Recent advances in calcium imaging enable simultaneous recordings of up to a million neurons in behaving animals, producing datasets of unprecedented scales. Although individual neurons and their activity traces can be extracted from these videos with automated algorithms, the results often require human curation to remove false positives, a laborious process called \emph{cell sorting}. To address this challenge, we introduce ActSort, an active-learning algorithm for sorting large-scale datasets that integrates features engineered by domain experts together with data formats with minimal memory requirements. By strategically bringing outlier cell candidates near the decision boundary up for annotation, ActSort reduces human labor to about 1-3\% of cell candidates and improves curation accuracy by mitigating annotator bias. To facilitate the algorithm's widespread adoption among experimental neuroscientists, we created a user-friendly software and conducted a first-of-its-kind benchmarking study involving about 160,000 annotations.

Modeling these sequences is key to understand disease mechanisms and is an active research area in computational biology. Recently, Large Language Models have shown great promise in solving certain biological tasks but current approaches are limited to a single sequence modality (DNA, RNA, or protein). Key problems in genomics intrinsically involve multiple modalities, but it remains unclear how to adapt general-purpose sequence models to those cases. In this work we propose a multi-modal model that connects DNA, RNA, and proteins by leveraging information from different pre-trained modality-specific encoders. We demonstrate its capabilities by applying it to the largely unsolved problem of predicting how multiple \rna transcript isoforms originate from the same gene (i.e.

Roughly 500 cold-stunned sea turtles were rescued in New England this winter. Helvetica is a loggerhead sea turtle. Breakthroughs, discoveries, and DIY tips sent six days a week. They're also a few of the new names bestowed upon sea turtles that a team from the New England Aquarium's turtle hospital rehabilitated this year. This winter, almost 500 live turtles washed up along the shores of Cape Cod Bay, with many suffering from hypothermia following the annual cold stunning season .

Motion forecasting for agents in autonomous driving is highly challenging due to the numerous possibilities for each agent's next action and their complex interactions in space and time. In real applications, motion forecasting takes place repeatedly and continuously as the self-driving car moves. However, existing forecasting methods typically process each driving scene within a certain range independently, totally ignoring the situational and contextual relationships between successive driving scenes. This significantly simplifies the forecasting task, making the solutions suboptimal and inefficient to use in practice. To address this fundamental limitation, we propose a novel motion forecasting framework for continuous driving, named RealMotion.It comprises two integral streams both at the scene level:(1) The scene context stream progressively accumulates historical scene information until the present moment, capturing temporal interactive relationships among scene elements.(2) The agent trajectory stream optimizes current forecasting by sequentially relaying past predictions.Besides, a data reorganization strategy is introduced to narrow the gap between existing benchmarks and real-world applications, consistent with our network. These approaches enable exploiting more broadly the situational and progressive insights of dynamic motion across space and time. Extensive experiments on Argoverse series with different settings demonstrate that our RealMotion achieves state-of-the-art performance, along with the advantage of efficient real-world inference.

Existing benchmarks for evaluating LLMs' cultural sensitivities are usually limited to a single language or online sources like Wikipedia, which may not reflect the daily habits, customs, and lifestyles of different regions. That is, information about the food people eat for their birthday celebrations, spices they typically use, musical instruments youngsters play or the sports they practice in school is not always explicitly written online. To address this issue, we introduce BLEnD, a hand-crafted benchmark designed to evaluate LLMs' everyday knowledge across diverse cultures and languages. The benchmark comprises 52.6k question-answer pairs from 16 countries/regions, in 13 different languages, including low-resource ones such as Amharic, Assamese, Azerbaijani, Hausa, and Sundanese. We evaluate LLMs in two formats: short-answer questions, and multiple-choice questions. We show that LLMs perform better in cultures that are more present online, with a maximum 57.34% difference in GPT-4, the best-performing model, in the short-answer format.Furthermore, we find that LLMs perform better in their local languages for mid-to-high-resource languages. Interestingly, for languages deemed to be low-resource, LLMs provide better answers in English. We make our dataset publicly available at: https://github.com/nlee0212/BLEnD.

Conditional independence tests are crucial across various disciplines in determining the independence of an outcome variable $Y$ from a treatment variable $X$, conditioning on a set of confounders $Z$. The Conditional Randomization Test (CRT) offers a powerful framework for such testing by assuming known distributions of $X \mid Z$; it controls the Type-I error exactly, allowing for the use of flexible, black-box test statistics. In practice, testing for conditional independence often involves using data from a source population to draw conclusions about a target population. This can be challenging due to covariate shift---differences in the distribution of $X$, $Z$, and surrogate variables, which can affect the conditional distribution of $Y \mid X, Z$---rendering traditional CRT approaches invalid. To address this issue, we propose a novel Covariate Shift Corrected Pearson Chi-squared Conditional Randomization (csPCR) test. This test adapts to covariate shifts by integrating importance weights and employing the control variates method to reduce variance in the test statistics and thus enhance power. Theoretically, we establish that the csPCR test controls the Type-I error asymptotically. Empirically, through simulation studies, we demonstrate that our method not only maintains control over Type-I errors but also exhibits superior power, confirming its efficacy and practical utility in real-world scenarios where covariate shifts are prevalent. Finally, we apply our methodology to a real-world dataset to assess the impact of a COVID-19 treatment on the 90-day mortality rate among patients.

Backdoor attacks pose a significant threat to Deep Neural Networks (DNNs) as they allow attackers to manipulate model predictions with backdoor triggers. To address these security vulnerabilities, various backdoor purification methods have been proposed to purify compromised models.

How (dis)similar are the learning trajectories of vision-language models and children? Recent modeling work has attempted to understand the gap between models' and humans' data efficiency by constructing models trained on less data, especially multimodal naturalistic data. However, such models are often evaluated on adult-level benchmarks, with limited breadth in language abilities tested, and without direct comparison to behavioral data. We introduce DevBench, a multimodal benchmark comprising seven language evaluation tasks spanning the domains of lexical, syntactic, and semantic ability, with behavioral data from both children and adults. We evaluate a set of vision-language models on these tasks, comparing models and humans on their response patterns, not their absolute performance. Across tasks, models exhibit variation in their closeness to human response patterns, and models that perform better on a task also more closely resemble human behavioral responses. We also examine the developmental trajectory of OpenCLIP over training, finding that greater training results in closer approximations to adult response patterns. DevBench thus provides a benchmark for comparing models to human language development. These comparisons highlight ways in which model and human language learning processes diverge, providing insight into entry points for improving language models.

Nanopore sequencing is the third-generation sequencing technology with capabilities of generating long-read sequences and directly measuring modifications on DNA/RNA molecules, which makes it ideal for biological applications such as human Telomere-to-Telomere (T2T) genome assembly, Ebola virus surveillance and COVID-19 mRNA vaccine development. However, accuracies of computational methods in various tasks of Nanopore sequencing data analysis are far from satisfactory. For instance, the base calling accuracy of Nanopore RNA sequencing is $\sim$90\%, while the aim is $\sim$99.9\%. This highlights an urgent need of contributions from the machine learning community. A bottleneck that prevents machine learning researchers from entering this field is the lack of a large integrated benchmark dataset.

Disease grading is a crucial task in medical image analysis. Due to the continuous progression of diseases, i.e., the variability within the same level and the similarity between adjacent stages, accurate grading is highly challenging.Furthermore, in real-world scenarios, models trained on limited source domain datasets should also be capable of handling data from unseen target domains.Due to the cross-domain variants, the feature distribution between source and unseen target domains can be dramatically different, leading to a substantial decrease in model performance.To address these challenges in cross-domain disease grading, we propose a Severity-aware Recurrent Modeling (Samba) method in this paper.As the core objective of most staging tasks is to identify the most severe lesions, which may only occupy a small portion of the image, we propose to encode image patches in a sequential and recurrent manner.Specifically, a state space model is tailored to store and transport the severity information by hidden states.Moreover, to mitigate the impact of cross-domain variants, an Expectation-Maximization (EM) based state recalibration mechanism is designed to map the patch embeddings into a more compact space.We model the feature distributions of different lesions through the Gaussian Mixture Model (GMM) and reconstruct the intermediate features based on learnable severity bases.Extensive experiments show the proposed Samba outperforms the VMamba baseline by an average accuracy of 23.5\%, 5.6\% and 4.1\% on the cross-domain grading of fatigue fracture, breast cancer and diabetic retinopathy, respectively. Source code is available at \url{https://github.com/BiQiWHU/Samba}.