Antibodies are crucial proteins produced by the immune system in response to foreign substances or antigens. The specificity of an antibody is determined by its complementarity-determining regions (CDRs), which are located in the variable domains of the antibody chains and form the antigen-binding site. Previous studies have utilized complex techniques to generate CDRs, but they suffer from inadequate geometric modeling. Moreover, the common iterative refinement strategies lead to an inefficient inference. In this paper, we propose a \textit{simple yet effective} model that can co-design 1D sequences and 3D structures of CDRs in a one-shot manner. To achieve this, we decouple the antibody CDR design problem into two stages: (i) geometric modeling of protein complex structures and (ii) sequence-structure co-learning. We develop a novel macromolecular structure invariant embedding, typically for protein complexes, that captures both intra- and inter-component interactions among the backbone atoms, including C$\alpha$, N, C, and O atoms, to achieve comprehensive geometric modeling. Then, we introduce a simple cross-gate MLP for sequence-structure co-learning, allowing sequence and structure representations to implicitly refine each other. This enables our model to design desired sequences and structures in a one-shot manner. Extensive experiments are conducted to evaluate our results at both the sequence and structure levels, which demonstrate that our model achieves superior performance compared to the state-of-the-art antibody CDR design methods.
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ACM/IEEE第23屆模型驅動工程語言和系統國際會議，是模型驅動軟件和系統工程的首要會議系列，由ACM-SIGSOFT和IEEE-TCSE支持組織。自1998年以來，模型涵蓋了建模的各個方面，從語言和方法到工具和應用程序。模特的參加者來自不同的背景，包括研究人員、學者、工程師和工業專業人士。MODELS 2019是一個論壇，參與者可以圍繞建模和模型驅動的軟件和系統交流前沿研究成果和創新實踐經驗。今年的版本將為建模社區提供進一步推進建模基礎的機會，并在網絡物理系統、嵌入式系統、社會技術系統、云計算、大數據、機器學習、安全、開源等新興領域提出建模的創新應用以及可持續性。
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Human learning is sensitive to rule-like structure and the curriculum of examples used for training. In tasks governed by succinct rules, learning is more robust when related examples are blocked across trials, but in the absence of such rules, interleaving is more effective. To date, no neural model has simultaneously captured these seemingly contradictory effects. Here we show that this same tradeoff spontaneously emerges with "in-context learning" (ICL) both in neural networks trained with metalearning and in large language models (LLMs). ICL is the ability to learn new tasks "in context" - without weight changes - via an inner-loop algorithm implemented in activation dynamics. Experiments with pretrained LLMs and metalearning transformers show that ICL exhibits the blocking advantage demonstrated in humans on a task involving rule-like structure, and conversely, that concurrent in-weight learning reproduces the interleaving advantage observed in humans on tasks lacking such structure.
Motivated by the success of Transformers when applied to sequences of discrete symbols, token-based world models (TBWMs) were recently proposed as sample-efficient methods. In TBWMs, the world model consumes agent experience as a language-like sequence of tokens, where each observation constitutes a sub-sequence. However, during imagination, the sequential token-by-token generation of next observations results in a severe bottleneck, leading to long training times, poor GPU utilization, and limited representations. To resolve this bottleneck, we devise a novel Parallel Observation Prediction (POP) mechanism. POP augments a Retentive Network (RetNet) with a novel forward mode tailored to our reinforcement learning setting. We incorporate POP in a novel TBWM agent named REM (Retentive Environment Model), showcasing a 15.4x faster imagination compared to prior TBWMs. REM attains superhuman performance on 12 out of 26 games of the Atari 100K benchmark, while training in less than 12 hours. Our code is available at \url{//github.com/leor-c/REM}.
An algorithm effects a causal representation of relations between features and labels in the human's perception. Such a representation might conflict with the human's prior belief. Explanations can direct the human's attention to the conflicting feature and away from other relevant features. This leads to causal overattribution and may adversely affect the human's information processing. In a field experiment we implemented an XGBoost-trained model as a decision-making aid for counselors at a public employment service to predict candidates' risk of long-term unemployment. The treatment group of counselors was also provided with SHAP. The results show that the quality of the human's decision-making is worse when a feature on which the human holds a conflicting prior belief is displayed as part of the explanation.
Advances towards more faithful and traceable answers of Large Language Models (LLMs) are crucial for various research and practical endeavors. One avenue in reaching this goal is basing the answers on reliable sources. However, this Evidence-Based QA has proven to work insufficiently with LLMs in terms of citing the correct sources (source quality) and truthfully representing the information within sources (answer attributability). In this work, we systematically investigate how to robustly fine-tune LLMs for better source quality and answer attributability. Specifically, we introduce a data generation pipeline with automated data quality filters, which can synthesize diversified high-quality training and testing data at scale. We further introduce four test sets to benchmark the robustness of fine-tuned specialist models. Extensive evaluation shows that fine-tuning on synthetic data improves performance on both in- and out-of-distribution. %Evidence-Based QA cases. Furthermore, we show that data quality, which can be drastically improved by proposed quality filters, matters more than quantity in improving Evidence-Based QA.
What counts as legitimate AI ethics labor, and consequently, what are the epistemic terms on which AI ethics claims are rendered legitimate? Based on 75 interviews with technologists including researchers, developers, open source contributors, artists, and activists, this paper explores various epistemic bases from which AI ethics is practiced. In the context of outside attacks on AI ethics as an impediment to "progress," I show how some AI ethics practices have reached toward scholarly authority, automation and quantification and achieved some legitimacy, while those based on richly embodied and situated lived experience have not. This paper draws the works of feminist Anthropology and Science and Technology Studies (STS) scholars Diana Forsythe and Lucy Suchman together with the works of postcolonial feminist theorist Sara Ahmed and Black feminist theorist Kristie Dotson to examine the implications of dominant AI ethics practices. I argue that by entrenching the epistemic power of quantification, dominant AI ethics practices risk legitimizing AI ethics as a project in equal and opposite measure to the extent that they delegitimize and marginalize embodied and lived experiences as legitimate parts of the same project. In response, I propose and sketch the idea of humble technical practices: quantified or technical practices which specifically seek to make their epistemic limits clear, with a view to flattening hierarchies of epistemic power.
Segmentations are crucial in medical imaging to obtain morphological, volumetric, and radiomics biomarkers. Manual segmentation is accurate but not feasible in the radiologist's clinical workflow, while automatic segmentation generally obtains sub-par performance. We therefore developed a minimally interactive deep learning-based segmentation method for soft-tissue tumors (STTs) on CT and MRI. The method requires the user to click six points near the tumor's extreme boundaries. These six points are transformed into a distance map and serve, with the image, as input for a Convolutional Neural Network. For training and validation, a multicenter dataset containing 514 patients and nine STT types in seven anatomical locations was used, resulting in a Dice Similarity Coefficient (DSC) of 0.85$\pm$0.11 (mean $\pm$ standard deviation (SD)) for CT and 0.84$\pm$0.12 for T1-weighted MRI, when compared to manual segmentations made by expert radiologists. Next, the method was externally validated on a dataset including five unseen STT phenotypes in extremities, achieving 0.81$\pm$0.08 for CT, 0.84$\pm$0.09 for T1-weighted MRI, and 0.88\pm0.08 for previously unseen T2-weighted fat-saturated (FS) MRI. In conclusion, our minimally interactive segmentation method effectively segments different types of STTs on CT and MRI, with robust generalization to previously unseen phenotypes and imaging modalities.
Recent artificial intelligence (AI) systems have reached milestones in "grand challenges" ranging from Go to protein-folding. The capability to retrieve medical knowledge, reason over it, and answer medical questions comparably to physicians has long been viewed as one such grand challenge. Large language models (LLMs) have catalyzed significant progress in medical question answering; Med-PaLM was the first model to exceed a "passing" score in US Medical Licensing Examination (USMLE) style questions with a score of 67.2% on the MedQA dataset. However, this and other prior work suggested significant room for improvement, especially when models' answers were compared to clinicians' answers. Here we present Med-PaLM 2, which bridges these gaps by leveraging a combination of base LLM improvements (PaLM 2), medical domain finetuning, and prompting strategies including a novel ensemble refinement approach. Med-PaLM 2 scored up to 86.5% on the MedQA dataset, improving upon Med-PaLM by over 19% and setting a new state-of-the-art. We also observed performance approaching or exceeding state-of-the-art across MedMCQA, PubMedQA, and MMLU clinical topics datasets. We performed detailed human evaluations on long-form questions along multiple axes relevant to clinical applications. In pairwise comparative ranking of 1066 consumer medical questions, physicians preferred Med-PaLM 2 answers to those produced by physicians on eight of nine axes pertaining to clinical utility (p < 0.001). We also observed significant improvements compared to Med-PaLM on every evaluation axis (p < 0.001) on newly introduced datasets of 240 long-form "adversarial" questions to probe LLM limitations. While further studies are necessary to validate the efficacy of these models in real-world settings, these results highlight rapid progress towards physician-level performance in medical question answering.
Inspired by the human cognitive system, attention is a mechanism that imitates the human cognitive awareness about specific information, amplifying critical details to focus more on the essential aspects of data. Deep learning has employed attention to boost performance for many applications. Interestingly, the same attention design can suit processing different data modalities and can easily be incorporated into large networks. Furthermore, multiple complementary attention mechanisms can be incorporated in one network. Hence, attention techniques have become extremely attractive. However, the literature lacks a comprehensive survey specific to attention techniques to guide researchers in employing attention in their deep models. Note that, besides being demanding in terms of training data and computational resources, transformers only cover a single category in self-attention out of the many categories available. We fill this gap and provide an in-depth survey of 50 attention techniques categorizing them by their most prominent features. We initiate our discussion by introducing the fundamental concepts behind the success of attention mechanism. Next, we furnish some essentials such as the strengths and limitations of each attention category, describe their fundamental building blocks, basic formulations with primary usage, and applications specifically for computer vision. We also discuss the challenges and open questions related to attention mechanism in general. Finally, we recommend possible future research directions for deep attention.
A sememe is defined as the minimum semantic unit of human languages. Sememe knowledge bases (KBs), which contain words annotated with sememes, have been successfully applied to many NLP tasks. However, existing sememe KBs are built on only a few languages, which hinders their widespread utilization. To address the issue, we propose to build a unified sememe KB for multiple languages based on BabelNet, a multilingual encyclopedic dictionary. We first build a dataset serving as the seed of the multilingual sememe KB. It manually annotates sememes for over $15$ thousand synsets (the entries of BabelNet). Then, we present a novel task of automatic sememe prediction for synsets, aiming to expand the seed dataset into a usable KB. We also propose two simple and effective models, which exploit different information of synsets. Finally, we conduct quantitative and qualitative analyses to explore important factors and difficulties in the task. All the source code and data of this work can be obtained on //github.com/thunlp/BabelNet-Sememe-Prediction.
The problem of Multiple Object Tracking (MOT) consists in following the trajectory of different objects in a sequence, usually a video. In recent years, with the rise of Deep Learning, the algorithms that provide a solution to this problem have benefited from the representational power of deep models. This paper provides a comprehensive survey on works that employ Deep Learning models to solve the task of MOT on single-camera videos. Four main steps in MOT algorithms are identified, and an in-depth review of how Deep Learning was employed in each one of these stages is presented. A complete experimental comparison of the presented works on the three MOTChallenge datasets is also provided, identifying a number of similarities among the top-performing methods and presenting some possible future research directions.
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