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Dec 8

Quantifying Language Models' Sensitivity to Spurious Features in Prompt Design or: How I learned to start worrying about prompt formatting

As large language models (LLMs) are adopted as a fundamental component of language technologies, it is crucial to accurately characterize their performance. Because choices in prompt design can strongly influence model behavior, this design process is critical in effectively using any modern pre-trained generative language model. In this work, we focus on LLM sensitivity to a quintessential class of meaning-preserving design choices: prompt formatting. We find that several widely used open-source LLMs are extremely sensitive to subtle changes in prompt formatting in few-shot settings, with performance differences of up to 76 accuracy points when evaluated using LLaMA-2-13B. Sensitivity remains even when increasing model size, the number of few-shot examples, or performing instruction tuning. Our analysis suggests that work evaluating LLMs with prompting-based methods would benefit from reporting a range of performance across plausible prompt formats, instead of the currently-standard practice of reporting performance on a single format. We also show that format performance only weakly correlates between models, which puts into question the methodological validity of comparing models with an arbitrarily chosen, fixed prompt format. To facilitate systematic analysis we propose FormatSpread, an algorithm that rapidly evaluates a sampled set of plausible prompt formats for a given task, and reports the interval of expected performance without accessing model weights. Furthermore, we present a suite of analyses that characterize the nature of this sensitivity, including exploring the influence of particular atomic perturbations and the internal representation of particular formats.

  • 4 authors
·
Oct 17, 2023

Sensitivity-Aware Visual Parameter-Efficient Fine-Tuning

Visual Parameter-Efficient Fine-Tuning (PEFT) has become a powerful alternative for full fine-tuning so as to adapt pre-trained vision models to downstream tasks, which only tunes a small number of parameters while freezing the vast majority ones to ease storage burden and optimization difficulty. However, existing PEFT methods introduce trainable parameters to the same positions across different tasks depending solely on human heuristics and neglect the domain gaps. To this end, we study where to introduce and how to allocate trainable parameters by proposing a novel Sensitivity-aware visual Parameter-efficient fine-Tuning (SPT) scheme, which adaptively allocates trainable parameters to task-specific important positions given a desired tunable parameter budget. Specifically, our SPT first quickly identifies the sensitive parameters that require tuning for a given task in a data-dependent way. Next, our SPT further boosts the representational capability for the weight matrices whose number of sensitive parameters exceeds a pre-defined threshold by utilizing existing structured tuning methods, e.g., LoRA [23] or Adapter [22], to replace directly tuning the selected sensitive parameters (unstructured tuning) under the budget. Extensive experiments on a wide range of downstream recognition tasks show that our SPT is complementary to the existing PEFT methods and largely boosts their performance, e.g., SPT improves Adapter with supervised pre-trained ViT-B/16 backbone by 4.2% and 1.4% mean Top-1 accuracy, reaching SOTA performance on FGVC and VTAB-1k benchmarks, respectively. Source code is at https://github.com/ziplab/SPT

  • 5 authors
·
Mar 15, 2023

Analytical sensitivity curves of the second-generation time-delay interferometry

Forthcoming space-based gravitational-wave (GW) detectors will employ second-generation time-delay interferometry (TDI) to suppress laser frequency noise and achieve the sensitivity required for GW detection. We introduce an inverse light-path operator P_{i_{1}i_{2}i_{3}ldots i_{n-1}i_{n}}, which enables simple representation of second-generation TDI combinations and a concise description of light propagation. Analytical expressions and high-accuracy approximate formulas are derived for the sky- and polarization-averaged response functions, noise power spectral densities (PSDs), and sensitivity curves of TDI Michelson, (alpha,beta,gamma), Monitor, Beacon, Relay, and Sagnac combinations, as well as their orthogonal A, E, T channels. Our results show that: (i) second-generation TDIs have the same sensitivities as their first-generation counterparts; (ii) the A, E, T sensitivities and the optimal sensitivity are independent of the TDI generation and specific combination; (iii) the A and E channels have equal averaged responses, noise PSDs, and sensitivities, while the T channel has much weaker response and sensitivity at low frequencies (2pi fL/clesssim3); (iv) except for the (alpha,beta,gamma) and zeta combinations and the T channel, all sensitivity curves exhibit a flat section in the range f_{n}<flesssim 1.5/(2pi L/c), where the noise-balance frequency f_{n} separates the proof-mass- and optical-path-dominated regimes, while the response-transition frequency sim 1.5/(2pi L/c) separates the response function's low- and high-frequency behaviors; (v) the averaged response, noise PSD, and sensitivity of zeta scales with those of the T channel. These analytical and approximate formulations provide useful benchmarks for instrument optimization and data-analysis studies for future space-based GW detectors.

  • 1 authors
·
Nov 3

Sharper Bounds for $\ell_p$ Sensitivity Sampling

In large scale machine learning, random sampling is a popular way to approximate datasets by a small representative subset of examples. In particular, sensitivity sampling is an intensely studied technique which provides provable guarantees on the quality of approximation, while reducing the number of examples to the product of the VC dimension d and the total sensitivity mathfrak S in remarkably general settings. However, guarantees going beyond this general bound of mathfrak S d are known in perhaps only one setting, for ell_2 subspace embeddings, despite intense study of sensitivity sampling in prior work. In this work, we show the first bounds for sensitivity sampling for ell_p subspace embeddings for pneq 2 that improve over the general mathfrak S d bound, achieving a bound of roughly mathfrak S^{2/p} for 1leq p<2 and mathfrak S^{2-2/p} for 2<p<infty. For 1leq p<2, we show that this bound is tight, in the sense that there exist matrices for which mathfrak S^{2/p} samples is necessary. Furthermore, our techniques yield further new results in the study of sampling algorithms, showing that the root leverage score sampling algorithm achieves a bound of roughly d for 1leq p<2, and that a combination of leverage score and sensitivity sampling achieves an improved bound of roughly d^{2/p}mathfrak S^{2-4/p} for 2<p<infty. Our sensitivity sampling results yield the best known sample complexity for a wide class of structured matrices that have small ell_p sensitivity.

  • 2 authors
·
Jun 1, 2023

Controllable Context Sensitivity and the Knob Behind It

When making predictions, a language model must trade off how much it relies on its context vs. its prior knowledge. Choosing how sensitive the model is to its context is a fundamental functionality, as it enables the model to excel at tasks like retrieval-augmented generation and question-answering. In this paper, we search for a knob which controls this sensitivity, determining whether language models answer from the context or their prior knowledge. To guide this search, we design a task for controllable context sensitivity. In this task, we first feed the model a context (Paris is in England) and a question (Where is Paris?); we then instruct the model to either use its prior or contextual knowledge and evaluate whether it generates the correct answer for both intents (either France or England). When fine-tuned on this task, instruction-tuned versions of Llama-3.1, Mistral-v0.3, and Gemma-2 can solve it with high accuracy (85-95%). Analyzing these high-performing models, we narrow down which layers may be important to context sensitivity using a novel linear time algorithm. Then, in each model, we identify a 1-D subspace in a single layer that encodes whether the model follows context or prior knowledge. Interestingly, while we identify this subspace in a fine-tuned model, we find that the exact same subspace serves as an effective knob in not only that model but also non-fine-tuned instruct and base models of that model family. Finally, we show a strong correlation between a model's performance and how distinctly it separates context-agreeing from context-ignoring answers in this subspace. These results suggest a single subspace facilitates how the model chooses between context and prior knowledge, hinting at a simple fundamental mechanism that controls this behavior.

  • 7 authors
·
Nov 11, 2024

Assessing the Sensitivity and Alignment of FOL Closeness Metrics

The recent successful paradigm of solving logical reasoning problems with tool-augmented large language models (LLMs) leverages translation of natural language (NL) statements into First-Order Logic~(FOL) and external theorem provers. However, the correctness of FOL statements, comprising operators and text, often go unverified due to the lack of a reliable evaluation metric for comparing generated and ground-truth FOLs. In this paper, we conduct a comprehensive study on the sensitivity of existing NL-, FOL-, and graph-based metrics to capture differences between a sampled FOL and its corresponding ground-truth. We then measure the alignment between a metric-based ranking of FOL outputs and a strong LLM as-a-judge. To do this, we first apply operator and text-based perturbations to ground-truth FOL statements to assess metric sensitivity. We then evaluate metric robustness by comparing the metrics against LLMs judgment. Our empirical findings highlight a clear oversensitivity in the n-gram metric BLEU for text perturbations. The operator perturbation affects the semantic graph metric Smatch++ for structural changes, and the FOL metric for specific operator changes. We observe a closer alignment between BertScore and LLM judgement, proving the importance of semantic evaluation. Additionally, we show that combining metrics enhances both robustness and sensitivity compared to using individual metrics.

  • 3 authors
·
Jan 15

Mask of truth: model sensitivity to unexpected regions of medical images

The development of larger models for medical image analysis has led to increased performance. However, it also affected our ability to explain and validate model decisions. Models can use non-relevant parts of images, also called spurious correlations or shortcuts, to obtain high performance on benchmark datasets but fail in real-world scenarios. In this work, we challenge the capacity of convolutional neural networks (CNN) to classify chest X-rays and eye fundus images while masking out clinically relevant parts of the image. We show that all models trained on the PadChest dataset, irrespective of the masking strategy, are able to obtain an Area Under the Curve (AUC) above random. Moreover, the models trained on full images obtain good performance on images without the region of interest (ROI), even superior to the one obtained on images only containing the ROI. We also reveal a possible spurious correlation in the Chaksu dataset while the performances are more aligned with the expectation of an unbiased model. We go beyond the performance analysis with the usage of the explainability method SHAP and the analysis of embeddings. We asked a radiology resident to interpret chest X-rays under different masking to complement our findings with clinical knowledge. Our code is available at https://github.com/TheoSourget/MMC_Masking and https://github.com/TheoSourget/MMC_Masking_EyeFundus

  • 5 authors
·
Dec 5, 2024

POSIX: A Prompt Sensitivity Index For Large Language Models

Despite their remarkable capabilities, Large Language Models (LLMs) are found to be surprisingly sensitive to minor variations in prompts, often generating significantly divergent outputs in response to minor variations in the prompts, such as spelling errors, alteration of wording or the prompt template. However, while assessing the quality of an LLM, the focus often tends to be solely on its performance on downstream tasks, while very little to no attention is paid to prompt sensitivity. To fill this gap, we propose POSIX - a novel PrOmpt Sensitivity IndeX as a reliable measure of prompt sensitivity, thereby offering a more comprehensive evaluation of LLM performance. The key idea behind POSIX is to capture the relative change in loglikelihood of a given response upon replacing the corresponding prompt with a different intent-preserving prompt. We provide thorough empirical evidence demonstrating the efficacy of POSIX in capturing prompt sensitivity and subsequently use it to measure and thereby compare prompt sensitivity of various open-source LLMs. We find that merely increasing the parameter count or instruction tuning does not necessarily reduce prompt sensitivity whereas adding some few-shot exemplars, even just one, almost always leads to significant decrease in prompt sensitivity. We also find that alterations to prompt template lead to the highest sensitivity in the case of MCQ type tasks, whereas paraphrasing results in the highest sensitivity in open-ended generation tasks. The code for reproducing our results is open-sourced at https://github.com/kowndinya-renduchintala/POSIX.

  • 4 authors
·
Oct 3, 2024

Quantifying the Sensitivity of Inverse Reinforcement Learning to Misspecification

Inverse reinforcement learning (IRL) aims to infer an agent's preferences (represented as a reward function R) from their behaviour (represented as a policy pi). To do this, we need a behavioural model of how pi relates to R. In the current literature, the most common behavioural models are optimality, Boltzmann-rationality, and causal entropy maximisation. However, the true relationship between a human's preferences and their behaviour is much more complex than any of these behavioural models. This means that the behavioural models are misspecified, which raises the concern that they may lead to systematic errors if applied to real data. In this paper, we analyse how sensitive the IRL problem is to misspecification of the behavioural model. Specifically, we provide necessary and sufficient conditions that completely characterise how the observed data may differ from the assumed behavioural model without incurring an error above a given threshold. In addition to this, we also characterise the conditions under which a behavioural model is robust to small perturbations of the observed policy, and we analyse how robust many behavioural models are to misspecification of their parameter values (such as e.g.\ the discount rate). Our analysis suggests that the IRL problem is highly sensitive to misspecification, in the sense that very mild misspecification can lead to very large errors in the inferred reward function.

  • 2 authors
·
Mar 11, 2024

AdjointDPM: Adjoint Sensitivity Method for Gradient Backpropagation of Diffusion Probabilistic Models

Existing customization methods require access to multiple reference examples to align pre-trained diffusion probabilistic models (DPMs) with user-provided concepts. This paper aims to address the challenge of DPM customization when the only available supervision is a differentiable metric defined on the generated contents. Since the sampling procedure of DPMs involves recursive calls to the denoising UNet, na\"ive gradient backpropagation requires storing the intermediate states of all iterations, resulting in extremely high memory consumption. To overcome this issue, we propose a novel method AdjointDPM, which first generates new samples from diffusion models by solving the corresponding probability-flow ODEs. It then uses the adjoint sensitivity method to backpropagate the gradients of the loss to the models' parameters (including conditioning signals, network weights, and initial noises) by solving another augmented ODE. To reduce numerical errors in both the forward generation and gradient backpropagation processes, we further reparameterize the probability-flow ODE and augmented ODE as simple non-stiff ODEs using exponential integration. Finally, we demonstrate the effectiveness of AdjointDPM on three interesting tasks: converting visual effects into identification text embeddings, finetuning DPMs for specific types of stylization, and optimizing initial noise to generate adversarial samples for security auditing.

  • 5 authors
·
Jul 20, 2023

Towards Explainable Anticancer Compound Sensitivity Prediction via Multimodal Attention-based Convolutional Encoders

In line with recent advances in neural drug design and sensitivity prediction, we propose a novel architecture for interpretable prediction of anticancer compound sensitivity using a multimodal attention-based convolutional encoder. Our model is based on the three key pillars of drug sensitivity: compounds' structure in the form of a SMILES sequence, gene expression profiles of tumors and prior knowledge on intracellular interactions from protein-protein interaction networks. We demonstrate that our multiscale convolutional attention-based (MCA) encoder significantly outperforms a baseline model trained on Morgan fingerprints, a selection of encoders based on SMILES as well as previously reported state of the art for multimodal drug sensitivity prediction (R2 = 0.86 and RMSE = 0.89). Moreover, the explainability of our approach is demonstrated by a thorough analysis of the attention weights. We show that the attended genes significantly enrich apoptotic processes and that the drug attention is strongly correlated with a standard chemical structure similarity index. Finally, we report a case study of two receptor tyrosine kinase (RTK) inhibitors acting on a leukemia cell line, showcasing the ability of the model to focus on informative genes and submolecular regions of the two compounds. The demonstrated generalizability and the interpretability of our model testify its potential for in-silico prediction of anticancer compound efficacy on unseen cancer cells, positioning it as a valid solution for the development of personalized therapies as well as for the evaluation of candidate compounds in de novo drug design.

  • 6 authors
·
Apr 25, 2019

SUGARCREPE++ Dataset: Vision-Language Model Sensitivity to Semantic and Lexical Alterations

Despite their remarkable successes, state-of-the-art large language models (LLMs), including vision-and-language models (VLMs) and unimodal language models (ULMs), fail to understand precise semantics. For example, semantically equivalent sentences expressed using different lexical compositions elicit diverging representations. The degree of this divergence and its impact on encoded semantics is not very well understood. In this paper, we introduce the SUGARCREPE++ dataset to analyze the sensitivity of VLMs and ULMs to lexical and semantic alterations. Each sample in SUGARCREPE++ dataset consists of an image and a corresponding triplet of captions: a pair of semantically equivalent but lexically different positive captions and one hard negative caption. This poses a 3-way semantic (in)equivalence problem to the language models. We comprehensively evaluate VLMs and ULMs that differ in architecture, pre-training objectives and datasets to benchmark the performance of SUGARCREPE++ dataset. Experimental results highlight the difficulties of VLMs in distinguishing between lexical and semantic variations, particularly in object attributes and spatial relations. Although VLMs with larger pre-training datasets, model sizes, and multiple pre-training objectives achieve better performance on SUGARCREPE++, there is a significant opportunity for improvement. We show that all the models which achieve better performance on compositionality datasets need not perform equally well on SUGARCREPE++, signifying that compositionality alone may not be sufficient for understanding semantic and lexical alterations. Given the importance of the property that the SUGARCREPE++ dataset targets, it serves as a new challenge to the vision-and-language community.

  • 6 authors
·
Jun 16, 2024

Does resistance to style-transfer equal Global Shape Bias? Measuring network sensitivity to global shape configuration

Deep learning models are known to exhibit a strong texture bias, while human tends to rely heavily on global shape structure for object recognition. The current benchmark for evaluating a model's global shape bias is a set of style-transferred images with the assumption that resistance to the attack of style transfer is related to the development of global structure sensitivity in the model. In this work, we show that networks trained with style-transfer images indeed learn to ignore style, but its shape bias arises primarily from local detail. We provide a Disrupted Structure Testbench (DiST) as a direct measurement of global structure sensitivity. Our test includes 2400 original images from ImageNet-1K, each of which is accompanied by two images with the global shapes of the original image disrupted while preserving its texture via the texture synthesis program. We found that black{(1) models that performed well on the previous cue-conflict dataset do not fare well in the proposed DiST; (2) the supervised trained Vision Transformer (ViT) lose its global spatial information from positional embedding, leading to no significant advantages over Convolutional Neural Networks (CNNs) on DiST. While self-supervised learning methods, especially mask autoencoder significantly improves the global structure sensitivity of ViT. (3) Improving the global structure sensitivity is orthogonal to resistance to style-transfer, indicating that the relationship between global shape structure and local texture detail is not an either/or relationship. Training with DiST images and style-transferred images are complementary, and can be combined to train network together to enhance the global shape sensitivity and robustness of local features.} Our code will be hosted in github: https://github.com/leelabcnbc/DiST

  • 4 authors
·
Oct 11, 2023

Navigating the Cultural Kaleidoscope: A Hitchhiker's Guide to Sensitivity in Large Language Models

As LLMs are increasingly deployed in global applications, the importance of cultural sensitivity becomes paramount, ensuring that users from diverse backgrounds feel respected and understood. Cultural harm can arise when these models fail to align with specific cultural norms, resulting in misrepresentations or violations of cultural values. This work addresses the challenges of ensuring cultural sensitivity in LLMs, especially in small-parameter models that often lack the extensive training data needed to capture global cultural nuances. We present two key contributions: (1) A cultural harm test dataset, created to assess model outputs across different cultural contexts through scenarios that expose potential cultural insensitivities, and (2) A culturally aligned preference dataset, aimed at restoring cultural sensitivity through fine-tuning based on feedback from diverse annotators. These datasets facilitate the evaluation and enhancement of LLMs, ensuring their ethical and safe deployment across different cultural landscapes. Our results show that integrating culturally aligned feedback leads to a marked improvement in model behavior, significantly reducing the likelihood of generating culturally insensitive or harmful content. Ultimately, this work paves the way for more inclusive and respectful AI systems, fostering a future where LLMs can safely and ethically navigate the complexities of diverse cultural landscapes.

  • 10 authors
·
Oct 15, 2024

TAG-WM: Tamper-Aware Generative Image Watermarking via Diffusion Inversion Sensitivity

AI-generated content (AIGC) enables efficient visual creation but raises copyright and authenticity risks. As a common technique for integrity verification and source tracing, digital image watermarking is regarded as a potential solution to above issues. However, the widespread adoption and advancing capabilities of generative image editing tools have amplified malicious tampering risks, while simultaneously posing new challenges to passive tampering detection and watermark robustness. To address these challenges, this paper proposes a Tamper-Aware Generative image WaterMarking method named TAG-WM. The proposed method comprises four key modules: a dual-mark joint sampling (DMJS) algorithm for embedding copyright and localization watermarks into the latent space while preserving generative quality, the watermark latent reconstruction (WLR) utilizing reversed DMJS, a dense variation region detector (DVRD) leveraging diffusion inversion sensitivity to identify tampered areas via statistical deviation analysis, and the tamper-aware decoding (TAD) guided by localization results. The experimental results demonstrate that TAG-WM achieves state-of-the-art performance in both tampering robustness and localization capability even under distortion, while preserving lossless generation quality and maintaining a watermark capacity of 256 bits. The code is available at: https://github.com/Suchenl/TAG-WM.

  • 5 authors
·
Jun 29

ACE2-SOM: Coupling to a slab ocean and learning the sensitivity of climate to changes in CO$_2$

While autoregressive machine-learning-based emulators have been trained to produce stable and accurate rollouts in the climate of the present-day and recent past, none so far have been trained to emulate the sensitivity of climate to substantial changes in CO_2 or other greenhouse gases. As an initial step we couple the Ai2 Climate Emulator version 2 to a slab ocean model (hereafter ACE2-SOM) and train it on output from a collection of equilibrium-climate physics-based reference simulations with varying levels of CO_2. We test it in equilibrium and non-equilibrium climate scenarios with CO_2 concentrations seen and unseen in training. ACE2-SOM performs well in equilibrium-climate inference with both in-sample and out-of-sample CO_2 concentrations, accurately reproducing the emergent time-mean spatial patterns of surface temperature and precipitation change with CO_2 doubling, tripling, or quadrupling. In addition, the vertical profile of atmospheric warming and change in extreme precipitation rates with increased CO_2 closely agree with the reference model. Non-equilibrium-climate inference is more challenging. With CO_2 increasing gradually at a rate of 2% year^{-1}, ACE2-SOM can accurately emulate the global annual mean trends of surface and lower-to-middle atmosphere fields but produces unphysical jumps in stratospheric fields. With an abrupt quadrupling of CO_2, ML-controlled fields transition unrealistically quickly to the 4xCO_2 regime. In doing so they violate global energy conservation and exhibit unphysical sensitivities of and surface and top of atmosphere radiative fluxes to instantaneous changes in CO_2. Future emulator development needed to address these issues should improve its generalizability to diverse climate change scenarios.

  • 9 authors
·
Dec 5, 2024

CPTQuant - A Novel Mixed Precision Post-Training Quantization Techniques for Large Language Models

Large language models have transformed the comprehension and generation of natural language tasks, but they come with substantial memory and computational requirements. Quantization techniques have emerged as a promising avenue for addressing these challenges while preserving accuracy and making energy efficient. We propose CPTQuant, a comprehensive strategy that introduces correlation-based (CMPQ), pruning-based (PMPQ), and Taylor decomposition-based (TDMPQ) mixed precision techniques. CMPQ adapts the precision level based on canonical correlation analysis of different layers. PMPQ optimizes precision layer-wise based on their sensitivity to sparsity. TDMPQ modifies precision using Taylor decomposition to assess each layer's sensitivity to input perturbation. These strategies allocate higher precision to more sensitive layers while diminishing precision to robust layers. CPTQuant assesses the performance across BERT, OPT-125M, OPT-350M, OPT-1.3B, and OPT-2.7B. We demonstrate up to 4x compression and a 2x-fold increase in efficiency with minimal accuracy drop compared to Hugging Face FP16. PMPQ stands out for achieving a considerably higher model compression. Sensitivity analyses across various LLMs show that the initial and final 30% of layers exhibit higher sensitivities than the remaining layers. PMPQ demonstrates an 11% higher compression ratio than other methods for classification tasks, while TDMPQ achieves a 30% greater compression ratio for language modeling tasks.

  • 3 authors
·
Dec 2, 2024

A study of a deterministic model for meningitis epidemic

A compartmental deterministic model that allows (1) immunity from two stages of infection and carriage, and (2) disease induced death, is used in studying the dynamics of meningitis epidemic process in a closed population. It allows for difference in the transmission rate of infection to a susceptible by a carrier and an infective. It is generalized to allow a proportion ({\phi}) of those susceptibles infected to progress directly to infectives in stage I. Both models are used in this study. The threshold conditions for the spread of carrier and infectives in stage I are derived for the two models. Sensitivity analysis is performed on the reproductive number derived from the next generation matrix. The case-carrier ratio profile for various parameters and threshold values are shown. So also are the graphs of the total number ever infected as influenced by {\epsilon} and {\phi}. The infection transmission rate (eta), the odds in favor of a carrier, over an infective, in transmitting an infection to a susceptible ({\epsilon}) and the carrier conversion rate ({\phi}) to an infective in stage I, are identified as key parameters that should be subject of attention for any control intervention strategy. The case-carrier ratio profiles provide evidence of a critical case-carrier ratio attained before the number of reported cases grows to an epidemic level. They also provide visual evidence of epidemiological context, in this case, epidemic incidence (in later part of dry season) and endemic incidence (during rainy season). Results from total proportion ever infected suggest that the model, in which {\phi}=0 obtained, can adequately represent, in essence, the generalized model for this study.

  • 2 authors
·
Mar 31, 2023

Lagrangian Coherent Track Initialisation (LCTI)

Advances in time-resolved Particle Tracking Velocimetry (4D-PTV) techniques have been consistently revealed more accurate Lagrangian particle motions. A novel track initialisation technique as a complementary part of 4D-PTV, based on local temporal and spatial coherency of neighbour trajectories, is proposed. The proposed Lagrangian Coherent Track Initialisation (LCTI) applies physics-based Finite Time Lyapunov Exponent (FTLE) to build four frame coherent tracks. We locally determine the boundaries (i.e., ridges) of Lagrangian Coherent Structures (LCS) among neighbour trajectories by using FTLE to distinguish clusters of coherent motions. To evaluate the proposed technique, we created an open-access synthetic Lagrangian and Eulerian dataset of the wake downstream of a smooth cylinder at a Reynolds number equal to 3900 obtained from 3D Direct Numerical Simulation (DNS). The dataset is available to the public. Performance of the proposed method based on three characteristic parameters, temporal scale, particle concentration (i.e., density), and noise ratio, showed robust behaviour in finding true tracks compared to the recent initialisation algorithms. Sensitivity of LCTI to the number of untracked and wrong tracks are also discussed. We address the capability of using the proposed method as a function of a 4D-PTV scheme in the Lagrangian Particle Tracking challenge for a flow with high particle densities. Finally, the LCTI behaviour was assessed in a real jet impingement experiment. LCTI was found to be a reliable tracking tool in complex flow motions, with a strength revealed for flows with high particle concentrations.

  • 4 authors
·
Jun 21, 2021

Training Transformers with Enforced Lipschitz Constants

Neural networks are often highly sensitive to input and weight perturbations. This sensitivity has been linked to pathologies such as vulnerability to adversarial examples, divergent training, and overfitting. To combat these problems, past research has looked at building neural networks entirely from Lipschitz components. However, these techniques have not matured to the point where researchers have trained a modern architecture such as a transformer with a Lipschitz certificate enforced beyond initialization. To explore this gap, we begin by developing and benchmarking novel, computationally-efficient tools for maintaining norm-constrained weight matrices. Applying these tools, we are able to train transformer models with Lipschitz bounds enforced throughout training. We find that optimizer dynamics matter: switching from AdamW to Muon improves standard methods -- weight decay and spectral normalization -- allowing models to reach equal performance with a lower Lipschitz bound. Inspired by Muon's update having a fixed spectral norm, we co-design a weight constraint method that improves the Lipschitz vs. performance tradeoff on MLPs and 2M parameter transformers. Our 2-Lipschitz transformer on Shakespeare text reaches validation accuracy 60%. Scaling to 145M parameters, our 10-Lipschitz transformer reaches 21% accuracy on internet text. However, to match the NanoGPT baseline validation accuracy of 39.4%, our Lipschitz upper bound increases to 10^264. Nonetheless, our Lipschitz transformers train without stability measures such as layer norm, QK norm, and logit tanh softcapping.

  • 6 authors
·
Jul 17

CodeJudgeBench: Benchmarking LLM-as-a-Judge for Coding Tasks

Large Language Models (LLMs) have significantly advanced the state-of-the-art in various coding tasks. Beyond directly answering user queries, LLMs can also serve as judges, assessing and comparing the quality of responses generated by other models. Such an evaluation capability is crucial both for benchmarking different LLMs and for improving response quality through response ranking. However, despite the growing adoption of the LLM-as-a-Judge paradigm, its effectiveness in coding scenarios remains underexplored due to the absence of dedicated benchmarks. To address this gap, we introduce CodeJudgeBench, a benchmark explicitly designed to evaluate the performance of LLM-as-a-Judge models across three critical coding tasks: code generation, code repair, and unit test generation. Through comprehensive benchmarking of 26 LLM-as-a-Judge models, we find that recent thinking models significantly outperform non-thinking models on our carefully designed code judging tasks. Notably, even relatively small thinking models, such as Qwen3-8B, can outperform specially trained LLM-as-a-Judge models up to 70B in size. Nevertheless, all models still exhibit significant randomness in their judgment of coding tasks. For pairwise judging tasks, simply changing the order in which responses are presented can substantially impact accuracy. In addition, when judging code and unit tests written by different LLMs, LLM-as-a-Judge models also show variance in performance. This sensitivity raises concerns about the reliability and consistency of LLM-as-a-Judge in coding scenarios. Lastly, we study optimal prompting strategies for LLM-as-a-Judge. We find that using pair-wise comparison outperforms scalar point-wise judging. Furthermore, retaining comments and reasoning in the full, unprocessed LLM response leads to improved judge performance.

  • 5 authors
·
Jul 14

KNN-MMD: Cross Domain Wireless Sensing via Local Distribution Alignment

Wireless sensing has recently found widespread applications in diverse environments, including homes, offices, and public spaces. By analyzing patterns in channel state information (CSI), it is possible to infer human actions for tasks such as person identification, gesture recognition, and fall detection. However, CSI is highly sensitive to environmental changes, where even minor alterations can significantly distort the CSI patterns. This sensitivity often leads to performance degradation or outright failure when applying wireless sensing models trained in one environment to another. To address this challenge, Domain Alignment (DAL) has been widely adopted for cross-domain classification tasks, as it focuses on aligning the global distributions of the source and target domains in feature space. Despite its popularity, DAL often neglects inter-category relationships, which can lead to misalignment between categories across domains, even when global alignment is achieved. To overcome these limitations, we propose K-Nearest Neighbors Maximum Mean Discrepancy (KNN-MMD), a novel few-shot method for cross-domain wireless sensing. Our approach begins by constructing a help set using KNN from the target domain, enabling local alignment between the source and target domains within each category using MMD. Additionally, we address a key instability issue commonly observed in cross-domain methods, where model performance fluctuates sharply between epochs. Further, most existing methods struggle to determine an optimal stopping point during training due to the absence of labeled data from the target domain. Our method resolves this by excluding the support set from the target domain during training and employing it as a validation set to determine the stopping criterion.The dataset and code are publicly available at https://github.com/RS2002/KNN-MMD .

  • 7 authors
·
Dec 6, 2024

Real-Time Prediction of Gas Flow Dynamics in Diesel Engines using a Deep Neural Operator Framework

We develop a data-driven deep neural operator framework to approximate multiple output states for a diesel engine and generate real-time predictions with reasonable accuracy. As emission norms become more stringent, the need for fast and accurate models that enable analysis of system behavior have become an essential requirement for system development. The fast transient processes involved in the operation of a combustion engine make it difficult to develop accurate physics-based models for such systems. As an alternative to physics based models, we develop an operator-based regression model (DeepONet) to learn the relevant output states for a mean-value gas flow engine model using the engine operating conditions as input variables. We have adopted a mean-value model as a benchmark for comparison, simulated using Simulink. The developed approach necessitates using the initial conditions of the output states to predict the accurate sequence over the temporal domain. To this end, a sequence-to-sequence approach is embedded into the proposed framework. The accuracy of the model is evaluated by comparing the prediction output to ground truth generated from Simulink model. The maximum mathcal L_2 relative error observed was approximately 6.5%. The sensitivity of the DeepONet model is evaluated under simulated noise conditions and the model shows relatively low sensitivity to noise. The uncertainty in model prediction is further assessed by using a mean ensemble approach. The worst-case error at the (mu + 2sigma) boundary was found to be 12%. The proposed framework provides the ability to predict output states in real-time and enables data-driven learning of complex input-output operator mapping. As a result, this model can be applied during initial development stages, where accurate models may not be available.

  • 4 authors
·
Apr 2, 2023

Machine learning applications to DNA subsequence and restriction site analysis

Based on the BioBricks standard, restriction synthesis is a novel catabolic iterative DNA synthesis method that utilizes endonucleases to synthesize a query sequence from a reference sequence. In this work, the reference sequence is built from shorter subsequences by classifying them as applicable or inapplicable for the synthesis method using three different machine learning methods: Support Vector Machines (SVMs), random forest, and Convolution Neural Networks (CNNs). Before applying these methods to the data, a series of feature selection, curation, and reduction steps are applied to create an accurate and representative feature space. Following these preprocessing steps, three different pipelines are proposed to classify subsequences based on their nucleotide sequence and other relevant features corresponding to the restriction sites of over 200 endonucleases. The sensitivity using SVMs, random forest, and CNNs are 94.9%, 92.7%, 91.4%, respectively. Moreover, each method scores lower in specificity with SVMs, random forest, and CNNs resulting in 77.4%, 85.7%, and 82.4%, respectively. In addition to analyzing these results, the misclassifications in SVMs and CNNs are investigated. Across these two models, different features with a derived nucleotide specificity visually contribute more to classification compared to other features. This observation is an important factor when considering new nucleotide sensitivity features for future studies.

  • 2 authors
·
Nov 7, 2020

DS6, Deformation-aware Semi-supervised Learning: Application to Small Vessel Segmentation with Noisy Training Data

Blood vessels of the brain provide the human brain with the required nutrients and oxygen. As a vulnerable part of the cerebral blood supply, pathology of small vessels can cause serious problems such as Cerebral Small Vessel Diseases (CSVD). It has also been shown that CSVD is related to neurodegeneration, such as Alzheimer's disease. With the advancement of 7 Tesla MRI systems, higher spatial image resolution can be achieved, enabling the depiction of very small vessels in the brain. Non-Deep Learning-based approaches for vessel segmentation, e.g., Frangi's vessel enhancement with subsequent thresholding, are capable of segmenting medium to large vessels but often fail to segment small vessels. The sensitivity of these methods to small vessels can be increased by extensive parameter tuning or by manual corrections, albeit making them time-consuming, laborious, and not feasible for larger datasets. This paper proposes a deep learning architecture to automatically segment small vessels in 7 Tesla 3D Time-of-Flight (ToF) Magnetic Resonance Angiography (MRA) data. The algorithm was trained and evaluated on a small imperfect semi-automatically segmented dataset of only 11 subjects; using six for training, two for validation, and three for testing. The deep learning model based on U-Net Multi-Scale Supervision was trained using the training subset and was made equivariant to elastic deformations in a self-supervised manner using deformation-aware learning to improve the generalisation performance. The proposed technique was evaluated quantitatively and qualitatively against the test set and achieved a Dice score of 80.44 pm 0.83. Furthermore, the result of the proposed method was compared against a selected manually segmented region (62.07 resultant Dice) and has shown a considerable improvement (18.98\%) with deformation-aware learning.

  • 10 authors
·
Jun 18, 2020

An error indicator-based adaptive reduced order model for nonlinear structural mechanics -- application to high-pressure turbine blades

The industrial application motivating this work is the fatigue computation of aircraft engines' high-pressure turbine blades. The material model involves nonlinear elastoviscoplastic behavior laws, for which the parameters depend on the temperature. For this application, the temperature loading is not accurately known and can reach values relatively close to the creep temperature: important nonlinear effects occur and the solution strongly depends on the used thermal loading. We consider a nonlinear reduced order model able to compute, in the exploitation phase, the behavior of the blade for a new temperature field loading. The sensitivity of the solution to the temperature makes {the classical unenriched proper orthogonal decomposition method} fail. In this work, we propose a new error indicator, quantifying the error made by the reduced order model in computational complexity independent of the size of the high-fidelity reference model. In our framework, when the {error indicator} becomes larger than a given tolerance, the reduced order model is updated using one time step solution of the high-fidelity reference model. The approach is illustrated on a series of academic test cases and applied on a setting of industrial complexity involving 5 million degrees of freedom, where the whole procedure is computed in parallel with distributed memory.

  • 2 authors
·
Apr 19, 2019

GWKokab: An Implementation to Identify the Properties of Multiple Population of Gravitational Wave Sources

The rapidly increasing sensitivity of gravitational wave detectors is enabling the detection of a growing number of compact binary mergers. These events are crucial for understanding the population properties of compact binaries. However, many previous studies rely on computationally expensive inference frameworks, limiting their scalability. In this work, we present GWKokab, a JAX-based framework that enables modular model building with independent rate for each subpopulation such as BBH, BNS, and NSBH binaries. It provides accelerated inference using the normalizing flow based sampler called flowMC and is also compatible with NumPyro samplers. To validate our framework, we generated two synthetic populations, one comprising spinning eccentric binaries and the other circular binaries using a multi-source model. We then recovered their injected parameters at significantly reduced computational cost and demonstrated that eccentricity distribution can be recovered even in spinning eccentric populations. We also reproduced results from two prior studies: one on non-spinning eccentric populations, and another on the BBH mass distribution using the third Gravitational Wave Transient Catalog (GWTC-3). We anticipate that GWKokab will not only reduce computational costs but also enable more detailed subpopulation analyses such as their mass, spin, eccentricity, and redshift distributions in gravitational wave events, offering deeper insights into compact binary formation and evolution.

  • 3 authors
·
Sep 16

Rethinking Brain Tumor Segmentation from the Frequency Domain Perspective

Precise segmentation of brain tumors, particularly contrast-enhancing regions visible in post-contrast MRI (areas highlighted by contrast agent injection), is crucial for accurate clinical diagnosis and treatment planning but remains challenging. However, current methods exhibit notable performance degradation in segmenting these enhancing brain tumor areas, largely due to insufficient consideration of MRI-specific tumor features such as complex textures and directional variations. To address this, we propose the Harmonized Frequency Fusion Network (HFF-Net), which rethinks brain tumor segmentation from a frequency-domain perspective. To comprehensively characterize tumor regions, we develop a Frequency Domain Decomposition (FDD) module that separates MRI images into low-frequency components, capturing smooth tumor contours and high-frequency components, highlighting detailed textures and directional edges. To further enhance sensitivity to tumor boundaries, we introduce an Adaptive Laplacian Convolution (ALC) module that adaptively emphasizes critical high-frequency details using dynamically updated convolution kernels. To effectively fuse tumor features across multiple scales, we design a Frequency Domain Cross-Attention (FDCA) integrating semantic, positional, and slice-specific information. We further validate and interpret frequency-domain improvements through visualization, theoretical reasoning, and experimental analyses. Extensive experiments on four public datasets demonstrate that HFF-Net achieves an average relative improvement of 4.48\% (ranging from 2.39\% to 7.72\%) in the mean Dice scores across the three major subregions, and an average relative improvement of 7.33% (ranging from 5.96% to 8.64%) in the segmentation of contrast-enhancing tumor regions, while maintaining favorable computational efficiency and clinical applicability. Code: https://github.com/VinyehShaw/HFF.

  • 8 authors
·
Jun 11

A Remote Sensing Image Change Detection Method Integrating Layer Exchange and Channel-Spatial Differences

Change detection in remote sensing imagery is a critical technique for Earth observation, primarily focusing on pixel-level segmentation of change regions between bi-temporal images. The essence of pixel-level change detection lies in determining whether corresponding pixels in bi-temporal images have changed. In deep learning, the spatial and channel dimensions of feature maps represent different information from the original images. In this study, we found that in change detection tasks, difference information can be computed not only from the spatial dimension of bi-temporal features but also from the channel dimension. Therefore, we designed the Channel-Spatial Difference Weighting (CSDW) module as an aggregation-distribution mechanism for bi-temporal features in change detection. This module enhances the sensitivity of the change detection model to difference features. Additionally, bi-temporal images share the same geographic location and exhibit strong inter-image correlations. To construct the correlation between bi-temporal images, we designed a decoding structure based on the Layer-Exchange (LE) method to enhance the interaction of bi-temporal features. Comprehensive experiments on the CLCD, PX-CLCD, LEVIR-CD, and S2Looking datasets demonstrate that the proposed LENet model significantly improves change detection performance. The code and pre-trained models will be available at: https://github.com/dyzy41/lenet.

  • 5 authors
·
Jan 18

RES-Q: Evaluating Code-Editing Large Language Model Systems at the Repository Scale

The instruction-following ability of Large Language Models (LLMs) has cultivated a class of LLM-based systems capable of approaching complex tasks such as making edits to large code repositories. Due to the high sensitivity and unpredictability of LLM behavior in response to changes in prompting, robust evaluation tools are needed to drive future iteration of these systems. We propose RES-Q, a natural language instruction-based benchmark for evaluating Repository Editing Systems, which consists of 100 repository editing tasks derived from real GitHub commits. Given an edit instruction and a code repository, RES-Q evaluates an LLM system's ability to gather information and construct an edit that satisfies the criteria set by the instruction. We argue that evaluating LLMs in this way addresses issues with traditional benchmarks and provides a more holistic assessment of a model's abilities. We evaluate various state-of-the-art LLMs as language agents in a repository-editing system built on Qurrent OS, our language agent development software. Despite their 1% pass@1 performance difference on HumanEval, we find Claude Sonnet 3.5 outperforms GPT-4o by 12% pass@1 on RES-Q, indicating RES-Q's capacity to differentiate model capability as traditional benchmarks approach saturation. We further investigate token efficiency, performance relationships with existing benchmarks, and interesting disparities between closed and open-source LLMs. Code and dataset are available at https://github.com/Qurrent-AI/RES-Q.

  • 4 authors
·
Jun 24, 2024

LLMCad: Fast and Scalable On-device Large Language Model Inference

Generative tasks, such as text generation and question answering, hold a crucial position in the realm of mobile applications. Due to their sensitivity to privacy concerns, there is a growing demand for their execution directly on mobile devices. Currently, the execution of these generative tasks heavily depends on Large Language Models (LLMs). Nevertheless, the limited memory capacity of these devices presents a formidable challenge to the scalability of such models. In our research, we introduce LLMCad, an innovative on-device inference engine specifically designed for efficient generative Natural Language Processing (NLP) tasks. The core idea behind LLMCad revolves around model collaboration: a compact LLM, residing in memory, takes charge of generating the most straightforward tokens, while a high-precision LLM steps in to validate these tokens and rectify any identified errors. LLMCad incorporates three novel techniques: (1) Instead of generating candidate tokens in a sequential manner, LLMCad employs the smaller LLM to construct a token tree, encompassing a wider range of plausible token pathways. Subsequently, the larger LLM can efficiently validate all of these pathways simultaneously. (2) It employs a self-adjusting fallback strategy, swiftly initiating the verification process whenever the smaller LLM generates an erroneous token. (3) To ensure a continuous flow of token generation, LLMCad speculatively generates tokens during the verification process by implementing a compute-IO pipeline. Through an extensive series of experiments, LLMCad showcases an impressive token generation speed, achieving rates up to 9.3x faster than existing inference engines.

  • 7 authors
·
Sep 8, 2023

Deep Synoptic Array Science: Searching for Long Duration Radio Transients with the DSA-110

We describe the design and commissioning tests for the DSA-110 Not-So-Fast Radio Burst (NSFRB) search pipeline, a 1.4 GHz image-plane single-pulse search sensitive to 134 ms-160.8 s radio bursts. Extending the pulse width range of the Fast Radio Burst (FRB) search by 3 orders of magnitude, the NSFRB search is sensitive to the recently-discovered Galactic Long Period Radio Transients (LPRTs). The NSFRB search operates in real-time, utilizing a custom GPU-accelerated search code, cerberus, implemented in Python with JAX. We summarize successful commissioning sensitivity tests with continuum sources and pulsar B0329+54, estimating the 6sigma flux (fluence) threshold to be ~290 mJy (~40 Jy ms). Future tests of recovery of longer timescale transients, e.g. CHIME J1634+44, are planned to supplement injection testing and B0329+54 observations. An offline DSA-110 NSFRB Galactic Plane Survey was conducted to search for LPRTs, covering -3.5^circ<b<5.7^circ and 141^circ<l<225^circ (~770 square degrees) in Galactic coordinates. We estimate an upper limit Poissonian burst rate ~1 hr^{-1} per square degree (~7 hr^{-1} per 3^circtimes3^circ survey grid cell) maximized across the inner |b|<0.25^circ of the surveyed region. By imposing the ~290 mJy flux limit on two representative models (the magnetar plastic flow model and the White Dwarf-M Dwarf binary model), we reject with 95% confidence the presence of White Dwarf-M Dwarf binary LPRTs with periods between ~10-70s within ~95% of the surveyed region. Combined with the prevalence of LPRTs in the Galactic Plane, our results motivate further consideration of both White Dwarf-M Dwarf binary models and isolated magnetar models. We will continue to explore novel LPRT search strategies during real-time operations, such as triggered periodicity searches and additional targeted surveys.

  • 13 authors
·
Oct 20

STROKEVISION-BENCH: A Multimodal Video And 2D Pose Benchmark For Tracking Stroke Recovery

Despite advancements in rehabilitation protocols, clinical assessment of upper extremity (UE) function after stroke largely remains subjective, relying heavily on therapist observation and coarse scoring systems. This subjectivity limits the sensitivity of assessments to detect subtle motor improvements, which are critical for personalized rehabilitation planning. Recent progress in computer vision offers promising avenues for enabling objective, quantitative, and scalable assessment of UE motor function. Among standardized tests, the Box and Block Test (BBT) is widely utilized for measuring gross manual dexterity and tracking stroke recovery, providing a structured setting that lends itself well to computational analysis. However, existing datasets targeting stroke rehabilitation primarily focus on daily living activities and often fail to capture clinically structured assessments such as block transfer tasks. Furthermore, many available datasets include a mixture of healthy and stroke-affected individuals, limiting their specificity and clinical utility. To address these critical gaps, we introduce StrokeVision-Bench, the first-ever dedicated dataset of stroke patients performing clinically structured block transfer tasks. StrokeVision-Bench comprises 1,000 annotated videos categorized into four clinically meaningful action classes, with each sample represented in two modalities: raw video frames and 2D skeletal keypoints. We benchmark several state-of-the-art video action recognition and skeleton-based action classification methods to establish performance baselines for this domain and facilitate future research in automated stroke rehabilitation assessment.

  • 5 authors
·
Sep 2

First Light And Reionization Epoch Simulations (FLARES) -- XIX: Supermassive black hole mergers in the early Universe and their environmental dependence

The upcoming space-based gravitational wave (GW) observatory, LISA, is expected to detect GW signals from supermassive black hole (SMBH) mergers occurring at high redshifts. However, understanding the origin and growth of SMBHs in the early Universe remains an open problem in astrophysics. In this work, we utilize the First Light And Reionization Epoch Simulations (FLARES), a suite of cosmological hydrodynamical zoom-in simulations, to study SMBH mergers at 5 lesssim z lesssim 10 across a wide range of environments. Most mergers in FLARES involve secondary SMBHs near the seed mass (m_{seed} approx 1.5 times 10^{5} M_{odot}) while primary SMBHs span up to 10^{9} M_{odot}, resulting in mass ratios from q sim 10^{-4} to 1, with a peak at q sim 1. The number of mergers increases rapidly towards lower redshifts, and the comoving total number density scales with overdensity as n_{merger} = 10^{-3.80} (1 + delta)^{4.56}. Denser regions host more massive mergers, with higher merger redshifts and lower mass ratios. Within the FLARES redshift range, LISA is expected to detect mergers with 10^{5} lesssim M_{tot} / M_{odot} lesssim 10^{8} and q gtrsim 10^{-2}, corresponding to a detection rate of 0.030 yr^{-1} for events with signal-to-noise ratio SNR geq 10. Our study demonstrates the sensitivity of GW predictions at high redshifts to SMBH seed models and merger time delays, highlighting the need for improved modeling in future cosmological simulations to maximize LISA's scientific return.

  • 13 authors
·
May 18

Applying the ACE2 Emulator to SST Green's Functions for the E3SMv3 Climate Model

Green's functions are a useful technique for interpreting atmospheric state responses to changes in the spatial pattern of sea surface temperature (SST). Here we train version 2 of the Ai2 Climate Emulator (ACE2) on reference historical SST simulations of the US Department of Energy's EAMv3 global atmosphere model. We compare how well the SST Green's functions generated by ACE2 match those of EAMv3, following the protocol of the Green's Function Model Intercomparison Project (GFMIP). The spatial patterns of top-of-atmosphere (TOA) radiative response from the individual GFMIP SST patch simulations are similar for ACE and the EAMv3 reference. The derived sensitivity of global net TOA radiation sensitivity to SST patch location is qualitatively similar in ACE as in EAMv3, but there are statistically significant discrepancies for some SST patches, especially over the subtropical northeast Pacific. These discrepancies may reflect insufficient diversity in the SST patterns sampled over the course of the EAMv3 AMIP simulation used for training ACE. Both ACE and EAMv3 Green's functions reconstruct the historical record of the global annual-mean TOA radiative flux from a reference EAMv3 AMIP simulation reasonably well. Notably, under our configuration and compute resources, ACE achieves these results approximately 100 times faster in wall-clock time compared to EAMv3, highlighting its potential as a powerful and efficient tool for tackling other computationally intensive problems in climate science.

  • 8 authors
·
May 13

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

Beyond Degradation Conditions: All-in-One Image Restoration via HOG Transformers

All-in-one image restoration, which aims to address diverse degradations within a unified framework, is critical for practical applications. However, existing methods rely on predicting and integrating degradation conditions, which can misactivate degradation-specific features in complex scenarios, limiting their restoration performance. To address this issue, we propose a novel all-in-one image restoration framework guided by Histograms of Oriented Gradients (HOG), named HOGformer. By leveraging the degradation-discriminative capability of HOG descriptors, HOGformer employs a dynamic self-attention mechanism that adaptively attends to long-range spatial dependencies based on degradation-aware HOG cues. To enhance the degradation sensitivity of attention inputs, we design a HOG-guided local dynamic-range convolution module that captures long-range degradation similarities while maintaining awareness of global structural information. Furthermore, we propose a dynamic interaction feed-forward module, efficiently increasing the model capacity to adapt to different degradations through channel-spatial interactions. Extensive experiments across diverse benchmarks, including adverse weather and natural degradations, demonstrate that HOGformer achieves state-of-the-art performance and generalizes effectively to complex real-world degradations. Code is available at https://github.com/Fire-friend/HOGformer.

  • 4 authors
·
Apr 12

ReynoldsFlow: Exquisite Flow Estimation via Reynolds Transport Theorem

Optical flow is a fundamental technique for motion estimation, widely applied in video stabilization, interpolation, and object tracking. Traditional optical flow estimation methods rely on restrictive assumptions like brightness constancy and slow motion constraints. Recent deep learning-based flow estimations require extensive training on large domain-specific datasets, making them computationally demanding. Also, artificial intelligence (AI) advances have enabled deep learning models to take advantage of optical flow as an important feature for object tracking and motion analysis. Since optical flow is commonly encoded in HSV for visualization, its conversion to RGB for neural network processing is nonlinear and may introduce perceptual distortions. These transformations amplify the sensitivity to estimation errors, potentially affecting the predictive accuracy of the networks. To address these challenges that are influential to the performance of downstream network models, we propose Reynolds flow, a novel training-free flow estimation inspired by the Reynolds transport theorem, offering a principled approach to modeling complex motion dynamics. In addition to conventional HSV-based visualization of Reynolds flow, we also introduce an RGB-encoded representation of Reynolds flow designed to improve flow visualization and feature enhancement for neural networks. We evaluated the effectiveness of Reynolds flow in video-based tasks. Experimental results on three benchmarks, tiny object detection on UAVDB, infrared object detection on Anti-UAV, and pose estimation on GolfDB, demonstrate that networks trained with RGB-encoded Reynolds flow achieve SOTA performance, exhibiting improved robustness and efficiency across all tasks.

  • 2 authors
·
Mar 6

MADE-for-ASD: A Multi-Atlas Deep Ensemble Network for Diagnosing Autism Spectrum Disorder

In response to the global need for efficient early diagnosis of Autism Spectrum Disorder (ASD), this paper bridges the gap between traditional, time-consuming diagnostic methods and potential automated solutions. We propose a multi-atlas deep ensemble network, MADE-for-ASD, that integrates multiple atlases of the brain's functional magnetic resonance imaging (fMRI) data through a weighted deep ensemble network. Our approach integrates demographic information into the prediction workflow, which enhances ASD diagnosis performance and offers a more holistic perspective on patient profiling. We experiment with the well-known publicly available ABIDE (Autism Brain Imaging Data Exchange) I dataset, consisting of resting state fMRI data from 17 different laboratories around the globe. Our proposed system achieves 75.20% accuracy on the entire dataset and 96.40% on a specific subset - both surpassing reported ASD diagnosis accuracy in ABIDE I fMRI studies. Specifically, our model improves by 4.4 percentage points over prior works on the same amount of data. The model exhibits a sensitivity of 82.90% and a specificity of 69.70% on the entire dataset, and 91.00% and 99.50%, respectively, on the specific subset. We leverage the F-score to pinpoint the top 10 ROI in ASD diagnosis, such as precuneus and anterior cingulate/ventromedial. The proposed system can potentially pave the way for more cost-effective, efficient and scalable strategies in ASD diagnosis. Codes and evaluations are publicly available at https://github.com/hasan-rakibul/MADE-for-ASD.

  • 4 authors
·
Jul 9, 2024

From Density to Geometry: YOLOv8 Instance Segmentation for Reverse Engineering of Optimized Structures

This paper introduces YOLOv8-TO, a novel approach for reverse engineering of topology-optimized structures into interpretable geometric parameters using the YOLOv8 instance segmentation model. Density-based topology optimization methods require post-processing to convert the optimal density distribution into a parametric representation for design exploration and integration with CAD tools. Traditional methods such as skeletonization struggle with complex geometries and require manual intervention. YOLOv8-TO addresses these challenges by training a custom YOLOv8 model to automatically detect and reconstruct structural components from binary density distributions. The model is trained on a diverse dataset of both optimized and random structures generated using the Moving Morphable Components method. A custom reconstruction loss function based on the dice coefficient of the predicted geometry is used to train the new regression head of the model via self-supervised learning. The method is evaluated on test sets generated from different topology optimization methods, including out-of-distribution samples, and compared against a skeletonization approach. Results show that YOLOv8-TO significantly outperforms skeletonization in reconstructing visually and structurally similar designs. The method showcases an average improvement of 13.84% in the Dice coefficient, with peak enhancements reaching 20.78%. The method demonstrates good generalization to complex geometries and fast inference times, making it suitable for integration into design workflows using regular workstations. Limitations include the sensitivity to non-max suppression thresholds. YOLOv8-TO represents a significant advancement in topology optimization post-processing, enabling efficient and accurate reverse engineering of optimized structures for design exploration and manufacturing.

  • 4 authors
·
Apr 29, 2024

Cosmic Evolution Early Release Science (CEERS) survey: The colour evolution of galaxies in the distant Universe

The wavelength-coverage and sensitivity of JWST now enables us to probe the rest-frame UV - optical spectral energy distributions (SEDs) of galaxies at high-redshift (z>4). From these SEDs it is, in principle, through SED fitting possible to infer key physical properties, including stellar masses, star formation rates, and dust attenuation. These in turn can be compared with the predictions of galaxy formation simulations allowing us to validate and refine the incorporated physics. However, the inference of physical properties, particularly from photometry alone, can lead to large uncertainties and potential biases. Instead, it is now possible, and common, for simulations to be forward-modelled to yield synthetic observations that can be compared directly to real observations. In this work, we measure the JWST broadband fluxes and colours of a robust sample of 5<z<10 galaxies using the Cosmic Evolution Early Release Science (CEERS) Survey. We then analyse predictions from a variety of models using the same methodology and compare the NIRCam/F277W magnitude distribution and NIRCam colours with observations. We find that the predicted and observed magnitude distributions are similar, at least at 5<z<8. At z>8 the distributions differ somewhat, though our observed sample size is small and thus susceptible to statistical fluctuations. Likewise, the predicted and observed colour evolution show broad agreement, at least at 5<z<8. There is however some disagreement between the observed and modelled strength of the strong line contribution. In particular all the models fails to reproduce the F410M-F444W colour at z>8, though, again, the sample size is small here.

  • 23 authors
·
Nov 14, 2023

GOALS-JWST: Gas Dynamics and Excitation in NGC7469 revealed by NIRSpec

We present new JWST-NIRSpec IFS data for the luminous infrared galaxy NGC7469: a nearby (70.6Mpc) active galaxy with a Sy 1.5 nucleus that drives a highly ionized gas outflow and a prominent nuclear star-forming ring. Using the superb sensitivity and high spatial resolution of the JWST instrument NIRSpec-IFS, we investigate the role of the Seyfert nucleus in the excitation and dynamics of the circumnuclear gas. Our analysis focuses on the [Fe ii], H2, and hydrogen recombination lines that trace the radiation/shocked-excited molecular and ionized ISM around the AGN. We investigate the gas excitation through H2/Br{\gamma} and [Fe ii]/Paeta emission line ratios and find that photoionization by the AGN dominates within the central 300 pc of the galaxy and together with a small region show ing signatures of shock-heated gas; these shock-heated regions are likely associated with a compact radio jet. In addition, the velocity field and velocity dispersion maps reveal complex gas kinematics. Rotation is the dominant feature, but we also identify non-circular motions consistent with gas inflows as traced by the velocity residuals and the spiral pattern in the Pa{\alpha} velocity dispersion map. The inflow is consistent with the mass outflow rate and two orders of magnitude higher than the AGN accretion rate. The compact nuclear radio jet has enough power to drive the highly ionized outflow. This scenario suggests that the inflow and outflow are in a self-regulating feeding-feedback process, with a contribution from the radio jet helping to drive the outflow.

  • 39 authors
·
Jul 31, 2023

Evaluating the Zero-shot Robustness of Instruction-tuned Language Models

Instruction fine-tuning has recently emerged as a promising approach for improving the zero-shot capabilities of Large Language Models (LLMs) on new tasks. This technique has shown particular strength in improving the performance of modestly sized LLMs, sometimes inducing performance competitive with much larger model variants. In this paper we ask two questions: (1) How sensitive are instruction-tuned models to the particular phrasings of instructions, and, (2) How can we make them more robust to such natural language variation? To answer the former, we collect a set of 319 instructions manually written by NLP practitioners for over 80 unique tasks included in widely used benchmarks, and we evaluate the variance and average performance of these instructions as compared to instruction phrasings observed during instruction fine-tuning. We find that using novel (unobserved) but appropriate instruction phrasings consistently degrades model performance, sometimes substantially so. Further, such natural instructions yield a wide variance in downstream performance, despite their semantic equivalence. Put another way, instruction-tuned models are not especially robust to instruction re-phrasings. We propose a simple method to mitigate this issue by introducing ``soft prompt'' embedding parameters and optimizing these to maximize the similarity between representations of semantically equivalent instructions. We show that this method consistently improves the robustness of instruction-tuned models.

  • 3 authors
·
Jun 19, 2023

SLUE Phase-2: A Benchmark Suite of Diverse Spoken Language Understanding Tasks

Spoken language understanding (SLU) tasks have been studied for many decades in the speech research community, but have not received as much attention as lower-level tasks like speech and speaker recognition. In particular, there are not nearly as many SLU task benchmarks, and many of the existing ones use data that is not freely available to all researchers. Recent work has begun to introduce such benchmark datasets for several tasks. In this work, we introduce several new annotated SLU benchmark tasks based on freely available speech data, which complement existing benchmarks and address gaps in the SLU evaluation landscape. We contribute four tasks: question answering and summarization involve inference over longer speech sequences; named entity localization addresses the speech-specific task of locating the targeted content in the signal; dialog act classification identifies the function of a given speech utterance. We follow the blueprint of the Spoken Language Understanding Evaluation (SLUE) benchmark suite. In order to facilitate the development of SLU models that leverage the success of pre-trained speech representations, we will be publishing for each task (i) annotations for a relatively small fine-tuning set, (ii) annotated development and test sets, and (iii) baseline models for easy reproducibility and comparisons. In this work, we present the details of data collection and annotation and the performance of the baseline models. We also perform sensitivity analysis of pipeline models' performance (speech recognizer + text model) to the speech recognition accuracy, using more than 20 state-of-the-art speech recognition models.

  • 10 authors
·
Dec 20, 2022

First Light And Reionisation Epoch Simulations (FLARES) VI: The colour evolution of galaxies $z=5-15$

With its exquisite sensitivity, wavelength coverage, and spatial and spectral resolution, the James Webb Space Telescope is poised to revolutionise our view of the distant, high-redshift (z>5) Universe. While Webb's spectroscopic observations will be transformative for the field, photometric observations play a key role in identifying distant objects and providing more comprehensive samples than accessible to spectroscopy alone. In addition to identifying objects, photometric observations can also be used to infer physical properties and thus be used to constrain galaxy formation models. However, inferred physical properties from broadband photometric observations, particularly in the absence of spectroscopic redshifts, often have large uncertainties. With the development of new tools for forward modelling simulations it is now routinely possible to predict observational quantities, enabling a direct comparison with observations. With this in mind, in this work, we make predictions for the colour evolution of galaxies at z=5-15 using the FLARES: First Light And Reionisation Epoch Simulations cosmological hydrodynamical simulation suite. We predict a complex evolution, driven predominantly by strong nebular line emission passing through individual bands. These predictions are in good agreement with existing constraints from Hubble and Spitzer as well as some of the first results from Webb. We also contrast our predictions with other models in the literature: while the general trends are similar we find key differences, particularly in the strength of features associated with strong nebular line emission. This suggests photometric observations alone should provide useful discriminating power between different models.

  • 9 authors
·
Jul 22, 2022

Learning Tubule-Sensitive CNNs for Pulmonary Airway and Artery-Vein Segmentation in CT

Training convolutional neural networks (CNNs) for segmentation of pulmonary airway, artery, and vein is challenging due to sparse supervisory signals caused by the severe class imbalance between tubular targets and background. We present a CNNs-based method for accurate airway and artery-vein segmentation in non-contrast computed tomography. It enjoys superior sensitivity to tenuous peripheral bronchioles, arterioles, and venules. The method first uses a feature recalibration module to make the best use of features learned from the neural networks. Spatial information of features is properly integrated to retain relative priority of activated regions, which benefits the subsequent channel-wise recalibration. Then, attention distillation module is introduced to reinforce representation learning of tubular objects. Fine-grained details in high-resolution attention maps are passing down from one layer to its previous layer recursively to enrich context. Anatomy prior of lung context map and distance transform map is designed and incorporated for better artery-vein differentiation capacity. Extensive experiments demonstrated considerable performance gains brought by these components. Compared with state-of-the-art methods, our method extracted much more branches while maintaining competitive overall segmentation performance. Codes and models are available at http://www.pami.sjtu.edu.cn/News/56

  • 9 authors
·
Dec 10, 2020

Deep Knowledge Tracing with Learning Curves

Knowledge tracing (KT) has recently been an active research area of computational pedagogy. The task is to model students' mastery level of knowledge concepts based on their responses to the questions in the past, as well as predict the probabilities that they correctly answer subsequent questions in the future. KT tasks were historically solved using statistical modeling methods such as Bayesian inference and factor analysis, but recent advances in deep learning have led to the successive proposals that leverage deep neural networks, including long short-term memory networks, memory-augmented networks and self-attention networks. While those deep models demonstrate superior performance over the traditional approaches, they all neglect the explicit modeling of the learning curve theory, which generally says that more practice on the same knowledge concept enhances one's mastery level of the concept. Based on this theory, we propose a Convolution-Augmented Knowledge Tracing (CAKT) model in this paper. The model employs three-dimensional convolutional neural networks to explicitly learn a student's recent experience on applying the same knowledge concept with that in the next question, and fuses the learnt feature with the feature representing her overall latent knowledge state obtained using a classic LSTM network. The fused feature is then fed into a second LSTM network to predict the student's response to the next question. Experimental results show that CAKT achieves the new state-of-the-art performance in predicting students' responses compared with existing models. We also conduct extensive sensitivity analysis and ablation study to show the stability of the results and justify the particular architecture of CAKT, respectively.

  • 3 authors
·
Jul 26, 2020

Semantic Topic Analysis of Traffic Camera Images

Traffic cameras are commonly deployed monitoring components in road infrastructure networks, providing operators visual information about conditions at critical points in the network. However, human observers are often limited in their ability to process simultaneous information sources. Recent advancements in computer vision, driven by deep learning methods, have enabled general object recognition, unlocking opportunities for camera-based sensing beyond the existing human observer paradigm. In this paper, we present a Natural Language Processing (NLP)-inspired approach, entitled Bag-of-Label-Words (BoLW), for analyzing image data sets using exclusively textual labels. The BoLW model represents the data in a conventional matrix form, enabling data compression and decomposition techniques, while preserving semantic interpretability. We apply the Latent Dirichlet Allocation (LDA) topic model to decompose the label data into a small number of semantic topics. To illustrate our approach, we use freeway camera images collected from the Boston area between December 2017-January 2018. We analyze the cameras' sensitivity to weather events; identify temporal traffic patterns; and analyze the impact of infrequent events, such as the winter holidays and the "bomb cyclone" winter storm. This study demonstrates the flexibility of our approach, which allows us to analyze weather events and freeway traffic using only traffic camera image labels.

  • 3 authors
·
Sep 27, 2018