2025

An adaptively inexact first-order method for bilevel optimization with application to hyperparameter learning

Various tasks in data science are modeled utilizing the variational regularization approach, where manually selecting regularization parameters presents a challenge. The difficulty gets exacerbated when employing regularizers involving a large number of hyperparameters. To overcome this challenge, bilevel learning can be employed to learn such parameters from data. However, neither exact function values nor exact gradients with respect to the hyperparameters are attainable, necessitating methods that only rely on inexact evaluation of such quantities. State-of-the-art inexact gradient-based methods a priori select a sequence of the required accuracies and cannot identify an appropriate step size since the Lipschitz constant of the hypergradient is unknown. In this work, we propose an algorithm with backtracking line search that only relies on inexact function evaluations and hypergradients and show convergence to a stationary point. Furthermore, the proposed algorithm determines the required accuracy dynamically rather than manually selected before running it. Our numerical experiments demonstrate the efficiency and feasibility of our approach for hyperparameter estimation on a range of relevant problems in imaging and data science such as total variation and field of experts denoising and multinomial logistic regression. Particularly, the results show that the algorithm is robust to its own hyperparameters such as the initial accuracies and step size.

  • 4 authors
·
Aug 19, 2023

Automatically identifying, counting, and describing wild animals in camera-trap images with deep learning

Having accurate, detailed, and up-to-date information about the location and behavior of animals in the wild would revolutionize our ability to study and conserve ecosystems. We investigate the ability to automatically, accurately, and inexpensively collect such data, which could transform many fields of biology, ecology, and zoology into "big data" sciences. Motion sensor "camera traps" enable collecting wildlife pictures inexpensively, unobtrusively, and frequently. However, extracting information from these pictures remains an expensive, time-consuming, manual task. We demonstrate that such information can be automatically extracted by deep learning, a cutting-edge type of artificial intelligence. We train deep convolutional neural networks to identify, count, and describe the behaviors of 48 species in the 3.2-million-image Snapshot Serengeti dataset. Our deep neural networks automatically identify animals with over 93.8% accuracy, and we expect that number to improve rapidly in years to come. More importantly, if our system classifies only images it is confident about, our system can automate animal identification for 99.3% of the data while still performing at the same 96.6% accuracy as that of crowdsourced teams of human volunteers, saving more than 8.4 years (at 40 hours per week) of human labeling effort (i.e. over 17,000 hours) on this 3.2-million-image dataset. Those efficiency gains immediately highlight the importance of using deep neural networks to automate data extraction from camera-trap images. Our results suggest that this technology could enable the inexpensive, unobtrusive, high-volume, and even real-time collection of a wealth of information about vast numbers of animals in the wild.

  • 7 authors
·
Mar 16, 2017

CAD2RL: Real Single-Image Flight without a Single Real Image

Deep reinforcement learning has emerged as a promising and powerful technique for automatically acquiring control policies that can process raw sensory inputs, such as images, and perform complex behaviors. However, extending deep RL to real-world robotic tasks has proven challenging, particularly in safety-critical domains such as autonomous flight, where a trial-and-error learning process is often impractical. In this paper, we explore the following question: can we train vision-based navigation policies entirely in simulation, and then transfer them into the real world to achieve real-world flight without a single real training image? We propose a learning method that we call CAD^2RL, which can be used to perform collision-free indoor flight in the real world while being trained entirely on 3D CAD models. Our method uses single RGB images from a monocular camera, without needing to explicitly reconstruct the 3D geometry of the environment or perform explicit motion planning. Our learned collision avoidance policy is represented by a deep convolutional neural network that directly processes raw monocular images and outputs velocity commands. This policy is trained entirely on simulated images, with a Monte Carlo policy evaluation algorithm that directly optimizes the network's ability to produce collision-free flight. By highly randomizing the rendering settings for our simulated training set, we show that we can train a policy that generalizes to the real world, without requiring the simulator to be particularly realistic or high-fidelity. We evaluate our method by flying a real quadrotor through indoor environments, and further evaluate the design choices in our simulator through a series of ablation studies on depth prediction. For supplementary video see: https://youtu.be/nXBWmzFrj5s

  • 2 authors
·
Nov 13, 2016

'Explaining RL Decisions with Trajectories': A Reproducibility Study

This work investigates the reproducibility of the paper 'Explaining RL decisions with trajectories'. The original paper introduces a novel approach in explainable reinforcement learning based on the attribution decisions of an agent to specific clusters of trajectories encountered during training. We verify the main claims from the paper, which state that (i) training on less trajectories induces a lower initial state value, (ii) trajectories in a cluster present similar high-level patterns, (iii) distant trajectories influence the decision of an agent, and (iv) humans correctly identify the attributed trajectories to the decision of the agent. We recover the environments used by the authors based on the partial original code they provided for one of the environments (Grid-World), and implemented the remaining from scratch (Seaquest, HalfCheetah, Breakout and Q*Bert). While we confirm that (i), (ii), and (iii) partially hold, we extend on the largely qualitative experiments from the authors by introducing a quantitative metric to further support (iii), and new experiments and visual results for (i). Moreover, we investigate the use of different clustering algorithms and encoder architectures to further support (ii). We could not support (iv), given the limited extent of the original experiments. We conclude that, while some of the claims can be supported, further investigations and experiments could be of interest. We recognise the novelty of the work from the authors and hope that our work paves the way for clearer and more transparent approaches.

  • 4 authors
·
Nov 11, 2024

SteloCoder: a Decoder-Only LLM for Multi-Language to Python Code Translation

With the recent focus on Large Language Models (LLMs), both StarCoder (Li et al., 2023) and Code Llama (Rozi\`ere et al., 2023) have demonstrated remarkable performance in code generation. However, there is still a need for improvement in code translation functionality with efficient training techniques. In response to this, we introduce SteloCoder, a decoder-only StarCoder-based LLM designed specifically for multi-programming language-to-Python code translation. In particular, SteloCoder achieves C++, C#, JavaScript, Java, or PHP-to-Python code translation without specifying the input programming language. We modified StarCoder model architecture by incorporating a Mixture-of-Experts (MoE) technique featuring five experts and a gating network for multi-task handling. Experts are obtained by StarCoder fine-tuning. Specifically, we use a Low-Rank Adaptive Method (LoRA) technique, limiting each expert size as only 0.06% of number of StarCoder's parameters. At the same time, to enhance training efficiency in terms of time, we adopt curriculum learning strategy and use self-instruct data for efficient fine-tuning. As a result, each expert takes only 6 hours to train on one single 80Gb A100 HBM. With experiments on XLCoST datasets, SteloCoder achieves an average of 73.76 CodeBLEU score in multi-programming language-to-Python translation, surpassing the top performance from the leaderboard by at least 3.5. This accomplishment is attributed to only 45M extra parameters with StarCoder as the backbone and 32 hours of valid training on one 80GB A100 HBM. The source code is release here: https://github.com/sade-adrien/SteloCoder.

  • 6 authors
·
Oct 24, 2023

Failing Forward: Improving Generative Error Correction for ASR with Synthetic Data and Retrieval Augmentation

Generative Error Correction (GEC) has emerged as a powerful post-processing method to enhance the performance of Automatic Speech Recognition (ASR) systems. However, we show that GEC models struggle to generalize beyond the specific types of errors encountered during training, limiting their ability to correct new, unseen errors at test time, particularly in out-of-domain (OOD) scenarios. This phenomenon amplifies with named entities (NEs), where, in addition to insufficient contextual information or knowledge about the NEs, novel NEs keep emerging. To address these issues, we propose DARAG (Data- and Retrieval-Augmented Generative Error Correction), a novel approach designed to improve GEC for ASR in in-domain (ID) and OOD scenarios. We augment the GEC training dataset with synthetic data generated by prompting LLMs and text-to-speech models, thereby simulating additional errors from which the model can learn. For OOD scenarios, we simulate test-time errors from new domains similarly and in an unsupervised fashion. Additionally, to better handle named entities, we introduce retrieval-augmented correction by augmenting the input with entities retrieved from a database. Our approach is simple, scalable, and both domain- and language-agnostic. We experiment on multiple datasets and settings, showing that DARAG outperforms all our baselines, achieving 8\% -- 30\% relative WER improvements in ID and 10\% -- 33\% improvements in OOD settings.

  • 7 authors
·
Oct 17, 2024 2

Feynman-Kac Correctors in Diffusion: Annealing, Guidance, and Product of Experts

While score-based generative models are the model of choice across diverse domains, there are limited tools available for controlling inference-time behavior in a principled manner, e.g. for composing multiple pretrained models. Existing classifier-free guidance methods use a simple heuristic to mix conditional and unconditional scores to approximately sample from conditional distributions. However, such methods do not approximate the intermediate distributions, necessitating additional 'corrector' steps. In this work, we provide an efficient and principled method for sampling from a sequence of annealed, geometric-averaged, or product distributions derived from pretrained score-based models. We derive a weighted simulation scheme which we call Feynman-Kac Correctors (FKCs) based on the celebrated Feynman-Kac formula by carefully accounting for terms in the appropriate partial differential equations (PDEs). To simulate these PDEs, we propose Sequential Monte Carlo (SMC) resampling algorithms that leverage inference-time scaling to improve sampling quality. We empirically demonstrate the utility of our methods by proposing amortized sampling via inference-time temperature annealing, improving multi-objective molecule generation using pretrained models, and improving classifier-free guidance for text-to-image generation. Our code is available at https://github.com/martaskrt/fkc-diffusion.

  • 9 authors
·
Mar 4, 2025 2

Re-imagine the Negative Prompt Algorithm: Transform 2D Diffusion into 3D, alleviate Janus problem and Beyond

Although text-to-image diffusion models have made significant strides in generating images from text, they are sometimes more inclined to generate images like the data on which the model was trained rather than the provided text. This limitation has hindered their usage in both 2D and 3D applications. To address this problem, we explored the use of negative prompts but found that the current implementation fails to produce desired results, particularly when there is an overlap between the main and negative prompts. To overcome this issue, we propose Perp-Neg, a new algorithm that leverages the geometrical properties of the score space to address the shortcomings of the current negative prompts algorithm. Perp-Neg does not require any training or fine-tuning of the model. Moreover, we experimentally demonstrate that Perp-Neg provides greater flexibility in generating images by enabling users to edit out unwanted concepts from the initially generated images in 2D cases. Furthermore, to extend the application of Perp-Neg to 3D, we conducted a thorough exploration of how Perp-Neg can be used in 2D to condition the diffusion model to generate desired views, rather than being biased toward the canonical views. Finally, we applied our 2D intuition to integrate Perp-Neg with the state-of-the-art text-to-3D (DreamFusion) method, effectively addressing its Janus (multi-head) problem. Our project page is available at https://Perp-Neg.github.io/

  • 5 authors
·
Apr 11, 2023

Site-Specific MIMO Channel Generation via Diffusion and Flow Matching: Fidelity, Efficiency, and Downstream Utility

This paper explores the use of generative models to synthesize high-quality, site-specific multiple-input multiple-output (MIMO) channel data, addressing the high cost of the extensive measurement campaigns required to acquire real-world data for AI-native wireless networks. Two location-conditioned generative paradigms are compared: a conditional denoising diffusion implicit model (cDDIM), and a conditional flow matching model (cFMM). Both these models generate MIMO channel matrices conditioned on user coordinates, to preserve the spatial structure of the deployment site. The approaches are evaluated across three dimensions: statistical fidelity (including beam consistency and effective rank), generation efficiency, and utility in downstream tasks such as channel-state information compression and beam alignment. Results across diverse propagation scenarios (28 GHz and 3.5 GHz, both line-of-sight and non-line-of-sight) demonstrate that both models accurately capture site-specific characteristics, even when trained on scarce ground-truth data. Notably, cFMM achieves a quality comparable to cDDIM with roughly an order of magnitude less inference time. Augmenting scarce site-specific datasets with these synthetic channels yields hefty performance gains in downstream physical layer tasks compared to using scarce data alone or stochastic channels.

  • 6 authors
·
Jun 17

Diffusion-based Frameworks for Unsupervised Speech Enhancement

This paper addresses unsupervised diffusion-based single-channel speech enhancement (SE). Prior work in this direction combines a score-based diffusion model trained on clean speech with a Gaussian noise model whose covariance is structured by non-negative matrix factorization (NMF). This combination is used within an iterative expectation-maximization (EM) scheme, in which a diffusion-based posterior-sampling E-step estimates the clean speech. We first revisit this framework and propose to explicitly model both speech and acoustic noise as latent variables, jointly sampling them in the E-step instead of sampling speech alone as in previous approaches. We then introduce a new unsupervised SE framework that replaces the NMF noise prior with a diffusion-based noise model, learned jointly with the speech prior in a single conditional score model. Within this framework, we derive two variants: one that implicitly accounts for noise and one that explicitly treats noise as a latent variable. Experiments on WSJ0-QUT and VoiceBank-DEMAND show that explicit noise modeling systematically improves SE performance for both NMF-based and diffusion-based noise priors. Under matched conditions, the diffusion-based noise model attains the best overall quality and intelligibility among unsupervised methods, while under mismatched conditions the proposed NMF-based explicit-noise framework is more robust and suffers less degradation than several supervised baselines.

  • 4 authors
·
Jan 29

Guardians of the Agentic System: Preventing Many Shots Jailbreak with Agentic System

The autonomous AI agents using large language models can create undeniable values in all span of the society but they face security threats from adversaries that warrants immediate protective solutions because trust and safety issues arise. Considering the many-shot jailbreaking and deceptive alignment as some of the main advanced attacks, that cannot be mitigated by the static guardrails used during the supervised training, points out a crucial research priority for real world robustness. The combination of static guardrails in dynamic multi-agent system fails to defend against those attacks. We intend to enhance security for LLM-based agents through the development of new evaluation frameworks which identify and counter threats for safe operational deployment. Our work uses three examination methods to detect rogue agents through a Reverse Turing Test and analyze deceptive alignment through multi-agent simulations and develops an anti-jailbreaking system by testing it with GEMINI 1.5 pro and llama-3.3-70B, deepseek r1 models using tool-mediated adversarial scenarios. The detection capabilities are strong such as 94\% accuracy for GEMINI 1.5 pro yet the system suffers persistent vulnerabilities when under long attacks as prompt length increases attack success rates (ASR) and diversity metrics become ineffective in prediction while revealing multiple complex system faults. The findings demonstrate the necessity of adopting flexible security systems based on active monitoring that can be performed by the agents themselves together with adaptable interventions by system admin as the current models can create vulnerabilities that can lead to the unreliable and vulnerable system. So, in our work, we try to address such situations and propose a comprehensive framework to counteract the security issues.

  • 6 authors
·
Feb 23, 2025 2

PyGen: A Collaborative Human-AI Approach to Python Package Creation

The principles of automation and innovation serve as foundational elements for advancement in contemporary science and technology. Here, we introduce Pygen, an automation platform designed to empower researchers, technologists, and hobbyists to bring abstract ideas to life as core, usable software tools written in Python. Pygen leverages the immense power of autoregressive large language models to augment human creativity during the ideation, iteration, and innovation process. By combining state-of-the-art language models with open-source code generation technologies, Pygen has significantly reduced the manual overhead of tool development. From a user prompt, Pygen automatically generates Python packages for a complete workflow from concept to package generation and documentation. The findings of our work show that Pygen considerably enhances the researcher's productivity by enabling the creation of resilient, modular, and well-documented packages for various specialized purposes. We employ a prompt enhancement approach to distill the user's package description into increasingly specific and actionable. While being inherently an open-ended task, we have evaluated the generated packages and the documentation using Human Evaluation, LLM-based evaluation, and CodeBLEU, with detailed results in the results section. Furthermore, we documented our results, analyzed the limitations, and suggested strategies to alleviate them. Pygen is our vision of ethical automation, a framework that promotes inclusivity, accessibility, and collaborative development. This project marks the beginning of a large-scale effort towards creating tools where intelligent agents collaborate with humans to improve scientific and technological development substantially. Our code and generated examples are open-sourced at [https://github.com/GitsSaikat/Pygen]

  • 6 authors
·
Nov 12, 2024

OrganLens: Organ-Specific Representation Learning for CT Foundation Models

A CT examination captures multiple organs, but many biomedical questions concern abnormalities, prognosis, or longitudinal change in a specific organ. These questions require a separate representation for each organ within the same CT volume. Existing CT foundation models commonly produce a single volume-level representation, while recent anatomy-aware methods either encode pre-separated organ volumes or explicitly disentangle images into organ token groups. The former may remove clinically relevant surrounding context, while the latter does not condition a shared encoder on a selected organ before its features are formed. We introduce OrganLens for organ-specific representation learning through self-supervision. An organ identity conditions a shared CT encoder, while organ-specific distillation and anatomy-mask supervision shape features for anatomy-weighted pooling into organ-specific representations. At inference, the shared model produces 11 organ-specific representations without external segmentation masks. We evaluate OrganLens on CT-RATE, RAD-ChestCT, INSPECT, and NLST across diverse acquisitions and downstream evaluations. Relative to CT-pretrained DINOv2, heart representations raise CT-RATE cardiomegaly AUROC from 0.910 to 0.953, while lung representations improve the Harrell C-index for NLST lung-cancer mortality by 14.2\%. The global representation reaches INSPECT Recall@10 of 33.09\% and 32.04\% for text-to-image and image-to-text retrieval, respectively. Across organ-related tasks, anatomically matched representations provide stronger task-relevant signal, while the global representation retains broad utility. OrganLens offers a scalable approach to organ-specific CT representation learning with a shared encoder. More broadly, it provides the medical research community with a reusable framework for studying organ-specific disease across cohorts and clinical endpoints.

  • 5 authors
·
Jul 27

Long-context Protein Language Model

Self-supervised training of language models (LMs) has seen great success for protein sequences in learning meaningful representations and for generative drug design. Most protein LMs are based on the Transformer architecture trained on individual proteins with short context lengths. Such protein LMs cannot extrapolate to longer proteins and protein complexes well. They also fail to account for the underlying biological mechanisms carried out by biomolecular interactions and dynamics i.e., proteins often interact with other proteins, molecules, and pathways in complex biological systems. In this work, we propose LC-PLM based on an alternative protein LM architecture, BiMamba-S, built off selective structured state-space models, to learn high-quality universal protein representations at the amino acid token level using masked language modeling. We also introduce its graph-contextual variant, LC-PLM-G, which contextualizes protein-protein interaction (PPI) graphs for a second stage of training. LC-PLM demonstrates favorable neural scaling laws, better length extrapolation capability, and a 7% to 34% improvement on protein downstream tasks than Transformer-based ESM-2. LC-PLM-G further trained within the context of PPI graphs shows promising results on protein structure and function prediction tasks. Our study demonstrates the benefit of increasing the context size with computationally efficient LM architecture (e.g. structured state space models) in learning universal protein representations and incorporating molecular interaction context contained in biological graphs.

  • 7 authors
·
Oct 29, 2024

On Calibration of Object Detectors: Pitfalls, Evaluation and Baselines

Reliable usage of object detectors require them to be calibrated -- a crucial problem that requires careful attention. Recent approaches towards this involve (1) designing new loss functions to obtain calibrated detectors by training them from scratch, and (2) post-hoc Temperature Scaling (TS) that learns to scale the likelihood of a trained detector to output calibrated predictions. These approaches are then evaluated based on a combination of Detection Expected Calibration Error (D-ECE) and Average Precision. In this work, via extensive analysis and insights, we highlight that these recent evaluation frameworks, evaluation metrics, and the use of TS have notable drawbacks leading to incorrect conclusions. As a step towards fixing these issues, we propose a principled evaluation framework to jointly measure calibration and accuracy of object detectors. We also tailor efficient and easy-to-use post-hoc calibration approaches such as Platt Scaling and Isotonic Regression specifically for object detection task. Contrary to the common notion, our experiments show that once designed and evaluated properly, post-hoc calibrators, which are extremely cheap to build and use, are much more powerful and effective than the recent train-time calibration methods. To illustrate, D-DETR with our post-hoc Isotonic Regression calibrator outperforms the recent train-time state-of-the-art calibration method Cal-DETR by more than 7 D-ECE on the COCO dataset. Additionally, we propose improved versions of the recently proposed Localization-aware ECE and show the efficacy of our method on these metrics as well. Code is available at: https://github.com/fiveai/detection_calibration.

  • 4 authors
·
May 30, 2024

Bidirectional Language Models Are Also Few-shot Learners

Large language models such as GPT-3 (Brown et al., 2020) can perform arbitrary tasks without undergoing fine-tuning after being prompted with only a few labeled examples. An arbitrary task can be reformulated as a natural language prompt, and a language model can be asked to generate the completion, indirectly performing the task in a paradigm known as prompt-based learning. To date, emergent prompt-based learning capabilities have mainly been demonstrated for unidirectional language models. However, bidirectional language models pre-trained on denoising objectives such as masked language modeling produce stronger learned representations for transfer learning. This motivates the possibility of prompting bidirectional models, but their pre-training objectives have made them largely incompatible with the existing prompting paradigm. We present SAP (Sequential Autoregressive Prompting), a technique that enables the prompting of bidirectional models. Utilizing the machine translation task as a case study, we prompt the bidirectional mT5 model (Xue et al., 2021) with SAP and demonstrate its few-shot and zero-shot translations outperform the few-shot translations of unidirectional models like GPT-3 and XGLM (Lin et al., 2021), despite mT5's approximately 50% fewer parameters. We further show SAP is effective on question answering and summarization. For the first time, our results demonstrate prompt-based learning is an emergent property of a broader class of language models, rather than only unidirectional models.

  • 6 authors
·
Sep 28, 2022