We seek to automate the generation of drug-like compounds conditioned to specific protein pocket targets. Most current methods approximate the protein-molecule distribution of a finite dataset and, therefore struggle to generate molecules with significant binding improvement over the training dataset. We instead frame the pocket-conditioned molecular generation task as an RL problem and develop TacoGFN, a target conditional Generative Flow Network model. Our method is explicitly encouraged to generate molecules with desired properties as opposed to fitting on a pre-existing data distribution. To this end, we develop transformer-based docking score prediction to speed up docking score computation and propose TacoGFN to explore molecule space efficiently. Furthermore, we incorporate several rounds of active learning where generated samples are queried using a docking oracle to improve the docking score prediction. This approach allows us to accurately explore as much of the molecule landscape as we can afford computationally. Empirically, molecules generated using TacoGFN and its variants significantly outperform all baseline methods across every property (Docking score, QED, SA, Lipinski), while being orders of magnitude faster.

Interpretability for machine learning models in medical imaging (MLMI) is an important direction of research. However, there is a general sense of murkiness in what interpretability means. Why does the need for interpretability in MLMI arise? What goals does one actually seek to address when interpretability is needed? To answer these questions, we identify a need to formalize the goals and elements of interpretability in MLMI. By reasoning about real-world tasks and goals common in both medical image analysis and its intersection with machine learning, we identify five core elements of interpretability: localization, visual recognizability, physical attribution, model transparency, and actionability. From this, we arrive at a framework for interpretability in MLMI, which serves as a step-by-step guide to approaching interpretability in this context. Overall, this paper formalizes interpretability needs in the context of medical imaging, and our applied perspective clarifies concrete MLMI-specific goals and considerations in order to guide method design and improve real-world usage. Our goal is to provide practical and didactic information for model designers and practitioners, inspire developers of models in the medical imaging field to reason more deeply about what interpretability is achieving, and suggest future directions of interpretability research.

The term life sciences refers to the disciplines that study living organisms and life processes, and include chemistry, biology, medicine, and a range of other related disciplines. Research efforts in life sciences are heavily data-driven, as they produce and consume vast amounts of scientific data, much of which is intrinsically relational and graph-structured. The volume of data and the complexity of scientific concepts and relations referred to therein promote the application of advanced knowledge-driven technologies for managing and interpreting data, with the ultimate aim to advance scientific discovery. In this survey and position paper, we discuss recent developments and advances in the use of graph-based technologies in life sciences and set out a vision for how these technologies will impact these fields into the future. We focus on three broad topics: the construction and management of Knowledge Graphs (KGs), the use of KGs and associated technologies in the discovery of new knowledge, and the use of KGs in artificial intelligence applications to support explanations (explainable AI). We select a few exemplary use cases for each topic, discuss the challenges and open research questions within these topics, and conclude with a perspective and outlook that summarizes the overarching challenges and their potential solutions as a guide for future research.

Modern language models capture a large body of factual knowledge. However, some facts can be incorrectly induced or become obsolete over time, resulting in factually incorrect generations. This has led to the development of various editing methods that allow updating facts encoded by the model. Evaluation of these methods has primarily focused on testing whether an individual fact has been successfully injected, and if similar predictions for other subjects have not changed. Here we argue that such evaluation is limited, since injecting one fact (e.g. ``Jack Depp is the son of Johnny Depp'') introduces a ``ripple effect'' in the form of additional facts that the model needs to update (e.g.``Jack Depp is the sibling of Lily-Rose Depp''). To address this issue, we propose a novel set of evaluation criteria that consider the implications of an edit on related facts. Using these criteria, we then construct RippleEdits, a diagnostic benchmark of 5K factual edits, capturing a variety of types of ripple effects. We evaluate prominent editing methods on RippleEdits, showing that current methods fail to introduce consistent changes in the model's knowledge. In addition, we find that a simple in-context editing baseline obtains the best scores on our benchmark, suggesting a promising research direction for model editing.

India has a rich linguistic landscape with languages from 4 major language families spoken by over a billion people. 22 of these languages are listed in the Constitution of India (referred to as scheduled languages) are the focus of this work. Given the linguistic diversity, high-quality and accessible Machine Translation (MT) systems are essential in a country like India. Prior to this work, there was (i) no parallel training data spanning all 22 languages, (ii) no robust benchmarks covering all these languages and containing content relevant to India, and (iii) no existing translation models which support all the 22 scheduled languages of India. In this work, we aim to address this gap by focusing on the missing pieces required for enabling wide, easy, and open access to good machine translation systems for all 22 scheduled Indian languages. We identify four key areas of improvement: curating and creating larger training datasets, creating diverse and high-quality benchmarks, training multilingual models, and releasing models with open access. Our first contribution is the release of the Bharat Parallel Corpus Collection (BPCC), the largest publicly available parallel corpora for Indic languages. BPCC contains a total of 230M bitext pairs, of which a total of 126M were newly added, including 644K manually translated sentence pairs created as part of this work. Our second contribution is the release of the first n-way parallel benchmark covering all 22 Indian languages, featuring diverse domains, Indian-origin content, and source-original test sets. Next, we present IndicTrans2, the first model to support all 22 languages, surpassing existing models on multiple existing and new benchmarks created as a part of this work. Lastly, to promote accessibility and collaboration, we release our models and associated data with permissive licenses at https://github.com/AI4Bharat/IndicTrans2.

Declarative process specifications define the behavior of processes by means of rules based on Linear Temporal Logic on Finite Traces (LTLf). In a mining context, these specifications are inferred from, and checked on, multi-sets of runs recorded by information systems (namely, event logs). To this end, being able to gauge the degree to which process data comply with a specification is key. However, existing mining and verification techniques analyze the rules in isolation, thereby disregarding their interplay. In this paper, we introduce a framework to devise probabilistic measures for declarative process specifications. Thereupon, we propose a technique that measures the degree of satisfaction of specifications over event logs. To assess our approach, we conduct an evaluation with real-world data, evidencing its applicability in discovery, checking, and drift detection contexts.

Accurate uncertainty quantification is necessary to enhance the reliability of deep learning models in real-world applications. In the case of regression tasks, prediction intervals (PIs) should be provided along with the deterministic predictions of deep learning models. Such PIs are useful or "high-quality" as long as they are sufficiently narrow and capture most of the probability density. In this paper, we present a method to learn prediction intervals for regression-based neural networks automatically in addition to the conventional target predictions. In particular, we train two companion neural networks: one that uses one output, the target estimate, and another that uses two outputs, the upper and lower bounds of the corresponding PI. Our main contribution is the design of a novel loss function for the PI-generation network that takes into account the output of the target-estimation network and has two optimization objectives: minimizing the mean prediction interval width and ensuring the PI integrity using constraints that maximize the prediction interval probability coverage implicitly. Furthermore, we introduce a self-adaptive coefficient that balances both objectives within the loss function, which alleviates the task of fine-tuning. Experiments using a synthetic dataset, eight benchmark datasets, and a real-world crop yield prediction dataset showed that our method was able to maintain a nominal probability coverage and produce significantly narrower PIs without detriment to its target estimation accuracy when compared to those PIs generated by three state-of-the-art neural-network-based methods. In other words, our method was shown to produce higher-quality PIs.

Graph neural networks (GNN) are increasingly used to classify EEG for tasks such as emotion recognition, motor imagery and neurological diseases and disorders. A wide range of methods have been proposed to design GNN-based classifiers. Therefore, there is a need for a systematic review and categorisation of these approaches. We exhaustively search the published literature on this topic and derive several categories for comparison. These categories highlight the similarities and differences among the methods. The results suggest a prevalence of spectral graph convolutional layers over spatial. Additionally, we identify standard forms of node features, with the most popular being the raw EEG signal and differential entropy. Our results summarise the emerging trends in GNN-based approaches for EEG classification. Finally, we discuss several promising research directions, such as exploring the potential of transfer learning methods and appropriate modelling of cross-frequency interactions.

Through this paper, we introduce a novel driver cognitive load assessment dataset, CL-Drive, which contains Electroencephalogram (EEG) signals along with other physiological signals such as Electrocardiography (ECG) and Electrodermal Activity (EDA) as well as eye tracking data. The data was collected from 21 subjects while driving in an immersive vehicle simulator, in various driving conditions, to induce different levels of cognitive load in the subjects. The tasks consisted of 9 complexity levels for 3 minutes each. Each driver reported their subjective cognitive load every 10 seconds throughout the experiment. The dataset contains the subjective cognitive load recorded as ground truth. In this paper, we also provide benchmark classification results for different machine learning and deep learning models for both binary and ternary label distributions. We followed 2 evaluation criteria namely 10-fold and leave-one-subject-out (LOSO). We have trained our models on both hand-crafted features as well as on raw data.

We tackle the problem of sampling from intractable high-dimensional density functions, a fundamental task that often appears in machine learning and statistics. We extend recent sampling-based approaches that leverage controlled stochastic processes to model approximate samples from these target densities. The main drawback of these approaches is that the training objective requires full trajectories to compute, resulting in sluggish credit assignment issues due to use of entire trajectories and a learning signal present only at the terminal time. In this work, we present Diffusion Generative Flow Samplers (DGFS), a sampling-based framework where the learning process can be tractably broken down into short partial trajectory segments, via parameterizing an additional "flow function". Our method takes inspiration from the theory developed for generative flow networks (GFlowNets), allowing us to make use of intermediate learning signals. Through various challenging experiments, we demonstrate that DGFS achieves more accurate estimates of the normalization constant than closely-related prior methods.