When learning an input-output mapping from very few examples, is it better to first infer a latent function that explains the examples, or is it better to directly predict new test outputs, e.g. using a neural network? We study this question on ARC by training neural models for induction (inferring latent functions) and transduction (directly predicting the test output for a given test input). We train on synthetically generated variations of Python programs that solve ARC training tasks. We find inductive and transductive models solve different kinds of test problems, despite having the same training problems and sharing the same neural architecture: Inductive program synthesis excels at precise computations, and at composing multiple concepts, while transduction succeeds on fuzzier perceptual concepts. Ensembling them approaches human-level performance on ARC.

In this paper, we propose shifting the focus of robustness evaluation for Neural Program Repair (NPR) techniques toward naturally-occurring data transformations. To accomplish this, we first examine the naturalness of semantic-preserving transformations through a two-stage human study. This study includes (1) interviews with senior software developers to establish concrete criteria for evaluating the naturalness of these transformations, and (2) a survey involving 10 developers to assess the naturalness of 1,178 transformations, i.e., pairs of original and transformed programs, applied to 225 real-world bugs. Our findings show that only 60% of these transformations are deemed natural, while 20% are considered unnatural, with strong agreement among annotators. Moreover, the unnaturalness of these transformations significantly impacts both their applicability to benchmarks and the conclusions drawn from robustness testing. Next, we conduct natural robustness testing on NPR techniques to assess their true effectiveness against real-world data variations. Our experimental results reveal a substantial number of prediction changes in NPR techniques, leading to significant reductions in both plausible and correct patch rates when comparing performance on the original and transformed datasets. Additionally, we observe notable differences in performance improvements between NPR techniques, suggesting potential biases on NPR evaluation introduced by limited datasets. Finally, we propose an LLM-based metric to automate the assessment of transformation naturalness, ensuring the scalability of natural robustness testing.

DNA-Encoded Libraries (DEL) are combinatorial small molecule libraries that offer an efficient way to characterize diverse chemical spaces. Selection experiments using DELs are pivotal to drug discovery efforts, enabling high-throughput screens for hit finding. However, limited availability of public DEL datasets hinders the advancement of computational techniques designed to utilize such data. To bridge this gap, we present KinDEL, one of the first large, publicly available DEL datasets on two kinases: Mitogen-Activated Protein Kinase 14 (MAPK14) and Discoidin Domain Receptor Tyrosine Kinase 1 (DDR1). Interest in this data modality is growing due to its ability to generate extensive supervised chemical data that densely samples around select molecular structures. Demonstrating one such application of the data, we benchmark different machine learning techniques to develop predictive models for hit identification; in particular, we highlight recent structure-based probabilistic approaches. Finally, we provide biophysical assay data, both on-and off-DNA, to validate our models on a smaller subset of molecules. Data and code for our benchmarks can be found at https://github.com/insitro/kindel. DNA-Encoded Libraries (DEL) have emerged as a powerful tool in drug discovery, enabling highly efficient screens of small molecule libraries against therapeutically relevant targets (Yuen & Franzini, 2017; Gironda-Martínez et al., 2021; Kunig et al., 2021; Peterson & Liu, 2023). These massive libraries are efficiently constructed through combinatorial synthesis of chemical building blocks, or synthons, with each resulting molecule being assigned a DNA barcode (see Figure 1). DELs are then used in selection experiments against proteins of interest, wherein multiple rounds of washing are conducted to remove any weak binders, and the DNA tags of surviving molecules are sequenced as a measure of binding affinity. Despite the highly efficient throughput of DELs, data generated through these experiments are intrinsically noisy with various sources of bias arising from the DEL synthesis and selection processes, necessitating modern machine learning methods to learn signal from the data. Unfortunately, there is still a lack of large, publicly available DEL datasets and benchmarking tasks to drive this important research area.

We propose GNNInfer, the first automatic property inference technique for GNNs. To tackle the challenge of varying input structures in GNNs, GNNInfer first identifies a set of representative influential structures that contribute significantly towards the prediction of a GNN. Using these structures, GNNInfer converts each pair of an influential structure and the GNN to their equivalent FNN and then leverages existing property inference techniques to effectively capture properties of the GNN that are specific to the influential structures. GNNINfer then generalizes the captured properties to any input graphs that contain the influential structures. Finally, GNNInfer improves the correctness of the inferred properties by building a model (either a decision tree or linear regression) that estimates the deviation of GNN output from the inferred properties given full input graphs. The learned model helps GNNInfer extend the inferred properties with constraints to the input and output of the GNN, obtaining stronger properties that hold on full input graphs. Our experiments show that GNNInfer is effective in inferring likely properties of popular real-world GNNs, and more importantly, these inferred properties help effectively defend against GNNs' backdoor attacks. In particular, out of the 13 ground truth properties, GNNInfer re-discovered 8 correct properties and discovered likely correct properties that approximate the remaining 5 ground truth properties. Using properties inferred by GNNInfer to defend against the state-of-the-art backdoor attack technique on GNNs, namely UGBA, experiments show that GNNInfer's defense success rate is up to 30 times better than existing baselines.

The Competition on Legal Information Extraction/Entailment (COLIEE) is held annually to encourage advancements in the automatic processing of legal texts. Processing legal documents is challenging due to the intricate structure and meaning of legal language. In this paper, we outline our strategies for tackling Task 2, Task 3, and Task 4 in the COLIEE 2023 competition. Our approach involved utilizing appropriate state-of-the-art deep learning methods, designing methods based on domain characteristics observation, and applying meticulous engineering practices and methodologies to the competition. As a result, our performance in these tasks has been outstanding, with first places in Task 2 and Task 3, and promising results in Task 4. Our source code is available at https://github.com/Nguyen2015/CAPTAIN-COLIEE2023/tree/coliee2023.

We introduce efficient deep learning-based methods for legal document processing including Legal Document Retrieval and Legal Question Answering tasks in the Automated Legal Question Answering Competition (ALQAC 2022). In this competition, we achieve 1\textsuperscript{st} place in the first task and 3\textsuperscript{rd} place in the second task. Our method is based on the XLM-RoBERTa model that is pre-trained from a large amount of unlabeled corpus before fine-tuning to the specific tasks. The experimental results showed that our method works well in legal retrieval information tasks with limited labeled data. Besides, this method can be applied to other information retrieval tasks in low-resource languages.