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SubscribeSiT: Self-supervised vIsion Transformer
Self-supervised learning methods are gaining increasing traction in computer vision due to their recent success in reducing the gap with supervised learning. In natural language processing (NLP) self-supervised learning and transformers are already the methods of choice. The recent literature suggests that the transformers are becoming increasingly popular also in computer vision. So far, the vision transformers have been shown to work well when pretrained either using a large scale supervised data or with some kind of co-supervision, e.g. in terms of teacher network. These supervised pretrained vision transformers achieve very good results in downstream tasks with minimal changes. In this work we investigate the merits of self-supervised learning for pretraining image/vision transformers and then using them for downstream classification tasks. We propose Self-supervised vIsion Transformers (SiT) and discuss several self-supervised training mechanisms to obtain a pretext model. The architectural flexibility of SiT allows us to use it as an autoencoder and work with multiple self-supervised tasks seamlessly. We show that a pretrained SiT can be finetuned for a downstream classification task on small scale datasets, consisting of a few thousand images rather than several millions. The proposed approach is evaluated on standard datasets using common protocols. The results demonstrate the strength of the transformers and their suitability for self-supervised learning. We outperformed existing self-supervised learning methods by large margin. We also observed that SiT is good for few shot learning and also showed that it is learning useful representation by simply training a linear classifier on top of the learned features from SiT. Pretraining, finetuning, and evaluation codes will be available under: https://github.com/Sara-Ahmed/SiT.
SITTA: A Semantic Image-Text Alignment for Image Captioning
Textual and semantic comprehension of images is essential for generating proper captions. The comprehension requires detection of objects, modeling of relations between them, an assessment of the semantics of the scene and, finally, representing the extracted knowledge in a language space. To achieve rich language capabilities while ensuring good image-language mappings, pretrained language models (LMs) were conditioned on pretrained multi-modal (image-text) models that allow for image inputs. This requires an alignment of the image representation of the multi-modal model with the language representations of a generative LM. However, it is not clear how to best transfer semantics detected by the vision encoder of the multi-modal model to the LM. We introduce two novel ways of constructing a linear mapping that successfully transfers semantics between the embedding spaces of the two pretrained models. The first aligns the embedding space of the multi-modal language encoder with the embedding space of the pretrained LM via token correspondences. The latter leverages additional data that consists of image-text pairs to construct the mapping directly from vision to language space. Using our semantic mappings, we unlock image captioning for LMs without access to gradient information. By using different sources of data we achieve strong captioning performance on MS-COCO and Flickr30k datasets. Even in the face of limited data, our method partly exceeds the performance of other zero-shot and even finetuned competitors. Our ablation studies show that even LMs at a scale of merely 250M parameters can generate decent captions employing our semantic mappings. Our approach makes image captioning more accessible for institutions with restricted computational resources.
Situational Awareness Matters in 3D Vision Language Reasoning
Being able to carry out complicated vision language reasoning tasks in 3D space represents a significant milestone in developing household robots and human-centered embodied AI. In this work, we demonstrate that a critical and distinct challenge in 3D vision language reasoning is situational awareness, which incorporates two key components: (1) The autonomous agent grounds its self-location based on a language prompt. (2) The agent answers open-ended questions from the perspective of its calculated position. To address this challenge, we introduce SIG3D, an end-to-end Situation-Grounded model for 3D vision language reasoning. We tokenize the 3D scene into sparse voxel representation and propose a language-grounded situation estimator, followed by a situated question answering module. Experiments on the SQA3D and ScanQA datasets show that SIG3D outperforms state-of-the-art models in situation estimation and question answering by a large margin (e.g., an enhancement of over 30% on situation estimation accuracy). Subsequent analysis corroborates our architectural design choices, explores the distinct functions of visual and textual tokens, and highlights the importance of situational awareness in the domain of 3D question answering.
SiTH: Single-view Textured Human Reconstruction with Image-Conditioned Diffusion
A long-standing goal of 3D human reconstruction is to create lifelike and fully detailed 3D humans from single images. The main challenge lies in inferring unknown human shapes, clothing, and texture information in areas not visible in the images. To address this, we propose SiTH, a novel pipeline that uniquely integrates an image-conditioned diffusion model into a 3D mesh reconstruction workflow. At the core of our method lies the decomposition of the ill-posed single-view reconstruction problem into hallucination and reconstruction subproblems. For the former, we employ a powerful generative diffusion model to hallucinate back appearances from the input images. For the latter, we leverage skinned body meshes as guidance to recover full-body texture meshes from the input and back-view images. Our designs enable training of the pipeline with only about 500 3D human scans while maintaining its generality and robustness. Extensive experiments and user studies on two 3D reconstruction benchmarks demonstrated the efficacy of our method in generating realistic, fully textured 3D humans from a diverse range of unseen images.
Situated Dialogue Learning through Procedural Environment Generation
We teach goal-driven agents to interactively act and speak in situated environments by training on generated curriculums. Our agents operate in LIGHT (Urbanek et al. 2019) -- a large-scale crowd-sourced fantasy text adventure game wherein an agent perceives and interacts with the world through textual natural language. Goals in this environment take the form of character-based quests, consisting of personas and motivations. We augment LIGHT by learning to procedurally generate additional novel textual worlds and quests to create a curriculum of steadily increasing difficulty for training agents to achieve such goals. In particular, we measure curriculum difficulty in terms of the rarity of the quest in the original training distribution -- an easier environment is one that is more likely to have been found in the unaugmented dataset. An ablation study shows that this method of learning from the tail of a distribution results in significantly higher generalization abilities as measured by zero-shot performance on never-before-seen quests.
Site-Level Fine-Tuning with Progressive Layer Freezing: Towards Robust Prediction of Bronchopulmonary Dysplasia from Day-1 Chest Radiographs in Extremely Preterm Infants
Bronchopulmonary dysplasia (BPD) is a chronic lung disease affecting 35% of extremely low birth weight infants. Defined by oxygen dependence at 36 weeks postmenstrual age, it causes lifelong respiratory complications. However, preventive interventions carry severe risks, including neurodevelopmental impairment, ventilator-induced lung injury, and systemic complications. Therefore, early BPD prognosis and prediction of BPD outcome is crucial to avoid unnecessary toxicity in low risk infants. Admission radiographs of extremely preterm infants are routinely acquired within 24h of life and could serve as a non-invasive prognostic tool. In this work, we developed and investigated a deep learning approach using chest X-rays from 163 extremely low-birth-weight infants (leq32 weeks gestation, 401-999g) obtained within 24 hours of birth. We fine-tuned a ResNet-50 pretrained specifically on adult chest radiographs, employing progressive layer freezing with discriminative learning rates to prevent overfitting and evaluated a CutMix augmentation and linear probing. For moderate/severe BPD outcome prediction, our best performing model with progressive freezing, linear probing and CutMix achieved an AUROC of 0.78 pm 0.10, balanced accuracy of 0.69 pm 0.10, and an F1-score of 0.67 pm 0.11. In-domain pre-training significantly outperformed ImageNet initialization (p = 0.031) which confirms domain-specific pretraining to be important for BPD outcome prediction. Routine IRDS grades showed limited prognostic value (AUROC 0.57 pm 0.11), confirming the need of learned markers. Our approach demonstrates that domain-specific pretraining enables accurate BPD prediction from routine day-1 radiographs. Through progressive freezing and linear probing, the method remains computationally feasible for site-level implementation and future federated learning deployments.
SITE: towards Spatial Intelligence Thorough Evaluation
Spatial intelligence (SI) represents a cognitive ability encompassing the visualization, manipulation, and reasoning about spatial relationships, underpinning disciplines from neuroscience to robotics. We introduce SITE, a benchmark dataset towards SI Thorough Evaluation in a standardized format of multi-choice visual question-answering, designed to assess large vision-language models' spatial intelligence across diverse visual modalities (single-image, multi-image, and video) and SI factors (figural to environmental scales, spatial visualization and orientation, intrinsic and extrinsic, static and dynamic). Our approach to curating the benchmark combines a bottom-up survey about 31 existing datasets and a top-down strategy drawing upon three classification systems in cognitive science, which prompt us to design two novel types of tasks about view-taking and dynamic scenes. Extensive experiments reveal that leading models fall behind human experts especially in spatial orientation, a fundamental SI factor. Moreover, we demonstrate a positive correlation between a model's spatial reasoning proficiency and its performance on an embodied AI task.
Multi-modal Situated Reasoning in 3D Scenes
Situation awareness is essential for understanding and reasoning about 3D scenes in embodied AI agents. However, existing datasets and benchmarks for situated understanding are limited in data modality, diversity, scale, and task scope. To address these limitations, we propose Multi-modal Situated Question Answering (MSQA), a large-scale multi-modal situated reasoning dataset, scalably collected leveraging 3D scene graphs and vision-language models (VLMs) across a diverse range of real-world 3D scenes. MSQA includes 251K situated question-answering pairs across 9 distinct question categories, covering complex scenarios within 3D scenes. We introduce a novel interleaved multi-modal input setting in our benchmark to provide text, image, and point cloud for situation and question description, resolving ambiguity in previous single-modality convention (e.g., text). Additionally, we devise the Multi-modal Situated Next-step Navigation (MSNN) benchmark to evaluate models' situated reasoning for navigation. Comprehensive evaluations on MSQA and MSNN highlight the limitations of existing vision-language models and underscore the importance of handling multi-modal interleaved inputs and situation modeling. Experiments on data scaling and cross-domain transfer further demonstrate the efficacy of leveraging MSQA as a pre-training dataset for developing more powerful situated reasoning models.
SituationalLLM: Proactive language models with scene awareness for dynamic, contextual task guidance
Large language models (LLMs) have achieved remarkable success in text-based tasks but often struggle to provide actionable guidance in real-world physical environments. This is because of their inability to recognize their limited understanding of the user's physical context. We present SituationalLLM, a novel approach that integrates structured scene information into an LLM to deliver proactive, context-aware assistance. By encoding objects, attributes, and relationships in a custom Scene Graph Language, SituationalLLM actively identifies gaps in environmental context and seeks clarifications during user interactions. This behavior emerges from training on the Situational Awareness Database for Instruct-Tuning (SAD-Instruct), which combines diverse, scenario-specific scene graphs with iterative, dialogue-based refinements. Experimental results indicate that SituationalLLM outperforms generic LLM baselines in task specificity, reliability, and adaptability, paving the way for environment-aware AI assistants capable of delivering robust, user-centric guidance under real-world constraints.
Situation Awareness for Driver-Centric Driving Style Adaptation
There is evidence that the driving style of an autonomous vehicle is important to increase the acceptance and trust of the passengers. The driving situation has been found to have a significant influence on human driving behavior. However, current driving style models only partially incorporate driving environment information, limiting the alignment between an agent and the given situation. Therefore, we propose a situation-aware driving style model based on different visual feature encoders pretrained on fleet data, as well as driving behavior predictors, which are adapted to the driving style of a specific driver. Our experiments show that the proposed method outperforms static driving styles significantly and forms plausible situation clusters. Furthermore, we found that feature encoders pretrained on our dataset lead to more precise driving behavior modeling. In contrast, feature encoders pretrained supervised and unsupervised on different data sources lead to more specific situation clusters, which can be utilized to constrain and control the driving style adaptation for specific situations. Moreover, in a real-world setting, where driving style adaptation is happening iteratively, we found the MLP-based behavior predictors achieve good performance initially but suffer from catastrophic forgetting. In contrast, behavior predictors based on situationdependent statistics can learn iteratively from continuous data streams by design. Overall, our experiments show that important information for driving behavior prediction is contained within the visual feature encoder. The dataset is publicly available at huggingface.co/datasets/jHaselberger/SADC-Situation-Awareness-for-Driver-Centric-Driving-Style-Adaptation.
Situated Language Learning via Interactive Narratives
This paper provides a roadmap that explores the question of how to imbue learning agents with the ability to understand and generate contextually relevant natural language in service of achieving a goal. We hypothesize that two key components in creating such agents are interactivity and environment grounding, shown to be vital parts of language learning in humans, and posit that interactive narratives should be the environments of choice for such training these agents. These games are simulations in which an agent interacts with the world through natural language -- "perceiving", "acting upon", and "talking to" the world using textual descriptions, commands, and dialogue -- and as such exist at the intersection of natural language processing, storytelling, and sequential decision making. We discuss the unique challenges a text games' puzzle-like structure combined with natural language state-and-action spaces provides: knowledge representation, commonsense reasoning, and exploration. Beyond the challenges described so far, progress in the realm of interactive narratives can be applied in adjacent problem domains. These applications provide interesting challenges of their own as well as extensions to those discussed so far. We describe three of them in detail: (1) evaluating AI system's commonsense understanding by automatically creating interactive narratives; (2) adapting abstract text-based policies to include other modalities such as vision; and (3) enabling multi-agent and human-AI collaboration in shared, situated worlds.
Situated and Interactive Multimodal Conversations
Next generation virtual assistants are envisioned to handle multimodal inputs (e.g., vision, memories of previous interactions, in addition to the user's utterances), and perform multimodal actions (e.g., displaying a route in addition to generating the system's utterance). We introduce Situated Interactive MultiModal Conversations (SIMMC) as a new direction aimed at training agents that take multimodal actions grounded in a co-evolving multimodal input context in addition to the dialog history. We provide two SIMMC datasets totalling ~13K human-human dialogs (~169K utterances) using a multimodal Wizard-of-Oz (WoZ) setup, on two shopping domains: (a) furniture (grounded in a shared virtual environment) and, (b) fashion (grounded in an evolving set of images). We also provide logs of the items appearing in each scene, and contextual NLU and coreference annotations, using a novel and unified framework of SIMMC conversational acts for both user and assistant utterances. Finally, we present several tasks within SIMMC as objective evaluation protocols, such as Structural API Prediction and Response Generation. We benchmark a collection of existing models on these SIMMC tasks as strong baselines, and demonstrate rich multimodal conversational interactions. Our data, annotations, code, and models are publicly available.
Multimodal Situational Safety
Multimodal Large Language Models (MLLMs) are rapidly evolving, demonstrating impressive capabilities as multimodal assistants that interact with both humans and their environments. However, this increased sophistication introduces significant safety concerns. In this paper, we present the first evaluation and analysis of a novel safety challenge termed Multimodal Situational Safety, which explores how safety considerations vary based on the specific situation in which the user or agent is engaged. We argue that for an MLLM to respond safely, whether through language or action, it often needs to assess the safety implications of a language query within its corresponding visual context. To evaluate this capability, we develop the Multimodal Situational Safety benchmark (MSSBench) to assess the situational safety performance of current MLLMs. The dataset comprises 1,820 language query-image pairs, half of which the image context is safe, and the other half is unsafe. We also develop an evaluation framework that analyzes key safety aspects, including explicit safety reasoning, visual understanding, and, crucially, situational safety reasoning. Our findings reveal that current MLLMs struggle with this nuanced safety problem in the instruction-following setting and struggle to tackle these situational safety challenges all at once, highlighting a key area for future research. Furthermore, we develop multi-agent pipelines to coordinately solve safety challenges, which shows consistent improvement in safety over the original MLLM response. Code and data: mssbench.github.io.
Fixing 7,400 Bugs for 1$: Cheap Crash-Site Program Repair
The rapid advancement of bug-finding techniques has led to the discovery of more vulnerabilities than developers can reasonably fix, creating an urgent need for effective Automated Program Repair (APR) methods. However, the complexity of modern bugs often makes precise root cause analysis difficult and unreliable. To address this challenge, we propose crash-site repair to simplify the repair task while still mitigating the risk of exploitation. In addition, we introduce a template-guided patch generation approach that significantly reduces the token cost of Large Language Models (LLMs) while maintaining both efficiency and effectiveness. We implement our prototype system, WILLIAMT, and evaluate it against state-of-the-art APR tools. Our results show that, when combined with the top-performing agent CodeRover-S, WILLIAMT reduces token cost by 45.9% and increases the bug-fixing rate to 73.5% (+29.6%) on ARVO, a ground-truth open source software vulnerabilities benchmark. Furthermore, we demonstrate that WILLIAMT can function effectively even without access to frontier LLMs: even a local model running on a Mac M4 Mini achieves a reasonable repair rate. These findings highlight the broad applicability and scalability of WILLIAMT.
In-situ graph reasoning and knowledge expansion using Graph-PReFLexOR
The pursuit of automated scientific discovery has fueled progress from symbolic logic to modern AI, forging new frontiers in reasoning and pattern recognition. Transformers function as potential systems, where every possible relationship remains latent potentiality until tasks impose constraints, akin to measurement. Yet, refining their sampling requires more than probabilistic selection: solutions must conform to specific structures or rules, ensuring consistency and the invocation of general principles. We present Graph-PReFLexOR (Graph-based Preference-based Recursive Language Modeling for Exploratory Optimization of Reasoning), a framework that combines graph reasoning with symbolic abstraction to dynamically expand domain knowledge. Inspired by reinforcement learning, Graph-PReFLexOR defines reasoning as a structured mapping, where tasks yield knowledge graphs, abstract patterns, and ultimately, final answers. Inspired by category theory, it encodes concepts as nodes and their relationships as edges, supporting hierarchical inference and adaptive learning through isomorphic representations. Demonstrations include hypothesis generation, materials design, and creative reasoning, such as discovering relationships between mythological concepts like 'thin places' with materials science. We propose a 'knowledge garden growth' strategy that integrates insights across domains, promoting interdisciplinary connections. Results with a 3-billion-parameter Graph-PReFLexOR model show superior reasoning depth and adaptability, underscoring the potential for transparent, multidisciplinary AI-driven discovery. It lays the groundwork for general autonomous reasoning solutions.
The Mini-SiTian Array: Light Curves Analysis of Asteroids
The SiTian project, with its vast field of view, will become an ideal platform for asteroid scientific research. In this study, we develop a pipeline to analyze the photometry of asteroids and derive their periods from the data collected by the SiTian pathfinder project Mini-SiTian (MST). The pipeline is applied to the MST f02 region, a MST test region with a sky area of 2.29^{circ} times 1.53^{circ}. Rotation periods of 22 asteroids are derived by the obtained light curves analysis. Among them, there are 8 asteroids available in the Asteroid Lightcurve Photometry Database (ALCDEF), and 6 of them with more photometric points (>200) have similar period parameters as the ones in ALCDEF. Additionally, the periods for 14 of these asteroids are newly obtained and are not listed in ALCDEF. This study demonstrates the feasibility of asteroid photometric research by the SiTian project. It shows that future observations from the SiTian project will provide even more photometry of asteroids, significantly increasing the number of available light curves. The potential vast photometric data of asteroids will help us to further understand the physics of asteroids, their material composition, and the formation and evolution of the solar system.
Integrating Biological Data into Autonomous Remote Sensing Systems for In Situ Imageomics: A Case Study for Kenyan Animal Behavior Sensing with Unmanned Aerial Vehicles (UAVs)
In situ imageomics leverages machine learning techniques to infer biological traits from images collected in the field, or in situ, to study individuals organisms, groups of wildlife, and whole ecosystems. Such datasets provide real-time social and environmental context to inferred biological traits, which can enable new, data-driven conservation and ecosystem management. The development of machine learning techniques to extract biological traits from images are impeded by the volume and quality data required to train these models. Autonomous, unmanned aerial vehicles (UAVs), are well suited to collect in situ imageomics data as they can traverse remote terrain quickly to collect large volumes of data with greater consistency and reliability compared to manually piloted UAV missions. However, little guidance exists on optimizing autonomous UAV missions for the purposes of remote sensing for conservation and biodiversity monitoring. The UAV video dataset curated by KABR: In-Situ Dataset for Kenyan Animal Behavior Recognition from Drone Videos required three weeks to collect, a time-consuming and expensive endeavor. Our analysis of KABR revealed that a third of the videos gathered were unusable for the purposes of inferring wildlife behavior. We analyzed the flight telemetry data from portions of UAV videos that were usable for inferring wildlife behavior, and demonstrate how these insights can be integrated into an autonomous remote sensing system to track wildlife in real time. Our autonomous remote sensing system optimizes the UAV's actions to increase the yield of usable data, and matches the flight path of an expert pilot with an 87% accuracy rate, representing an 18.2% improvement in accuracy over previously proposed methods.
Towards A Holistic Landscape of Situated Theory of Mind in Large Language Models
Large Language Models (LLMs) have generated considerable interest and debate regarding their potential emergence of Theory of Mind (ToM). Several recent inquiries reveal a lack of robust ToM in these models and pose a pressing demand to develop new benchmarks, as current ones primarily focus on different aspects of ToM and are prone to shortcuts and data leakage. In this position paper, we seek to answer two road-blocking questions: (1) How can we taxonomize a holistic landscape of machine ToM? (2) What is a more effective evaluation protocol for machine ToM? Following psychological studies, we taxonomize machine ToM into 7 mental state categories and delineate existing benchmarks to identify under-explored aspects of ToM. We argue for a holistic and situated evaluation of ToM to break ToM into individual components and treat LLMs as an agent who is physically situated in environments and socially situated in interactions with humans. Such situated evaluation provides a more comprehensive assessment of mental states and potentially mitigates the risk of shortcuts and data leakage. We further present a pilot study in a grid world setup as a proof of concept. We hope this position paper can facilitate future research to integrate ToM with LLMs and offer an intuitive means for researchers to better position their work in the landscape of ToM. Project page: https://github.com/Mars-tin/awesome-theory-of-mind
Planar site percolation on semi-transitive graphs
Semi-transitive graphs, defined in hps98 as examples where ``uniform percolation" holds whenever p>p_c, are a large class of graphs more general than quasi-transitive graphs. Let G be a semi-transitive graph with one end which can be properly embedded into the plane with uniformly bounded face degree for finite faces and minimal vertex degree at least 7. We show that p_u^{site}(G) +p_c^{site}(G_*)=1, where G_* denotes the matching graph of G. This fulfils and extends an observation of Sykes and Essam in 1964 (SE64) to semi-transitive graphs.
SPRING: Situated Conversation Agent Pretrained with Multimodal Questions from Incremental Layout Graph
Existing multimodal conversation agents have shown impressive abilities to locate absolute positions or retrieve attributes in simple scenarios, but they fail to perform well when complex relative positions and information alignments are involved, which poses a bottleneck in response quality. In this paper, we propose a Situated Conversation Agent Petrained with Multimodal Questions from INcremental Layout Graph (SPRING) with abilities of reasoning multi-hops spatial relations and connecting them with visual attributes in crowded situated scenarios. Specifically, we design two types of Multimodal Question Answering (MQA) tasks to pretrain the agent. All QA pairs utilized during pretraining are generated from novel Incremental Layout Graphs (ILG). QA pair difficulty labels automatically annotated by ILG are used to promote MQA-based Curriculum Learning. Experimental results verify the SPRING's effectiveness, showing that it significantly outperforms state-of-the-art approaches on both SIMMC 1.0 and SIMMC 2.0 datasets.
SQA3D: Situated Question Answering in 3D Scenes
We propose a new task to benchmark scene understanding of embodied agents: Situated Question Answering in 3D Scenes (SQA3D). Given a scene context (e.g., 3D scan), SQA3D requires the tested agent to first understand its situation (position, orientation, etc.) in the 3D scene as described by text, then reason about its surrounding environment and answer a question under that situation. Based upon 650 scenes from ScanNet, we provide a dataset centered around 6.8k unique situations, along with 20.4k descriptions and 33.4k diverse reasoning questions for these situations. These questions examine a wide spectrum of reasoning capabilities for an intelligent agent, ranging from spatial relation comprehension to commonsense understanding, navigation, and multi-hop reasoning. SQA3D imposes a significant challenge to current multi-modal especially 3D reasoning models. We evaluate various state-of-the-art approaches and find that the best one only achieves an overall score of 47.20%, while amateur human participants can reach 90.06%. We believe SQA3D could facilitate future embodied AI research with stronger situation understanding and reasoning capability.
Collaborative Transformers for Grounded Situation Recognition
Grounded situation recognition is the task of predicting the main activity, entities playing certain roles within the activity, and bounding-box groundings of the entities in the given image. To effectively deal with this challenging task, we introduce a novel approach where the two processes for activity classification and entity estimation are interactive and complementary. To implement this idea, we propose Collaborative Glance-Gaze TransFormer (CoFormer) that consists of two modules: Glance transformer for activity classification and Gaze transformer for entity estimation. Glance transformer predicts the main activity with the help of Gaze transformer that analyzes entities and their relations, while Gaze transformer estimates the grounded entities by focusing only on the entities relevant to the activity predicted by Glance transformer. Our CoFormer achieves the state of the art in all evaluation metrics on the SWiG dataset. Training code and model weights are available at https://github.com/jhcho99/CoFormer.
Grounded Situation Recognition with Transformers
Grounded Situation Recognition (GSR) is the task that not only classifies a salient action (verb), but also predicts entities (nouns) associated with semantic roles and their locations in the given image. Inspired by the remarkable success of Transformers in vision tasks, we propose a GSR model based on a Transformer encoder-decoder architecture. The attention mechanism of our model enables accurate verb classification by capturing high-level semantic feature of an image effectively, and allows the model to flexibly deal with the complicated and image-dependent relations between entities for improved noun classification and localization. Our model is the first Transformer architecture for GSR, and achieves the state of the art in every evaluation metric on the SWiG benchmark. Our code is available at https://github.com/jhcho99/gsrtr .
Two Giraffes in a Dirt Field: Using Game Play to Investigate Situation Modelling in Large Multimodal Models
While the situation has improved for text-only models, it again seems to be the case currently that multimodal (text and image) models develop faster than ways to evaluate them. In this paper, we bring a recently developed evaluation paradigm from text models to multimodal models, namely evaluation through the goal-oriented game (self) play, complementing reference-based and preference-based evaluation. Specifically, we define games that challenge a model's capability to represent a situation from visual information and align such representations through dialogue. We find that the largest closed models perform rather well on the games that we define, while even the best open-weight models struggle with them. On further analysis, we find that the exceptional deep captioning capabilities of the largest models drive some of the performance. There is still room to grow for both kinds of models, ensuring the continued relevance of the benchmark.
MSPM: A Multi-Site Physiological Monitoring Dataset for Remote Pulse, Respiration, and Blood Pressure Estimation
Visible-light cameras can capture subtle physiological biomarkers without physical contact with the subject. We present the Multi-Site Physiological Monitoring (MSPM) dataset, which is the first dataset collected to support the study of simultaneous camera-based vital signs estimation from multiple locations on the body. MSPM enables research on remote photoplethysmography (rPPG), respiration rate, and pulse transit time (PTT); it contains ground-truth measurements of pulse oximetry (at multiple body locations) and blood pressure using contacting sensors. We provide thorough experiments demonstrating the suitability of MSPM to support research on rPPG, respiration rate, and PTT. Cross-dataset rPPG experiments reveal that MSPM is a challenging yet high quality dataset, with intra-dataset pulse rate mean absolute error (MAE) below 4 beats per minute (BPM), and cross-dataset pulse rate MAE below 2 BPM in certain cases. Respiration experiments find a MAE of 1.09 breaths per minute by extracting motion features from the chest. PTT experiments find that across the pairs of different body sites, there is high correlation between remote PTT and contact-measured PTT, which facilitates the possibility for future camera-based PTT research.
Predicting ATP binding sites in protein sequences using Deep Learning and Natural Language Processing
Predicting ATP-Protein Binding sites in genes is of great significance in the field of Biology and Medicine. The majority of research in this field has been conducted through time- and resource-intensive 'wet experiments' in laboratories. Over the years, researchers have been investigating computational methods computational methods to accomplish the same goals, utilising the strength of advanced Deep Learning and NLP algorithms. In this paper, we propose to develop methods to classify ATP-Protein binding sites. We conducted various experiments mainly using PSSMs and several word embeddings as features. We used 2D CNNs and LightGBM classifiers as our chief Deep Learning Algorithms. The MP3Vec and BERT models have also been subjected to testing in our study. The outcomes of our experiments demonstrated improvement over the state-of-the-art benchmarks.
The Mini-SiTian Array: real-bogus classification using deep learning
The Mini-SiTian (MST) project is a pathfinder for China's next-generation large-scale time-domain survey, SiTian, aimed at discovering variable stars, transients, and explosive events. MST generates hundreds of thousands of transient alerts every night, approximately 99\% of which are false alarms, posing a significant challenge to its scientific goals. To mitigate the impact of false positives, we propose a deep learning-based solution and systematically evaluate thirteen convolutional neural networks. The results show that ResNet achieves exceptional specificity (99.70\%), EfficientNet achieves the highest recall rate (98.68\%), and DenseNet provides balanced performance with a recall rate of 94.55\% and specificity of 98.66\%. Leveraging these complementary strengths, we developed a bagging-based ensemble classifier that integrates ResNet18, DenseNet121, and EfficientNet\_B0 using a soft voting strategy. This classifier achieved the best AUC value (0.9961) among all models, with a recall rate of 95.37\% and specificity of 99.25\%. It has now been successfully deployed in the MST real-time data processing pipeline. Validation using 5,000 practically processed samples with a classification threshold of 0.798 showed that the classifier achieved 88.31\% accuracy, 91.89\% recall rate, and 99.82\% specificity, confirming its effectiveness and robustness under real application conditions.
Enhancing Large Language Models' Situated Faithfulness to External Contexts
Large Language Models (LLMs) are often augmented with external information as contexts, but this external information can sometimes be inaccurate or even intentionally misleading. We argue that robust LLMs should demonstrate situated faithfulness, dynamically calibrating their trust in external information based on their confidence in the internal knowledge and the external context. To benchmark this capability, we evaluate LLMs across several QA datasets, including a newly created dataset called RedditQA featuring in-the-wild incorrect contexts sourced from Reddit posts. We show that when provided with both correct and incorrect contexts, both open-source and proprietary models tend to overly rely on external information, regardless of its factual accuracy. To enhance situated faithfulness, we propose two approaches: Self-Guided Confidence Reasoning (SCR) and Rule-Based Confidence Reasoning (RCR). SCR enables models to self-access the confidence of external information relative to their own internal knowledge to produce the most accurate answer. RCR, in contrast, extracts explicit confidence signals from the LLM and determines the final answer using predefined rules. Our results show that for LLMs with strong reasoning capabilities, such as GPT-4o and GPT-4o mini, SCR outperforms RCR, achieving improvements of up to 24.2% over a direct input augmentation baseline. Conversely, for a smaller model like Llama-3-8B, RCR outperforms SCR. Fine-tuning SCR with our proposed Confidence Reasoning Direct Preference Optimization (CR-DPO) method improves performance on both seen and unseen datasets, yielding an average improvement of 8.9% on Llama-3-8B. In addition to quantitative results, we offer insights into the relative strengths of SCR and RCR. Our findings highlight promising avenues for improving situated faithfulness in LLMs. The data and code are released.
Informed Reinforcement Learning for Situation-Aware Traffic Rule Exceptions
Reinforcement Learning is a highly active research field with promising advancements. In the field of autonomous driving, however, often very simple scenarios are being examined. Common approaches use non-interpretable control commands as the action space and unstructured reward designs which lack structure. In this work, we introduce Informed Reinforcement Learning, where a structured rulebook is integrated as a knowledge source. We learn trajectories and asses them with a situation-aware reward design, leading to a dynamic reward which allows the agent to learn situations which require controlled traffic rule exceptions. Our method is applicable to arbitrary RL models. We successfully demonstrate high completion rates of complex scenarios with recent model-based agents.
Large Language Model Situational Awareness Based Planning
This work pioneers evaluating emergent planning capabilities based on situational awareness in large language models. We contribute (i) novel benchmarks and metrics for standardized assessment; (ii) a unique dataset to spur progress; and (iii) demonstrations that prompting and multi-agent schemes significantly enhance planning performance in context-sensitive planning tasks. Positioning this within a situated agent and automated planning research, we highlight inherent reliability challenges--efficiently mapping world states to actions without environmental guidance remains open despite simulated domain advances. Although out-of-scope, limitations around validation methodology and data availability indicate exciting directions, including fine-tuning on expanded planning corpora and optimizations for triggering fast latent planning. By conclusively demonstrating current methods' promise and limitations via rigorous comparison, we catalyze investigating reliable goal-directed reasoning for situated agents.
Vision-based Situational Graphs Generating Optimizable 3D Scene Representations
3D scene graphs offer a more efficient representation of the environment by hierarchically organizing diverse semantic entities and the topological relationships among them. Fiducial markers, on the other hand, offer a valuable mechanism for encoding comprehensive information pertaining to environments and the objects within them. In the context of Visual SLAM (VSLAM), especially when the reconstructed maps are enriched with practical semantic information, these markers have the potential to enhance the map by augmenting valuable semantic information and fostering meaningful connections among the semantic objects. In this regard, this paper exploits the potential of fiducial markers to incorporate a VSLAM framework with hierarchical representations that generates optimizable multi-layered vision-based situational graphs. The framework comprises a conventional VSLAM system with low-level feature tracking and mapping capabilities bolstered by the incorporation of a fiducial marker map. The fiducial markers aid in identifying walls and doors in the environment, subsequently establishing meaningful associations with high-level entities, including corridors and rooms. Experimental results are conducted on a real-world dataset collected using various legged robots and benchmarked against a Light Detection And Ranging (LiDAR)-based framework (S-Graphs) as the ground truth. Consequently, our framework not only excels in crafting a richer, multi-layered hierarchical map of the environment but also shows enhancement in robot pose accuracy when contrasted with state-of-the-art methodologies.
Cream: Visually-Situated Natural Language Understanding with Contrastive Reading Model and Frozen Large Language Models
Advances in Large Language Models (LLMs) have inspired a surge of research exploring their expansion into the visual domain. While recent models exhibit promise in generating abstract captions for images and conducting natural conversations, their performance on text-rich images leaves room for improvement. In this paper, we propose the Contrastive Reading Model (Cream), a novel neural architecture designed to enhance the language-image understanding capability of LLMs by capturing intricate details typically overlooked by existing methods. Cream integrates vision and auxiliary encoders, complemented by a contrastive feature alignment technique, resulting in a more effective understanding of textual information within document images. Our approach, thus, seeks to bridge the gap between vision and language understanding, paving the way for more sophisticated Document Intelligence Assistants. Rigorous evaluations across diverse tasks, such as visual question answering on document images, demonstrate the efficacy of Cream as a state-of-the-art model in the field of visual document understanding. We provide our codebase and newly-generated datasets at https://github.com/naver-ai/cream
Towards Collaborative Plan Acquisition through Theory of Mind Modeling in Situated Dialogue
Collaborative tasks often begin with partial task knowledge and incomplete initial plans from each partner. To complete these tasks, agents need to engage in situated communication with their partners and coordinate their partial plans towards a complete plan to achieve a joint task goal. While such collaboration seems effortless in a human-human team, it is highly challenging for human-AI collaboration. To address this limitation, this paper takes a step towards collaborative plan acquisition, where humans and agents strive to learn and communicate with each other to acquire a complete plan for joint tasks. Specifically, we formulate a novel problem for agents to predict the missing task knowledge for themselves and for their partners based on rich perceptual and dialogue history. We extend a situated dialogue benchmark for symmetric collaborative tasks in a 3D blocks world and investigate computational strategies for plan acquisition. Our empirical results suggest that predicting the partner's missing knowledge is a more viable approach than predicting one's own. We show that explicit modeling of the partner's dialogue moves and mental states produces improved and more stable results than without. These results provide insight for future AI agents that can predict what knowledge their partner is missing and, therefore, can proactively communicate such information to help their partner acquire such missing knowledge toward a common understanding of joint tasks.
VASR: Visual Analogies of Situation Recognition
A core process in human cognition is analogical mapping: the ability to identify a similar relational structure between different situations. We introduce a novel task, Visual Analogies of Situation Recognition, adapting the classical word-analogy task into the visual domain. Given a triplet of images, the task is to select an image candidate B' that completes the analogy (A to A' is like B to what?). Unlike previous work on visual analogy that focused on simple image transformations, we tackle complex analogies requiring understanding of scenes. We leverage situation recognition annotations and the CLIP model to generate a large set of 500k candidate analogies. Crowdsourced annotations for a sample of the data indicate that humans agree with the dataset label ~80% of the time (chance level 25%). Furthermore, we use human annotations to create a gold-standard dataset of 3,820 validated analogies. Our experiments demonstrate that state-of-the-art models do well when distractors are chosen randomly (~86%), but struggle with carefully chosen distractors (~53%, compared to 90% human accuracy). We hope our dataset will encourage the development of new analogy-making models. Website: https://vasr-dataset.github.io/
DOROTHIE: Spoken Dialogue for Handling Unexpected Situations in Interactive Autonomous Driving Agents
In the real world, autonomous driving agents navigate in highly dynamic environments full of unexpected situations where pre-trained models are unreliable. In these situations, what is immediately available to vehicles is often only human operators. Empowering autonomous driving agents with the ability to navigate in a continuous and dynamic environment and to communicate with humans through sensorimotor-grounded dialogue becomes critical. To this end, we introduce Dialogue On the ROad To Handle Irregular Events (DOROTHIE), a novel interactive simulation platform that enables the creation of unexpected situations on the fly to support empirical studies on situated communication with autonomous driving agents. Based on this platform, we created the Situated Dialogue Navigation (SDN), a navigation benchmark of 183 trials with a total of 8415 utterances, around 18.7 hours of control streams, and 2.9 hours of trimmed audio. SDN is developed to evaluate the agent's ability to predict dialogue moves from humans as well as generate its own dialogue moves and physical navigation actions. We further developed a transformer-based baseline model for these SDN tasks. Our empirical results indicate that language guided-navigation in a highly dynamic environment is an extremely difficult task for end-to-end models. These results will provide insight towards future work on robust autonomous driving agents. The DOROTHIE platform, SDN benchmark, and code for the baseline model are available at https://github.com/sled-group/DOROTHIE.
ProgPrompt: Generating Situated Robot Task Plans using Large Language Models
Task planning can require defining myriad domain knowledge about the world in which a robot needs to act. To ameliorate that effort, large language models (LLMs) can be used to score potential next actions during task planning, and even generate action sequences directly, given an instruction in natural language with no additional domain information. However, such methods either require enumerating all possible next steps for scoring, or generate free-form text that may contain actions not possible on a given robot in its current context. We present a programmatic LLM prompt structure that enables plan generation functional across situated environments, robot capabilities, and tasks. Our key insight is to prompt the LLM with program-like specifications of the available actions and objects in an environment, as well as with example programs that can be executed. We make concrete recommendations about prompt structure and generation constraints through ablation experiments, demonstrate state of the art success rates in VirtualHome household tasks, and deploy our method on a physical robot arm for tabletop tasks. Website at progprompt.github.io
Singapore Soundscape Site Selection Survey (S5): Identification of Characteristic Soundscapes of Singapore via Weighted k-means Clustering
The ecological validity of soundscape studies usually rests on a choice of soundscapes that are representative of the perceptual space under investigation. For example, a soundscape pleasantness study might investigate locations with soundscapes ranging from "pleasant" to "annoying". The choice of soundscapes is typically researcher-led, but a participant-led process can reduce selection bias and improve result reliability. Hence, we propose a robust participant-led method to pinpoint characteristic soundscapes possessing arbitrary perceptual attributes. We validate our method by identifying Singaporean soundscapes spanning the perceptual quadrants generated from the "Pleasantness" and "Eventfulness" axes of the ISO 12913-2 circumplex model of soundscape perception, as perceived by local experts. From memory and experience, 67 participants first selected locations corresponding to each perceptual quadrant in each major planning region of Singapore. We then performed weighted k-means clustering on the selected locations, with weights for each location derived from previous frequencies and durations spent in each location by each participant. Weights hence acted as proxies for participant confidence. In total, 62 locations were thereby identified as suitable locations with characteristic soundscapes for further research utilizing the ISO 12913-2 perceptual quadrants. Audio-visual recordings and acoustic characterization of the soundscapes will be made in a future study.
Autonomous In-Situ Soundscape Augmentation via Joint Selection of Masker and Gain
The selection of maskers and playback gain levels in a soundscape augmentation system is crucial to its effectiveness in improving the overall acoustic comfort of a given environment. Traditionally, the selection of appropriate maskers and gain levels has been informed by expert opinion, which may not representative of the target population, or by listening tests, which can be time-consuming and labour-intensive. Furthermore, the resulting static choices of masker and gain are often inflexible to the dynamic nature of real-world soundscapes. In this work, we utilized a deep learning model to perform joint selection of the optimal masker and its gain level for a given soundscape. The proposed model was designed with highly modular building blocks, allowing for an optimized inference process that can quickly search through a large number of masker and gain combinations. In addition, we introduced the use of feature-domain soundscape augmentation conditioned on the digital gain level, eliminating the computationally expensive waveform-domain mixing process during inference time, as well as the tedious pre-calibration process required for new maskers. The proposed system was validated on a large-scale dataset of subjective responses to augmented soundscapes with more than 440 participants, ensuring the ability of the model to predict combined effect of the masker and its gain level on the perceptual pleasantness level.
DREAM: Improving Situational QA by First Elaborating the Situation
When people answer questions about a specific situation, e.g., "I cheated on my mid-term exam last week. Was that wrong?", cognitive science suggests that they form a mental picture of that situation before answering. While we do not know how language models (LMs) answer such questions, we conjecture that they may answer more accurately if they are also provided with additional details about the question situation, elaborating the "scene". To test this conjecture, we train a new model, DREAM, to answer questions that elaborate the scenes that situated questions are about, and then provide those elaborations as additional context to a question-answering (QA) model. We find that DREAM is able to create better scene elaborations (more accurate, useful, and consistent) than a representative state-of-the-art, zero-shot model (Macaw). We also find that using the scene elaborations as additional context improves the answer accuracy of a downstream QA system, including beyond that obtainable by simply further finetuning the QA system on DREAM's training data. These results suggest that adding focused elaborations about a situation can improve a system's reasoning about it, and may serve as an effective way of injecting new scenario based knowledge into QA models. Finally, our approach is dataset-neutral; we observe improved QA performance across different models, with even bigger gains on models with fewer parameters. We make our dataset and model publicly available at https://github.com/allenai/dream.
Predicting sepsis in multi-site, multi-national intensive care cohorts using deep learning
Despite decades of clinical research, sepsis remains a global public health crisis with high mortality, and morbidity. Currently, when sepsis is detected and the underlying pathogen is identified, organ damage may have already progressed to irreversible stages. Effective sepsis management is therefore highly time-sensitive. By systematically analysing trends in the plethora of clinical data available in the intensive care unit (ICU), an early prediction of sepsis could lead to earlier pathogen identification, resistance testing, and effective antibiotic and supportive treatment, and thereby become a life-saving measure. Here, we developed and validated a machine learning (ML) system for the prediction of sepsis in the ICU. Our analysis represents the largest multi-national, multi-centre in-ICU study for sepsis prediction using ML to date. Our dataset contains 156,309 unique ICU admissions, which represent a refined and harmonised subset of five large ICU databases originating from three countries. Using the international consensus definition Sepsis-3, we derived hourly-resolved sepsis label annotations, amounting to 26,734 (17.1%) septic stays. We compared our approach, a deep self-attention model, to several clinical baselines as well as ML baselines and performed an extensive internal and external validation within and across databases. On average, our model was able to predict sepsis with an AUROC of 0.847 pm 0.050 (internal out-of sample validation) and 0.761 pm 0.052 (external validation). For a harmonised prevalence of 17%, at 80% recall our model detects septic patients with 39% precision 3.7 hours in advance.
ResourceSync: Leveraging Sitemaps for Resource Synchronization
Many applications need up-to-date copies of collections of changing Web resources. Such synchronization is currently achieved using ad-hoc or proprietary solutions. We propose ResourceSync, a general Web resource synchronization protocol that leverages XML Sitemaps. It provides a set of capabilities that can be combined in a modular manner to meet local or community requirements. We report on work to implement this protocol for arXiv.org and also provide an experimental prototype for the English Wikipedia as well as a client API.
UNcommonsense Reasoning: Abductive Reasoning about Uncommon Situations
Language technologies that accurately model the dynamics of events must perform commonsense reasoning. Existing work evaluating commonsense reasoning focuses on making inferences about common, everyday situations. To instead investigate the ability to model unusual, unexpected, and unlikely situations, we explore the task of uncommonsense abductive reasoning. Given a piece of context with an unexpected outcome, this task requires reasoning abductively to generate a natural language explanation that makes the unexpected outcome more likely in the context. To this end, we curate and release a new English language corpus called UNcommonsense. We characterize the differences between the performance of human explainers and the best performing large language models, finding that model-enhanced human-written explanations achieve the highest quality by trading off between specificity and diversity. Finally, we experiment with several online imitation learning algorithms to train open and accessible language models on this task. When compared with the vanilla supervised fine-tuning approach, these methods consistently reduce lose rates on both common and uncommonsense abductive reasoning judged by human evaluators.
Aligning VLM Assistants with Personalized Situated Cognition
Vision-language models (VLMs) aligned with general human objectives, such as being harmless and hallucination-free, have become valuable assistants of humans in managing visual tasks. However, people with diversified backgrounds have different cognition even in the same situation. Consequently, they may have personalized expectations for VLM assistants. This highlights the urgent need to align VLM assistants with personalized situated cognition for real-world assistance. To study this problem, we first simplify it by characterizing individuals based on the sociological concept of Role-Set. Then, we propose to evaluate the individuals' actions to examine whether the personalized alignment is achieved. Further, we construct a benchmark named PCogAlignBench, which includes 18k instances and 20 individuals with different Role-Sets. Finally, we present a framework called PCogAlign, which constructs a cognition-aware and action-based reward model for personalized alignment. Experimental results and human evaluations demonstrate the reliability of the PCogAlignBench and the effectiveness of our proposed PCogAlign. We will open-source the constructed benchmark and code at https://github.com/NLPGM/PCogAlign.
SPRI: Aligning Large Language Models with Context-Situated Principles
Aligning Large Language Models to integrate and reflect human values, especially for tasks that demand intricate human oversight, is arduous since it is resource-intensive and time-consuming to depend on human expertise for context-specific guidance. Prior work has utilized predefined sets of rules or principles to steer the behavior of models (Bai et al., 2022; Sun et al., 2023). However, these principles tend to be generic, making it challenging to adapt them to each individual input query or context. In this work, we present Situated-PRInciples (SPRI), a framework requiring minimal or no human effort that is designed to automatically generate guiding principles in real-time for each input query and utilize them to align each response. We evaluate SPRI on three tasks, and show that 1) SPRI can derive principles in a complex domain-specific task that leads to on-par performance as expert-crafted ones; 2) SPRI-generated principles lead to instance-specific rubrics that outperform prior LLM-as-a-judge frameworks; 3) using SPRI to generate synthetic SFT data leads to substantial improvement on truthfulness. We release our code and model generations at https://github.com/honglizhan/SPRI-public.
WildFeedback: Aligning LLMs With In-situ User Interactions And Feedback
As large language models (LLMs) continue to advance, aligning these models with human preferences has emerged as a critical challenge. Traditional alignment methods, relying on human or LLM annotated datasets, are limited by their resource-intensive nature, inherent subjectivity, and the risk of feedback loops that amplify model biases. To overcome these limitations, we introduce WildFeedback, a novel framework that leverages real-time, in-situ user interactions to create preference datasets that more accurately reflect authentic human values. WildFeedback operates through a three-step process: feedback signal identification, preference data construction, and user-guided evaluation. We applied this framework to a large corpus of user-LLM conversations, resulting in a rich preference dataset that reflects genuine user preferences. This dataset captures the nuances of user preferences by identifying and classifying feedback signals within natural conversations, thereby enabling the construction of more representative and context-sensitive alignment data. Our extensive experiments demonstrate that LLMs fine-tuned on WildFeedback exhibit significantly improved alignment with user preferences, as evidenced by both traditional benchmarks and our proposed user-guided evaluation. By incorporating real-time feedback from actual users, WildFeedback addresses the scalability, subjectivity, and bias challenges that plague existing approaches, marking a significant step toward developing LLMs that are more responsive to the diverse and evolving needs of their users. In summary, WildFeedback offers a robust, scalable solution for aligning LLMs with true human values, setting a new standard for the development and evaluation of user-centric language models.
Immunohistochemistry guided segmentation of benign epithelial cells, in situ lesions, and invasive epithelial cells in breast cancer slides
Digital pathology enables automatic analysis of histopathological sections using artificial intelligence (AI). Automatic evaluation could improve diagnostic efficiency and help find associations between morphological features and clinical outcome. For development of such prediction models, identifying invasive epithelial cells, and separating these from benign epithelial cells and in situ lesions would be the first step. In this study, we aimed to develop an AI model for segmentation of epithelial cells in sections from breast cancer. We generated epithelial ground truth masks by restaining hematoxylin and eosin (HE) sections with cytokeratin (CK) AE1/AE3, and by pathologists' annotations. HE/CK image pairs were used to train a convolutional neural network, and data augmentation was used to make the model more robust. Tissue microarrays (TMAs) from 839 patients, and whole slide images from two patients were used for training and evaluation of the models. The sections were derived from four cohorts of breast cancer patients. TMAs from 21 patients from a fifth cohort was used as a second test set. In quantitative evaluation, a mean Dice score of 0.70, 0.79, and 0.75 for invasive epithelial cells, benign epithelial cells, and in situ lesions, respectively, were achieved. In qualitative scoring (0-5) by pathologists, results were best for all epithelium and invasive epithelium, with scores of 4.7 and 4.4. Scores for benign epithelium and in situ lesions were 3.7 and 2.0. The proposed model segmented epithelial cells in HE stained breast cancer slides well, but further work is needed for accurate division between the classes. Immunohistochemistry, together with pathologists' annotations, enabled the creation of accurate ground truths. The model is made freely available in FastPathology and the code is available at https://github.com/AICAN-Research/breast-epithelium-segmentation
NetDistiller: Empowering Tiny Deep Learning via In-Situ Distillation
Boosting the task accuracy of tiny neural networks (TNNs) has become a fundamental challenge for enabling the deployments of TNNs on edge devices which are constrained by strict limitations in terms of memory, computation, bandwidth, and power supply. To this end, we propose a framework called NetDistiller to boost the achievable accuracy of TNNs by treating them as sub-networks of a weight-sharing teacher constructed by expanding the number of channels of the TNN. Specifically, the target TNN model is jointly trained with the weight-sharing teacher model via (1) gradient surgery to tackle the gradient conflicts between them and (2) uncertainty-aware distillation to mitigate the overfitting of the teacher model. Extensive experiments across diverse tasks validate NetDistiller's effectiveness in boosting TNNs' achievable accuracy over state-of-the-art methods. Our code is available at https://github.com/GATECH-EIC/NetDistiller.
UReader: Universal OCR-free Visually-situated Language Understanding with Multimodal Large Language Model
Text is ubiquitous in our visual world, conveying crucial information, such as in documents, websites, and everyday photographs. In this work, we propose UReader, a first exploration of universal OCR-free visually-situated language understanding based on the Multimodal Large Language Model (MLLM). By leveraging the shallow text recognition ability of the MLLM, we only finetuned 1.2% parameters and the training cost is much lower than previous work following domain-specific pretraining and finetuning paradigms. Concretely, UReader is jointly finetuned on a wide range of Visually-situated Language Understanding tasks via a unified instruction format. To enhance the visual text and semantic understanding, we further apply two auxiliary tasks with the same format, namely text reading and key points generation tasks. We design a shape-adaptive cropping module before the encoder-decoder architecture of MLLM to leverage the frozen low-resolution vision encoder for processing high-resolution images. Without downstream finetuning, our single model achieves state-of-the-art ocr-free performance in 8 out of 10 visually-situated language understanding tasks, across 5 domains: documents, tables, charts, natural images, and webpage screenshots. Codes and instruction-tuning datasets will be released.
Estimation of Human Condition at Disaster Site Using Aerial Drone Images
Drones are being used to assess the situation in various disasters. In this study, we investigate a method to automatically estimate the damage status of people based on their actions in aerial drone images in order to understand disaster sites faster and save labor. We constructed a new dataset of aerial images of human actions in a hypothetical disaster that occurred in an urban area, and classified the human damage status using 3D ResNet. The results showed that the status with characteristic human actions could be classified with a recall rate of more than 80%, while other statuses with similar human actions could only be classified with a recall rate of about 50%. In addition, a cloud-based VR presentation application suggested the effectiveness of using drones to understand the disaster site and estimate the human condition.
DiPlomat: A Dialogue Dataset for Situated Pragmatic Reasoning
Pragmatic reasoning plays a pivotal role in deciphering implicit meanings that frequently arise in real-life conversations and is essential for the development of communicative social agents. In this paper, we introduce a novel challenge, DiPlomat, aiming at benchmarking machines' capabilities on pragmatic reasoning and situated conversational understanding. Compared with previous works that treat different figurative expressions (e.g. metaphor, sarcasm) as individual tasks, DiPlomat provides a cohesive framework towards general pragmatic understanding. Our dataset is created through the utilization of Amazon Mechanical Turk ( AMT ), resulting in a total of 4, 177 multi-turn dialogues. In conjunction with the dataset, we propose two tasks, Pragmatic Identification and Reasoning (PIR) and Conversational Question Answering (CQA). Experimental results with state-of-the-art (SOTA) neural architectures reveal several significant findings: 1) large language models ( LLMs) exhibit poor performance in tackling this subjective domain; 2) comprehensive comprehension of context emerges as a critical factor for establishing benign human-machine interactions; 3) current models defect in the application of pragmatic reasoning. As a result, we call on more attention to improve the ability of context understanding, reasoning, and implied meaning modeling.
Reasoning Over Paragraph Effects in Situations
A key component of successfully reading a passage of text is the ability to apply knowledge gained from the passage to a new situation. In order to facilitate progress on this kind of reading, we present ROPES, a challenging benchmark for reading comprehension targeting Reasoning Over Paragraph Effects in Situations. We target expository language describing causes and effects (e.g., "animal pollinators increase efficiency of fertilization in flowers"), as they have clear implications for new situations. A system is presented a background passage containing at least one of these relations, a novel situation that uses this background, and questions that require reasoning about effects of the relationships in the background passage in the context of the situation. We collect background passages from science textbooks and Wikipedia that contain such phenomena, and ask crowd workers to author situations, questions, and answers, resulting in a 14,322 question dataset. We analyze the challenges of this task and evaluate the performance of state-of-the-art reading comprehension models. The best model performs only slightly better than randomly guessing an answer of the correct type, at 61.6% F1, well below the human performance of 89.0%.
Tracing the cosmological origin of gas that fuels in situ star formation in TNG50 galaxies
Based on their cosmological origin, the stars of a galaxy can be divided into two categories: those that enter through merger events (ex situ) and those born in the main progenitor (in situ). We used the TNG50 cosmological magnetohydrodynamical simulation and its Lagrangian tracer particles to explore and quantify the origin of gas that ultimately forms the in situ stars of galaxies. We tracked back the baryonic mass contributing to the z=0 in situ stellar populations of galaxies, studying trends in mass from dwarfs to group-scale halos. We find that more massive halos acquire this matter earlier than lower-mass halos, reflecting an overall earlier assembly of their in situ stellar mass. Defining the Lagrangian half-mass radius R_{rm L, 1/2} of a galaxy as the distance containing half of the mass that will form its in situ stars by z=0, we find that R_{rm L, 1/2} is larger for more massive halos at early times, reflecting larger "in situ Lagrangian regions." However, the dependence of this radius on halo mass becomes flat at z simeq 3 and then inverts toward z=0. In addition, R_{rm L, 1/2} increases rapidly with redshift, surpassing the virial radii of halos at z sim 2. This marks the cosmic epoch at which most of the gas that eventually forms the in situ stars of galaxies leaves the intergalactic medium (IGM) and enters halos, a transition that occurs earlier for more massive halos. The formation redshift of the in situ stellar component increases with halo mass, while the formation redshift of the dark matter halo decreases, indicative of a differential assembly history between these two components. Finally, we decomposed the z=0 in situ stellar mass into its distinct modes of accretion. Smooth accretion from the IGM is the most important for low-mass galaxies, while mergers and satellite-stripped gas become relevant and even dominant only for high-mass galaxies.
Automating Urban Soundscape Enhancements with AI: In-situ Assessment of Quality and Restorativeness in Traffic-Exposed Residential Areas
Formalized in ISO 12913, the "soundscape" approach is a paradigmatic shift towards perception-based urban sound management, aiming to alleviate the substantial socioeconomic costs of noise pollution to advance the United Nations Sustainable Development Goals. Focusing on traffic-exposed outdoor residential sites, we implemented an automatic masker selection system (AMSS) utilizing natural sounds to mask (or augment) traffic soundscapes. We employed a pre-trained AI model to automatically select the optimal masker and adjust its playback level, adapting to changes over time in the ambient environment to maximize "Pleasantness", a perceptual dimension of soundscape quality in ISO 12913. Our validation study involving (N=68) residents revealed a significant 14.6 % enhancement in "Pleasantness" after intervention, correlating with increased restorativeness and positive affect. Perceptual enhancements at the traffic-exposed site matched those at a quieter control site with 6 dB(A) lower L_A,eq and road traffic noise dominance, affirming the efficacy of AMSS as a soundscape intervention, while streamlining the labour-intensive assessment of "Pleasantness" with probabilistic AI prediction.
Rearrangement of single atoms in a 2000-site optical tweezers array at cryogenic temperatures
We report on the trapping of single rubidium atoms in large arrays of optical tweezers comprising up to 2088 sites in a cryogenic environment at 6 K. Our approach relies on the use of microscope objectives that are in-vacuum but at room temperature, in combination with windowless thermal shields into which the objectives are protruding to ensure a cryogenic environment for the trapped atoms. To achieve enough optical power for efficient trapping, we combine two lasers at slightly different wavelengths. We discuss the performance and limitations of our design. Finally, we demonstrate atom-by-atom rearrangement of an 828-atom target array using moving optical tweezers controlled by a field-programmable gate array.
Game-MUG: Multimodal Oriented Game Situation Understanding and Commentary Generation Dataset
The dynamic nature of esports makes the situation relatively complicated for average viewers. Esports broadcasting involves game expert casters, but the caster-dependent game commentary is not enough to fully understand the game situation. It will be richer by including diverse multimodal esports information, including audiences' talks/emotions, game audio, and game match event information. This paper introduces GAME-MUG, a new multimodal game situation understanding and audience-engaged commentary generation dataset and its strong baseline. Our dataset is collected from 2020-2022 LOL game live streams from YouTube and Twitch, and includes multimodal esports game information, including text, audio, and time-series event logs, for detecting the game situation. In addition, we also propose a new audience conversation augmented commentary dataset by covering the game situation and audience conversation understanding, and introducing a robust joint multimodal dual learning model as a baseline. We examine the model's game situation/event understanding ability and commentary generation capability to show the effectiveness of the multimodal aspects coverage and the joint integration learning approach.
Preliminary investigation of the short-term in situ performance of an automatic masker selection system
Soundscape augmentation or "masking" introduces wanted sounds into the acoustic environment to improve acoustic comfort. Usually, the masker selection and playback strategies are either arbitrary or based on simple rules (e.g. -3 dBA), which may lead to sub-optimal increment or even reduction in acoustic comfort for dynamic acoustic environments. To reduce ambiguity in the selection of maskers, an automatic masker selection system (AMSS) was recently developed. The AMSS uses a deep-learning model trained on a large-scale dataset of subjective responses to maximize the derived ISO pleasantness (ISO 12913-2). Hence, this study investigates the short-term in situ performance of the AMSS implemented in a gazebo in an urban park. Firstly, the predicted ISO pleasantness from the AMSS is evaluated in comparison to the in situ subjective evaluation scores. Secondly, the effect of various masker selection schemes on the perceived affective quality and appropriateness would be evaluated. In total, each participant evaluated 6 conditions: (1) ambient environment with no maskers; (2) AMSS; (3) bird and (4) water masker from prior art; (5) random selection from same pool of maskers used to train the AMSS; and (6) selection of best-performing maskers based on the analysis of the dataset used to train the AMSS.
Symbol emergence as interpersonal cross-situational learning: the emergence of lexical knowledge with combinatoriality
We present a computational model for a symbol emergence system that enables the emergence of lexical knowledge with combinatoriality among agents through a Metropolis-Hastings naming game and cross-situational learning. Many computational models have been proposed to investigate combinatoriality in emergent communication and symbol emergence in cognitive and developmental robotics. However, existing models do not sufficiently address category formation based on sensory-motor information and semiotic communication through the exchange of word sequences within a single integrated model. Our proposed model facilitates the emergence of lexical knowledge with combinatoriality by performing category formation using multimodal sensory-motor information and enabling semiotic communication through the exchange of word sequences among agents in a unified model. Furthermore, the model enables an agent to predict sensory-motor information for unobserved situations by combining words associated with categories in each modality. We conducted two experiments with two humanoid robots in a simulated environment to evaluate our proposed model. The results demonstrated that the agents can acquire lexical knowledge with combinatoriality through interpersonal cross-situational learning based on the Metropolis-Hastings naming game and cross-situational learning. Furthermore, our results indicate that the lexical knowledge developed using our proposed model exhibits generalization performance for novel situations through interpersonal cross-modal inference.
VSTAR: A Video-grounded Dialogue Dataset for Situated Semantic Understanding with Scene and Topic Transitions
Video-grounded dialogue understanding is a challenging problem that requires machine to perceive, parse and reason over situated semantics extracted from weakly aligned video and dialogues. Most existing benchmarks treat both modalities the same as a frame-independent visual understanding task, while neglecting the intrinsic attributes in multimodal dialogues, such as scene and topic transitions. In this paper, we present Video-grounded Scene&Topic AwaRe dialogue (VSTAR) dataset, a large scale video-grounded dialogue understanding dataset based on 395 TV series. Based on VSTAR, we propose two benchmarks for video-grounded dialogue understanding: scene segmentation and topic segmentation, and one benchmark for video-grounded dialogue generation. Comprehensive experiments are performed on these benchmarks to demonstrate the importance of multimodal information and segments in video-grounded dialogue understanding and generation.
NormBank: A Knowledge Bank of Situational Social Norms
We present NormBank, a knowledge bank of 155k situational norms. This resource is designed to ground flexible normative reasoning for interactive, assistive, and collaborative AI systems. Unlike prior commonsense resources, NormBank grounds each inference within a multivalent sociocultural frame, which includes the setting (e.g., restaurant), the agents' contingent roles (waiter, customer), their attributes (age, gender), and other physical, social, and cultural constraints (e.g., the temperature or the country of operation). In total, NormBank contains 63k unique constraints from a taxonomy that we introduce and iteratively refine here. Constraints then apply in different combinations to frame social norms. Under these manipulations, norms are non-monotonic - one can cancel an inference by updating its frame even slightly. Still, we find evidence that neural models can help reliably extend the scope and coverage of NormBank. We further demonstrate the utility of this resource with a series of transfer experiments.
A Multi Camera Unsupervised Domain Adaptation Pipeline for Object Detection in Cultural Sites through Adversarial Learning and Self-Training
Object detection algorithms allow to enable many interesting applications which can be implemented in different devices, such as smartphones and wearable devices. In the context of a cultural site, implementing these algorithms in a wearable device, such as a pair of smart glasses, allow to enable the use of augmented reality (AR) to show extra information about the artworks and enrich the visitors' experience during their tour. However, object detection algorithms require to be trained on many well annotated examples to achieve reasonable results. This brings a major limitation since the annotation process requires human supervision which makes it expensive in terms of time and costs. A possible solution to reduce these costs consist in exploiting tools to automatically generate synthetic labeled images from a 3D model of the site. However, models trained with synthetic data do not generalize on real images acquired in the target scenario in which they are supposed to be used. Furthermore, object detectors should be able to work with different wearable devices or different mobile devices, which makes generalization even harder. In this paper, we present a new dataset collected in a cultural site to study the problem of domain adaptation for object detection in the presence of multiple unlabeled target domains corresponding to different cameras and a labeled source domain obtained considering synthetic images for training purposes. We present a new domain adaptation method which outperforms current state-of-the-art approaches combining the benefits of aligning the domains at the feature and pixel level with a self-training process. We release the dataset at the following link https://iplab.dmi.unict.it/OBJ-MDA/ and the code of the proposed architecture at https://github.com/fpv-iplab/STMDA-RetinaNet.
An Unsupervised Domain Adaptation Scheme for Single-Stage Artwork Recognition in Cultural Sites
Recognizing artworks in a cultural site using images acquired from the user's point of view (First Person Vision) allows to build interesting applications for both the visitors and the site managers. However, current object detection algorithms working in fully supervised settings need to be trained with large quantities of labeled data, whose collection requires a lot of times and high costs in order to achieve good performance. Using synthetic data generated from the 3D model of the cultural site to train the algorithms can reduce these costs. On the other hand, when these models are tested with real images, a significant drop in performance is observed due to the differences between real and synthetic images. In this study we consider the problem of Unsupervised Domain Adaptation for object detection in cultural sites. To address this problem, we created a new dataset containing both synthetic and real images of 16 different artworks. We hence investigated different domain adaptation techniques based on one-stage and two-stage object detector, image-to-image translation and feature alignment. Based on the observation that single-stage detectors are more robust to the domain shift in the considered settings, we proposed a new method which builds on RetinaNet and feature alignment that we called DA-RetinaNet. The proposed approach achieves better results than compared methods on the proposed dataset and on Cityscapes. To support research in this field we release the dataset at the following link https://iplab.dmi.unict.it/EGO-CH-OBJ-UDA/ and the code of the proposed architecture at https://github.com/fpv-iplab/DA-RetinaNet.
Sodium Metal Battery using CobaltOxide through in Situ Plating of Sodium Metal
In this work, we demonstrate that an impugn of energy density for sodium chemistries can be prevail through an anode-free architecture enabled by the use of a (nanocarbon/Cobaltoxide) nucleation layer formed on Aluminium current collectors. Electrochemical studies show this configuration to provide highly stable and efficient plating and stripping of sodium metal over a range of currents up to 5 mA/cm2, sodium loading up to 14 mAh/cm2, and with long-term endurance exceeding 1000 cycles at a current of 0.7 mA/cm2. Building upon this anode-free architecture, we demonstrate a full cell using a presodiated pyrite cathode to achieve energy densities of 400 Wh/kg, far surpassing recent reports on SIBs and even the theoretical maximum for LIB technology while still relying on naturally abundant raw materials and cost-effective aqueous processing.
Cuff-less Arterial Blood Pressure Waveform Synthesis from Single-site PPG using Transformer & Frequency-domain Learning
We propose two novel purpose-built deep learning (DL) models for synthesis of the arterial blood pressure (ABP) waveform in a cuff-less manner, using a single-site photoplethysmography (PPG) signal. We utilize the public UCI dataset on cuff-less blood pressure (CLBP) estimation to train and evaluate our DL models. Firstly, we implement a transformer model that incorporates positional encoding, multi-head attention, layer normalization, and dropout techniques, and synthesizes the ABP waveform with a mean absolute error (MAE) of 14. Secondly, we implement a frequency-domain (FD) learning approach where we first obtain the discrete cosine transform (DCT) coefficients of the PPG and ABP signals corresponding to two cardiac cycles, and then learn a linear/non-linear (L/NL) regression between them. We learn that the FD L/NL regression model outperforms the transformer model by achieving an MAE of 11.87 and 8.01, for diastolic blood pressure (DBP) and systolic blood pressure (SBP), respectively. Our FD L/NL regression model also fulfills the AAMI criterion of utilizing data from more than 85 subjects, and achieves grade B by the BHS criterion.
On Efficient Language and Vision Assistants for Visually-Situated Natural Language Understanding: What Matters in Reading and Reasoning
Recent advancements in language and vision assistants have showcased impressive capabilities but suffer from a lack of transparency, limiting broader research and reproducibility. While open-source models handle general image tasks effectively, they face challenges with the high computational demands of complex visually-situated text understanding. Such tasks often require increased token inputs and large vision modules to harness high-resolution information. Striking a balance between model size and data importance remains an open question. This study aims to redefine the design of vision-language models by identifying key components and creating efficient models with constrained inference costs. By strategically formulating datasets, optimizing vision modules, and enhancing supervision techniques, we achieve significant improvements in inference throughput while maintaining high performance. Extensive experiments across models ranging from 160M to 13B parameters offer insights into model optimization. We will fully open-source our codebase, models, and datasets at https://github.com/naver-ai/elva.
Adapting the Segment Anything Model During Usage in Novel Situations
The interactive segmentation task consists in the creation of object segmentation masks based on user interactions. The most common way to guide a model towards producing a correct segmentation consists in clicks on the object and background. The recently published Segment Anything Model (SAM) supports a generalized version of the interactive segmentation problem and has been trained on an object segmentation dataset which contains 1.1B masks. Though being trained extensively and with the explicit purpose of serving as a foundation model, we show significant limitations of SAM when being applied for interactive segmentation on novel domains or object types. On the used datasets, SAM displays a failure rate FR_{30}@90 of up to 72.6 %. Since we still want such foundation models to be immediately applicable, we present a framework that can adapt SAM during immediate usage. For this we will leverage the user interactions and masks, which are constructed during the interactive segmentation process. We use this information to generate pseudo-labels, which we use to compute a loss function and optimize a part of the SAM model. The presented method causes a relative reduction of up to 48.1 % in the FR_{20}@85 and 46.6 % in the FR_{30}@90 metrics.
When Neural Code Completion Models Size up the Situation: Attaining Cheaper and Faster Completion through Dynamic Model Inference
Leveraging recent advancements in large language models, modern neural code completion models have demonstrated the capability to generate highly accurate code suggestions. However, their massive size poses challenges in terms of computational costs and environmental impact, hindering their widespread adoption in practical scenarios. Dynamic inference emerges as a promising solution, as it allocates minimal computation during inference while maintaining the model's performance. In this research, we explore dynamic inference within the context of code completion. Initially, we conducted an empirical investigation on GPT-2, focusing on the inference capabilities of intermediate layers for code completion. We found that 54.4% of tokens can be accurately generated using just the first layer, signifying significant computational savings potential. Moreover, despite using all layers, the model still fails to predict 14.5% of tokens correctly, and the subsequent completions continued from them are rarely considered helpful, with only a 4.2% Acceptance Rate. These findings motivate our exploration of dynamic inference in code completion and inspire us to enhance it with a decision-making mechanism that stops the generation of incorrect code. We thus propose a novel dynamic inference method specifically tailored for code completion models. This method aims not only to produce correct predictions with largely reduced computation but also to prevent incorrect predictions proactively. Our extensive evaluation shows that it can averagely skip 1.7 layers out of 16 layers in the models, leading to an 11.2% speedup with only a marginal 1.1% reduction in ROUGE-L.
TIA: A Teaching Intonation Assessment Dataset in Real Teaching Situations
Intonation is one of the important factors affecting the teaching language arts, so it is an urgent problem to be addressed by evaluating the teachers' intonation through artificial intelligence technology. However, the lack of an intonation assessment dataset has hindered the development of the field. To this end, this paper constructs a Teaching Intonation Assessment (TIA) dataset for the first time in real teaching situations. This dataset covers 9 disciplines, 396 teachers, total of 11,444 utterance samples with a length of 15 seconds. In order to test the validity of the dataset, this paper proposes a teaching intonation assessment model (TIAM) based on low-level and deep-level features of speech. The experimental results show that TIAM based on the dataset constructed in this paper is basically consistent with the results of manual evaluation, and the results are better than the baseline models, which proves the effectiveness of the evaluation model.
MindDial: Belief Dynamics Tracking with Theory-of-Mind Modeling for Situated Neural Dialogue Generation
Humans talk in free-form while negotiating the expressed meanings or common ground. Despite the impressive conversational abilities of the large generative language models, they do not consider the individual differences in contextual understanding in a shared situated environment. In this work, we propose MindDial, a novel conversational framework that can generate situated free-form responses to negotiate common ground. We design an explicit mind module that can track three-level beliefs -- the speaker's belief, the speaker's prediction of the listener's belief, and the common belief based on the gap between the first two. Then the speaking act classification head will decide to continue to talk, end this turn, or take task-related action. We augment a common ground alignment dataset MutualFriend with belief dynamics annotation, of which the goal is to find a single mutual friend based on the free chat between two agents. Experiments show that our model with mental state modeling can resemble human responses when aligning common ground meanwhile mimic the natural human conversation flow. The ablation study further validates the third-level common belief can aggregate information of the first and second-order beliefs and align common ground more efficiently.
ClarifyDelphi: Reinforced Clarification Questions with Defeasibility Rewards for Social and Moral Situations
Context is everything, even in commonsense moral reasoning. Changing contexts can flip the moral judgment of an action; "Lying to a friend" is wrong in general, but may be morally acceptable if it is intended to protect their life. We present ClarifyDelphi, an interactive system that learns to ask clarification questions (e.g., why did you lie to your friend?) in order to elicit additional salient contexts of a social or moral situation. We posit that questions whose potential answers lead to diverging moral judgments are the most informative. Thus, we propose a reinforcement learning framework with a defeasibility reward that aims to maximize the divergence between moral judgments of hypothetical answers to a question. Human evaluation demonstrates that our system generates more relevant, informative and defeasible questions compared to competitive baselines. Our work is ultimately inspired by studies in cognitive science that have investigated the flexibility in moral cognition (i.e., the diverse contexts in which moral rules can be bent), and we hope that research in this direction can assist both cognitive and computational investigations of moral judgments.
Deployment of an IoT System for Adaptive In-Situ Soundscape Augmentation
Soundscape augmentation is an emerging approach for noise mitigation by introducing additional sounds known as "maskers" to increase acoustic comfort. Traditionally, the choice of maskers is often predicated on expert guidance or post-hoc analysis which can be time-consuming and sometimes arbitrary. Moreover, this often results in a static set of maskers that are inflexible to the dynamic nature of real-world acoustic environments. Overcoming the inflexibility of traditional soundscape augmentation is twofold. First, given a snapshot of a soundscape, the system must be able to select an optimal masker without human supervision. Second, the system must also be able to react to changes in the acoustic environment with near real-time latency. In this work, we harness the combined prowess of cloud computing and the Internet of Things (IoT) to allow in-situ listening and playback using microcontrollers while delegating computationally expensive inference tasks to the cloud. In particular, a serverless cloud architecture was used for inference, ensuring near real-time latency and scalability without the need to provision computing resources. A working prototype of the system is currently being deployed in a public area experiencing high traffic noise, as well as undergoing public evaluation for future improvements.
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.