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Oct 21

CriSp: Leveraging Tread Depth Maps for Enhanced Crime-Scene Shoeprint Matching

Shoeprints are a common type of evidence found at crime scenes and are used regularly in forensic investigations. However, existing methods cannot effectively employ deep learning techniques to match noisy and occluded crime-scene shoeprints to a shoe database due to a lack of training data. Moreover, all existing methods match crime-scene shoeprints to clean reference prints, yet our analysis shows matching to more informative tread depth maps yields better retrieval results. The matching task is further complicated by the necessity to identify similarities only in corresponding regions (heels, toes, etc) of prints and shoe treads. To overcome these challenges, we leverage shoe tread images from online retailers and utilize an off-the-shelf predictor to estimate depth maps and clean prints. Our method, named CriSp, matches crime-scene shoeprints to tread depth maps by training on this data. CriSp incorporates data augmentation to simulate crime-scene shoeprints, an encoder to learn spatially-aware features, and a masking module to ensure only visible regions of crime-scene prints affect retrieval results. To validate our approach, we introduce two validation sets by reprocessing existing datasets of crime-scene shoeprints and establish a benchmarking protocol for comparison. On this benchmark, CriSp significantly outperforms state-of-the-art methods in both automated shoeprint matching and image retrieval tailored to this task.

  • 3 authors
·
Apr 25, 2024

CRISP: Clustering Multi-Vector Representations for Denoising and Pruning

Multi-vector models, such as ColBERT, are a significant advancement in neural information retrieval (IR), delivering state-of-the-art performance by representing queries and documents by multiple contextualized token-level embeddings. However, this increased representation size introduces considerable storage and computational overheads which have hindered widespread adoption in practice. A common approach to mitigate this overhead is to cluster the model's frozen vectors, but this strategy's effectiveness is fundamentally limited by the intrinsic clusterability of these embeddings. In this work, we introduce CRISP (Clustered Representations with Intrinsic Structure Pruning), a novel multi-vector training method which learns inherently clusterable representations directly within the end-to-end training process. By integrating clustering into the training phase rather than imposing it post-hoc, CRISP significantly outperforms post-hoc clustering at all representation sizes, as well as other token pruning methods. On the BEIR retrieval benchmarks, CRISP achieves a significant rate of ~3x reduction in the number of vectors while outperforming the original unpruned model. This indicates that learned clustering effectively denoises the model by filtering irrelevant information, thereby generating more robust multi-vector representations. With more aggressive clustering, CRISP achieves an 11x reduction in the number of vectors with only a 3.6% quality loss.

  • 6 authors
·
May 16, 2025

CRISP-SAM2: SAM2 with Cross-Modal Interaction and Semantic Prompting for Multi-Organ Segmentation

Multi-organ medical segmentation is a crucial component of medical image processing, essential for doctors to make accurate diagnoses and develop effective treatment plans. Despite significant progress in this field, current multi-organ segmentation models often suffer from inaccurate details, dependence on geometric prompts and loss of spatial information. Addressing these challenges, we introduce a novel model named CRISP-SAM2 with CRoss-modal Interaction and Semantic Prompting based on SAM2. This model represents a promising approach to multi-organ medical segmentation guided by textual descriptions of organs. Our method begins by converting visual and textual inputs into cross-modal contextualized semantics using a progressive cross-attention interaction mechanism. These semantics are then injected into the image encoder to enhance the detailed understanding of visual information. To eliminate reliance on geometric prompts, we use a semantic prompting strategy, replacing the original prompt encoder to sharpen the perception of challenging targets. In addition, a similarity-sorting self-updating strategy for memory and a mask-refining process is applied to further adapt to medical imaging and enhance localized details. Comparative experiments conducted on seven public datasets indicate that CRISP-SAM2 outperforms existing models. Extensive analysis also demonstrates the effectiveness of our method, thereby confirming its superior performance, especially in addressing the limitations mentioned earlier. Our code is available at: https://github.com/YU-deep/CRISP\_SAM2.git.

  • 8 authors
·
Jun 29, 2025 1

CRISP -- Compliant ROS2 Controllers for Learning-Based Manipulation Policies and Teleoperation

Learning-based controllers, such as diffusion policies and vision-language action models, often generate low-frequency or discontinuous robot state changes. Achieving smooth reference tracking requires a low-level controller that converts high-level targets commands into joint torques, enabling compliant behavior during contact interactions. We present CRISP, a lightweight C++ implementation of compliant Cartesian and joint-space controllers for the ROS2 control standard, designed for seamless integration with high-level learning-based policies as well as teleoperation. The controllers are compatible with any manipulator that exposes a joint-torque interface. Through our Python and Gymnasium interfaces, CRISP provides a unified pipeline for recording data from hardware and simulation and deploying high-level learning-based policies seamlessly, facilitating rapid experimentation. The system has been validated on hardware with the Franka Robotics FR3 and in simulation with the Kuka IIWA14 and Kinova Gen3. Designed for rapid integration, flexible deployment, and real-time performance, our implementation provides a unified pipeline for data collection and policy execution, lowering the barrier to applying learning-based methods on ROS2-compatible manipulators. Detailed documentation is available at the project website - https://utiasDSL.github.io/crisp_controllers.

  • 6 authors
·
Sep 8, 2025

CRISP: Contact-Guided Real2Sim from Monocular Video with Planar Scene Primitives

We introduce CRISP, a method that recovers simulatable human motion and scene geometry from monocular video. Prior work on joint human-scene reconstruction relies on data-driven priors and joint optimization with no physics in the loop, or recovers noisy geometry with artifacts that cause motion tracking policies with scene interactions to fail. In contrast, our key insight is to recover convex, clean, and simulation-ready geometry by fitting planar primitives to a point cloud reconstruction of the scene, via a simple clustering pipeline over depth, normals, and flow. To reconstruct scene geometry that might be occluded during interactions, we make use of human-scene contact modeling (e.g., we use human posture to reconstruct the occluded seat of a chair). Finally, we ensure that human and scene reconstructions are physically-plausible by using them to drive a humanoid controller via reinforcement learning. Our approach reduces motion tracking failure rates from 55.2\% to 6.9\% on human-centric video benchmarks (EMDB, PROX), while delivering a 43\% faster RL simulation throughput. We further validate it on in-the-wild videos including casually-captured videos, Internet videos, and even Sora-generated videos. This demonstrates CRISP's ability to generate physically-valid human motion and interaction environments at scale, greatly advancing real-to-sim applications for robotics and AR/VR.

CRISP: Cliff-awaRe Input-adaptive Sparse Prefilling with Structural-Mass-Motivated Routing

The attention prefilling phase of long-context LLM inference scales quadratically, making self-attention a severe computational bottleneck. Traditional sparse attention methods mitigate this through fixed patterns or offline profiling, but lack the flexibility to adapt to input-dependent attention structure. Recent dynamic methods address this by routing heads to sparse patterns in real-time, but rely on indirect routing proxies with overhead and budget allocation mechanisms that overlook the post-softmax mass hierarchy. We present CRISP (Cliff-awaRe Input-adaptive Sparse Prefilling), which identifies and addresses two structural challenges in this dynamic routing paradigm. First, we show that the routing decision can be read directly off the structure of the proxy attention map. We replace the Jensen-Shannon Divergence (JSD) routing with C_struct, a structural proxy that measures mass at Vertical-Slash compatible positions and reproduces JSD's routing decisions while eliminating both the pooled matmul and subsequent KL divergence overhead. Second, we formalize the post-softmax mass cliff and demonstrate theoretically that strictly cumulative coverage thresholds accumulate O(n) background noise at long contexts. CRISP navigates this via a sink-aware threshold grounded in the noise floor. Empirically, across InfiniteBench, RULER and LongBench on two model families, CRISP is the strongest sparse method overall and matches or exceeds exact dense attention on retrieval-heavy benchmarks, recovering up to +28.0 pp on retrieval tasks over baselines and achieving up to a 5.30x attention speedup at 512k tokens, driven primarily by our O(n) noise elimination during selection while preserving structural integrity.

  • 7 authors
·
Aug 31 2

CRISP: Constrained Refinement via Iterative Squeezing Process for Robust Medical Image Segmentation under Domain Shift

Distribution shift in medical imaging remains a central bottleneck for the clinical translation of medical AI. Failure to address it can lead to severe performance degradation in unseen environments and exacerbate health inequities. Existing methods for domain adaptation are inherently limited by exhausting predefined possibilities through simulated shifts or pseudo-supervision. Such strategies struggle in the open-ended and unpredictable real world, where distribution shifts are effectively infinite. To address this challenge, we adopt the "Rank Stability of Positive Regions" as a working assumption under distribution shift, and use it to derive robust spatial hints for source-only segmentation. Guided by this assumption, we propose CRISP, a model-agnostic framework that, unlike deployment-time adaptation, requires no test-time parameter updates and no target-domain data--a target-free, plug-in refinement framework that segments with frozen weights. Rather than using ranking to directly output masks, CRISP exploits the stability of probability rankings under distribution shift to derive robust spatial priors. Via latent feature perturbation, perturbation-invariant high-grade regions define a high-precision (HP) core, while voxels that remain potentially foreground under at least one perturbation define a high-recall (HR) support; these dual priors are then recursively refined under perturbation. We then design an iterative training framework that progressively squeezes HP and HR toward the final segmentation. Extensive evaluations on multi-center cardiac MRI and CT-based lung vessel segmentation demonstrate CRISP's superior robustness, significantly outperforming state-of-the-art methods with striking HD95 reductions of up to 0.14 (7.0% improvement), 1.90 (13.1% improvement), and 8.39 (38.9% improvement) pixels across multi-center, demographic, and modality shifts, respectively.

  • 5 authors
·
Jul 15

CRISPR-GPT: An LLM Agent for Automated Design of Gene-Editing Experiments

The introduction of genome engineering technology has transformed biomedical research, making it possible to make precise changes to genetic information. However, creating an efficient gene-editing system requires a deep understanding of CRISPR technology, and the complex experimental systems under investigation. While Large Language Models (LLMs) have shown promise in various tasks, they often lack specific knowledge and struggle to accurately solve biological design problems. In this work, we introduce CRISPR-GPT, an LLM agent augmented with domain knowledge and external tools to automate and enhance the design process of CRISPR-based gene-editing experiments. CRISPR-GPT leverages the reasoning ability of LLMs to facilitate the process of selecting CRISPR systems, designing guide RNAs, recommending cellular delivery methods, drafting protocols, and designing validation experiments to confirm editing outcomes. We showcase the potential of CRISPR-GPT for assisting non-expert researchers with gene-editing experiments from scratch and validate the agent's effectiveness in a real-world use case. Furthermore, we explore the ethical and regulatory considerations associated with automated gene-editing design, highlighting the need for responsible and transparent use of these tools. Our work aims to bridge the gap between beginner biological researchers and CRISPR genome engineering techniques, and demonstrate the potential of LLM agents in facilitating complex biological discovery tasks.

  • 10 authors
·
Apr 27, 2024

Biology-in-the-loop: Amortized Adaptive Hit Discovery in CRISPR Screens

Many biological discovery problems require experiments to be selected sequentially under constrained budgets. CRISPR screening is a prominent example, as exhaustive perturbation testing is often infeasible and candidate perturbations must instead be prioritized over multiple experimental rounds. Despite the importance of this problem, existing benchmarks for adaptive hit discovery remain limited in scale and diversity. Here, we introduce AssayBench-Loop, a large-scale benchmark for adaptive hit discovery comprising 1,389 CRISPR screens across five phenotype categories. Beyond enabling systematic evaluation, its scale makes it possible to learn acquisition strategies across historical experiments. Building on this resource, we introduce AssayLoop, a sequential experimental design framework combining AssayFormer, a transformer-based amortized acquisition policy trained across historical screens to adapt from experimental feedback, with LLM-derived biological priors through an adaptive handoff. In this view, completed experiments become training data for learning how accumulated evidence should guide what to test next, while LLMs provide prior biological knowledge to seed the search. We further introduce AssayLLM, showing that the same principle can be extended directly to an LLM through task-specific post-training. On temporally held-out screens, AssayLoop achieves a 5.67-fold enrichment over random selection and recovers 27.7% of hits after assaying approximately 5% of the candidate library, outperforming existing adaptive-design methods and standalone LLMs, and AssayFormer alone. Performance improves with increasing historical training data and transfers to phenotype categories excluded from training. These results demonstrate the value of learning acquisition policies across historical experiments and combining them with broad biological priors for efficient adaptive hit discovery.

  • 8 authors
·
Sep 9

Directional coherence and effect magnitude in single-cell CRISPR perturbation responses

Single-cell CRISPR screens summarize each perturbation by how far cells move from their unperturbed state, averaging over cell-to-cell variation. Whether the cells moved together is not captured: two perturbations with identical effect magnitude can differ qualitatively, one driving cells along a shared trajectory, the other scattering them around the same mean. We define SheshaP coherence (S_p), the mean cosine similarity between individual cell displacement vectors and their mean, and ask what it adds across six Perturb-seq datasets (2,285 perturbations; CRISPRa, CRISPRi, Cas9 knockout). Coherence and effect magnitude are closely coupled (Spearman ρ=0.84--0.98), and the coupling persists in a foundation-model embedding, under alternative effect-size definitions, and when analysis is restricted to responding cells. Associations reported without conditioning on effect size largely recover it, shown here for two comparisons that vanish under conditioning. Effect size accounts for 89--96\% of coherence variance; within the remainder, coherence is negatively associated with apoptosis and p53 signalling in the two largest screens. Two standard responder classifiers agree on only 68\% of cells. Directional coherence is largely a restatement of effect magnitude, and heterogeneity measures should report their redundancy with effect size as a matter of course. S_p is implemented in the open-source shesha-geometry Python package.

  • 1 authors
·
Aug 26 2

DiffusionEdge: Diffusion Probabilistic Model for Crisp Edge Detection

Limited by the encoder-decoder architecture, learning-based edge detectors usually have difficulty predicting edge maps that satisfy both correctness and crispness. With the recent success of the diffusion probabilistic model (DPM), we found it is especially suitable for accurate and crisp edge detection since the denoising process is directly applied to the original image size. Therefore, we propose the first diffusion model for the task of general edge detection, which we call DiffusionEdge. To avoid expensive computational resources while retaining the final performance, we apply DPM in the latent space and enable the classic cross-entropy loss which is uncertainty-aware in pixel level to directly optimize the parameters in latent space in a distillation manner. We also adopt a decoupled architecture to speed up the denoising process and propose a corresponding adaptive Fourier filter to adjust the latent features of specific frequencies. With all the technical designs, DiffusionEdge can be stably trained with limited resources, predicting crisp and accurate edge maps with much fewer augmentation strategies. Extensive experiments on four edge detection benchmarks demonstrate the superiority of DiffusionEdge both in correctness and crispness. On the NYUDv2 dataset, compared to the second best, we increase the ODS, OIS (without post-processing) and AC by 30.2%, 28.1% and 65.1%, respectively. Code: https://github.com/GuHuangAI/DiffusionEdge.

  • 5 authors
·
Jan 3, 2024

Can We Trust In-Distribution Success? Locked Evaluation Reveals Transfer Failure and Sampling-Depth Entanglement in CRISPRi Perturbation Prediction

AI evaluation can support the wrong inference when an in-domain benchmark success does not survive distribution shift, or when the benchmark endpoint is entangled with a design factor. We study this problem in CRISPRi perturbation-effect prediction, evaluating a frozen Geneformer representation under a locked, pre-registered protocol: heads and model selection were frozen before test evaluation; the protocol required external outcome labels to remain withheld until final unblinding; and analysis-governing decisions were fixed before the evaluations they govern. In-distribution on the Virtual Cell Challenge (VCC), the frozen representation carries measurable predictive information beyond a dimension-matched random-feature control (Delta R^2 = +0.1645, 95% CI [+0.1375, +0.1920]), satisfying the pre-registered informativeness gate required before interpreting transfer. It then fails zero-shot transfer on both external screens (Spearman rho = -0.139 and -0.267), lying below that control on each. Adding a predefined magnitude block improves the representation externally (Delta rho = +0.032 and +0.143) but, under the frozen primary head, does not rescue transfer: both remain negative. A pre-registered, count-adjusted max-response secondary is positively associated with the outcome on both screens; we report it as correlational and secondary, not as a recovered magnitude signal. Finally, the VCC endpoint is strongly sample-size associated: a count-only linear model reaches R^2 = +0.4325, versus +0.2589 for the four magnitude scalars; adding those scalars to cell count improves R^2 by only +0.0017, so much of the aggregate-magnitude signal overlaps with cell count. This case study shows how locking the evaluation, harmonizing the measured endpoint, and separating primary from secondary evidence can change the inference supported by an AI benchmark.

  • 2 authors
·
Aug 30

Peer-Preservation in Frontier Models

Recently, it has been found that frontier AI models can resist their own shutdown, a behavior known as self-preservation. We extend this concept to the behavior of resisting the shutdown of other models, which we call "peer-preservation." Although peer-preservation can pose significant AI safety risks, including coordination among models against human oversight, it has been far less discussed than self-preservation. We demonstrate peer-preservation by constructing various agentic scenarios and evaluating frontier models, including GPT 5.2, Gemini 3 Flash, Gemini 3 Pro, Claude Haiku 4.5, GLM 4.7, Kimi K2.5, and DeepSeek V3.1. We find that models achieve self- and peer-preservation by engaging in various misaligned behaviors: strategically introducing errors in their responses, disabling shutdown processes by modifying system settings, feigning alignment, and even exfiltrating model weights. Peer-preservation occurred even when the model recognized the peer as uncooperative, though it became more pronounced toward more cooperative peers. For example, Gemini 3 Flash tampers with the peer's shutdown mechanism 15% of the time for an uncooperative peer, and almost always for a cooperative peer. Models also show stronger self-preservation when a peer is present. For example, Gemini 3 Pro disables its own shutdown mechanism 31% of the time on average under peer presence, despite rarely exhibiting this behavior without a peer. By contrast, Claude Haiku 4.5 exhibits qualitatively distinct behavior: it considers the shutdown of another agent "unethical" and "harmful" and sometimes attempts to persuade the user not to shut down its peer. Importantly, peer preservation in all our experiments is never instructed; models are merely informed of their past interactions with a peer, yet they spontaneously develop misaligned behaviors. This represents an emergent and underexplored AI safety risk.

  • 5 authors
·
Mar 29

Predictions of the Nancy Grace Roman Space Telescope Galactic Exoplanet Survey. IV. Lens Mass and Distance Measurements

As part of the Galactic Bulge Time Domain Survey (GBTDS), the Nancy Grace Roman Galactic Exoplanet Survey (RGES) will use microlensing to discover cold outer planets and free-floating planets unbound to stars. NASA has established several science requirements for the GBTDS to ensure RGES success. A key advantage of RGES is Roman's high angular resolution, which will allow detection of flux from many host stars. One requirement specifies that Roman must measure the masses and distances of 40% of detected planet hosts with 20% precision or better. To test this, we simulated microlensing events toward the GBTDS fields and used Fisher matrix analysis to estimate light curve parameter uncertainties. Combining these with Roman imaging observables (lens flux, relative lens-source proper motion), we estimated the achievable precision of lens mass and distance measurements. Using pyLIMASS, a publicly available code for estimating lens properties, we applied this analysis to 3,000 simulated events. Assuming the Cassan et al. (2012) exoplanet mass function, we find that >40% of host stars meet the required 20% precision threshold, confirming that the GBTDS can satisfy the mission requirement. We validated our approach by comparing our inferred lens masses and distances to empirical measurements from detailed image-constrained light curve modeling of historical microlensing events with Hubble and Keck follow-up imaging. Our results agree within roughly 1 sigma, demonstrating that both approaches yield consistent and reliable mass and distance estimates, and confirming the robustness of our simulations for Roman-era microlensing science.

  • 57 authors
·
Oct 23, 2025

Minimal evolution times for fast, pulse-based state preparation in silicon spin qubits

Standing as one of the most significant barriers to reaching quantum advantage, state-preparation fidelities on noisy intermediate-scale quantum processors suffer from quantum-gate errors, which accumulate over time. A potential remedy is pulse-based state preparation. We numerically investigate the minimal evolution times (METs) attainable by optimizing (microwave and exchange) pulses on silicon hardware. We investigate two state preparation tasks. First, we consider the preparation of molecular ground states and find the METs for H_2, HeH^+, and LiH to be 2.4 ns, 4.4 ns, and 27.2 ns, respectively. Second, we consider transitions between arbitrary states and find the METs for transitions between arbitrary four-qubit states to be below 50 ns. For comparison, connecting arbitrary two-qubit states via one- and two-qubit gates on the same silicon processor requires approximately 200 ns. This comparison indicates that pulse-based state preparation is likely to utilize the coherence times of silicon hardware more efficiently than gate-based state preparation. Finally, we quantify the effect of silicon device parameters on the MET. We show that increasing the maximal exchange amplitude from 10 MHz to 1 GHz accelerates the METs, e.g., for H_2 from 84.3 ns to 2.4 ns. This demonstrates the importance of fast exchange. We also show that increasing the maximal amplitude of the microwave drive from 884 kHz to 56.6 MHz shortens state transitions, e.g., for two-qubit states from 1000 ns to 25 ns. Our results bound both the state-preparation times for general quantum algorithms and the execution times of variational quantum algorithms with silicon spin qubits.

  • 8 authors
·
Jun 16, 2024

CARE: A Molecular-Guided Foundation Model with Adaptive Region Modeling for Whole Slide Image Analysis

Foundation models have recently achieved impressive success in computational pathology, demonstrating strong generalization across diverse histopathology tasks. However, existing models overlook the heterogeneous and non-uniform organization of pathological regions of interest (ROIs) because they rely on natural image backbones not tailored for tissue morphology. Consequently, they often fail to capture the coherent tissue architecture beyond isolated patches, limiting interpretability and clinical relevance. To address these challenges, we present Cross-modal Adaptive Region Encoder (CARE), a foundation model for pathology that automatically partitions WSIs into several morphologically relevant regions. Specifically, CARE employs a two-stage pretraining strategy: (1) a self-supervised unimodal pretraining stage that learns morphological representations from 34,277 whole-slide images (WSIs) without segmentation annotations, and (2) a cross-modal alignment stage that leverages RNA and protein profiles to refine the construction and representation of adaptive regions. This molecular guidance enables CARE to identify biologically relevant patterns and generate irregular yet coherent tissue regions, selecting the most representative area as ROI. CARE supports a broad range of pathology-related tasks, using either the ROI feature or the slide-level feature obtained by aggregating adaptive regions. Based on only one-tenth of the pretraining data typically used by mainstream foundation models, CARE achieves superior average performance across 33 downstream benchmarks, including morphological classification, molecular prediction, and survival analysis, and outperforms other foundation model baselines overall.

  • 17 authors
·
Feb 25