AntBO optimizes antibody design using Bayesian optimization for efficient and effective CDRH3 sequence generation.
problem Designing optimal antigen-specific CDRH3 regions in antibody design due to combinatorial sequence space.
method Combinatorial Bayesian optimization framework with trust region for developability.
result AntBO designs CDRH3 regions with diverse biophysical properties and outperforms existing methods.
K-Models clusters functional data with ordinal constraints for better interpretability.
problem Challenges in extracting meaningful insights from functional data due to lack of interpretability.
method Integrates ordinal constraints into clustering to improve interpretability and structure identification.
result Enhances interpretability of clustering results while maintaining performance.
Antibodies are a critical part of the immune system, having the function of directly neutralising or tagging undesirable objects (the antigens) for future destruction. Being able to predict which amino acids belong to the paratope, the region on the antibody which binds to the antigen, can facilitate antibody design an…
Method infers TCR effects on disease using patient data.
problem Estimating causal effects of TCR sequences on patient outcomes.
method Corrects for confounders using pre-selection TCR data and neural-network estimator.
result Identifies potentially therapeutic TCRs for COVID-19 severity.
Active learning speeds up antibody affinity prediction.
problem Challenging to identify mutations enhancing antibody affinity.
method Iterative proposal of promising sequences for simulation.
result Accelerates search for improved binders.
We attempt to set a mathematical foundation of immunology and amino acid chains. To measure the similarities of these chains, a kernel on strings is defined using only the sequence of the chains and a good amino acid substitution matrix (e.g. BLOSUM62). The kernel is used in learning machines to predict binding affinit…
MINN-SA enhances cancer detection using TCR sequences with better interpretability.
problem Challenges in detecting cancers using TCR sequences due to one-to-many correspondence.
method Multiple Instance Neural Networks based on Sparse Attention (MINN-SA).
result MINN-SA achieves highest AUC scores on 10 cancer types compared to existing MIL approaches.
Feature selection predicts immune state changes in RA mouse model.
problem Predicting the immune state change after RA immunotherapy.
method Feature selection algorithms applied to mouse CIA model data.
result Selected features predict both T cell markers and treatment efficacy.
Research proposes a risk-free machine learning model for COVID screening from routine blood tests.
problem Rapid antigen tests have low sensitivity and are not suitable for widespread screening.
method Stacked Ensemble Machine Learning model using routine blood tests.
result 100% accuracy, precision, recall and F1-score in identifying COVID patients.
Topolow embeds dissimilarity data into Euclidean space robustly against non-metricity and sparsity.
problem Embedding dissimilarity data into Euclidean space when dissimilarities are non-metric or sparse.
method Topolow uses a physics-inspired, gradient-free optimization framework to maximize likelihood under a Laplace error model.
result Topolow outperforms standard MDS methods in reconstructing sparse and non-Euclidean data.
NOTMAD estimates context-specific Bayesian networks without breaking datasets.
problem Non-convexity of acyclic graphs limits sharing information between context-specific estimators.
method NOTMAD models context-specific Bayesian networks as mixtures of archetypal DAGs, estimating structures and parameters jointly.
result NOTMAD shares information between context-specific acyclic graphs, enabling single-sample resolution.
Investigates physical properties on surfaces of rotation using Clairaut's theorem.
problem Understanding specific energy and angular momentum on surfaces of rotation.
method Used Clairaut's theorem with geodesic conditions to derive specific energy and angular momentum.
result Physical expressions for specific energy and angular momentum on surfaces of rotation were derived.
Most current methods for learning from demonstrations assume that those demonstrations alone are sufficient to learn the underlying task. This is often untrue, especially if extra safety specifications exist which were not present in the original demonstrations. In this paper, we allow an expert to elaborate on their o…
In this paper we formulate a probabilistic model for class-specific discriminant subspace learning. The proposed model can naturally incorporate the multi-modal structure of the negative class, which is neglected by existing class-specific methods. Moreover, it can be directly used to define a class-specific probabilis…
Introduces CStrees for modeling context-specific causal models from observational and interventional data.
problem Modeling context-specific causal relationships from mixed data types.
method Introduces CStrees with a novel factorization criterion and graphical characterization for context-specific conditional independence models.
result Derives a graphical characterization of model equivalence for observational CStrees and extends it to CStree models under context-specific interventions.
In this note we study whether specific elements in the second homology of specific simply connected closed 4-manifolds can be represented by smooth or topologically flat embedded spheres.
Statistical model checking for PCTL on MDPs using reinforcement learning.
problem Model checking PCTL specifications on MDPs with statistical methods.
method Reinforcement learning for policy search, statistical model checking with UCB-based Q-learning.
result Provably guaranteed statistical model checking method for PCTL specifications on MDPs.
Prior work on neural network verification has focused on specifications that are linear functions of the output of the network, e.g., invariance of the classifier output under adversarial perturbations of the input. In this paper, we extend verification algorithms to be able to certify richer properties of neural netwo…
New bounds on specific torsion lengths for periodic mapping classes.
problem Understanding specific torsion lengths in periodic mapping classes.
method Introduced stable specific torsion length and used it to bound Dehn twists.
result Bounded the stable specific torsion length of Dehn twists by six.
New model identifies patient-specific disease root causes.
problem Identifying root causes of complex diseases varying between patients.
method Generalized Root Causal Inference (GRCI) algorithm for heteroscedastic noise model.
result GRCI accurately extracts patient-specific root causes.
Formulates approach for guiding explanation types based on user specifications.
problem Creating explainable AI components from user-defined specifications.
method Develops a method for generating explanations based on user-defined specifications.
result Demonstrates feasibility of user-defined explanations for complex models like Bayesian networks and graph neural networks.
A site-specific Gordian distance between two spatial embeddings of an abstract graph is the minimal number of crossing changes from one to another where each crossing change is performed between two previously specified abstract edges of the graph. It is infinite in some cases. We determine the site-specific Gordian di…
IFGAN uses feature-specific GANs for missing value imputation.
problem Missing value imputation in data mining.
method Feature-specific Generative Adversarial Networks (GAN).
result IFGAN outperforms state-of-the-art algorithms in various missing conditions.
A novel validation method improves feature importance analysis in subject-specific ML models.
problem Limited effectiveness of general ML models trained on large datasets for individual patient outcomes.
method A novel validation approach using a general ML model with repeated trials and random seed variation.
result Consistent identification of key features at the subject level and improved group-level feature importance analysis.
We address the problem of tuning word embeddings for specific use cases and domains. We propose a new method that automatically combines multiple domain-specific embeddings, selected from a wide range of pre-trained domain-specific embeddings, to improve their combined expressive power. Our approach relies on two key c…
Site-specific recombination is an enzymatic process where two sites of precise sequence and orientation along a circle come together, are cleaved, and the ends are recombined. Site-specific recombination on a knotted substrate produces another knot or a two-component link depending on the relative orientation of the si…
Region-specific linear models are widely used in practical applications because of their non-linear but highly interpretable model representations. One of the key challenges in their use is non-convexity in simultaneous optimization of regions and region-specific models. This paper proposes novel convex region-specific…
Extends specific relative entropy to multidimensional continuous martingales.
problem Mutual singularity of martingale laws in continuous time.
method Extension of specific relative entropy from one to multiple dimensions, including closed-form expressions for simple examples.
result Establishes that the lower bound on specific relative entropy from Gantert carries over to higher dimensions and is tight.
Firms delay write-downs for adverse macroeconomic and industry outcomes but not for firm-specific issues.
problem Timeliness of write-downs for adverse macroeconomic and industry outcomes versus firm-specific issues.
method Comparative analysis of write-downs driven by macroeconomic and industry outcomes versus firm-specific outcomes.
result Firms delay write-downs for adverse macroeconomic and industry outcomes but not for firm-specific issues.
Scalable method learns context-specific models for hundreds of variables.
problem Learning context-specific models for large numbers of variables.
method Order-based Markov chain Monte-Carlo search with context-specific sparsity assumption.
result Method scales to hundreds of variables and learns accurate models.
This work defines observation-specific explanations for black-box models.
problem Assigning importance to data points in black-box model predictions.
method Surrogate model construction using scattered data approximation and orthogonal matching pursuit.
result Validated approach on simulated and real-world datasets.
Research in deep learning for multi-speaker source separation has received a boost in the last years. However, most studies are restricted to mixtures of a specific number of speakers, called a specific scenario. While some works included experiments for different scenarios, research towards combining data of different…
Specifying utility functions is a key step towards applying the discrete choice framework for understanding the behaviour processes that govern user choices. However, identifying the utility function specifications that best model and explain the observed choices can be a very challenging and time-consuming task. This …
Efficiently fine-tunes patient-independent seizure detection models with tensor kernel machine.
problem Improving seizure detection accuracy for wearable devices.
method Transfer learning with tensor kernel machine using canonical polyadic decomposition.
result Patient fine-tuned model achieves high performance with smaller model size.
Site-specific recombination on supercoiled circular DNA molecules can yield a variety of knots and catenanes. Twist knots are some of the most common conformations of these products and they can act as substrates for further rounds of site-specific recombination. They are also one of the simplest families of knots and …
CSD learns a common component for domain generalization, outperforming existing methods.
problem Training models to generalize across unseen domains.
method CSD decomposes the model into a common and specific component, discarding the latter.
result CSD outperforms state-of-the-art domain generalization methods.
Study evaluates if LLMs have company-specific biases in financial sentiment analysis.
problem Evaluating if large language models exhibit company-specific biases in financial sentiment analysis.
method Comparing sentiment scores with and without company names, constructing economic models, and empirical analysis.
result LLMs show company-specific biases in sentiment analysis, impacting investor behavior and stock prices.
QuantNet learns global market trends to improve trading strategies.
problem Developing global trading strategies from multiple markets' data.
method QuantNet integrates transfer and meta-learning to learn market-agnostic trends and market-specific strategies.
result QuantNet outperformed top baseline strategies by 51% Sharpe and 69% Calmar ratios.
In this paper we propose a boosting based multiview learning algorithm, referred to as PB-MVBoost, which iteratively learns i) weights over view-specific voters capturing view-specific information; and ii) weights over views by optimizing a PAC-Bayes multiview C-Bound that takes into account the accuracy of view-specif…
Low-rank framework for task-specific LLM ranking from sparse comparisons.
problem Challenges in reliable task-specific ranking of LLMs under sparse, imbalanced comparisons.
method Low-rank modeling of task-by-model ability matrix, max-norm accurate estimator, task-wise top-K recovery guarantees, uncertainty quantification framework.
result Improves sample efficiency and produces tighter, better-calibrated ranking certificates.
This paper aims to optimize incident-specific cyber insurance design.
problem Complexity in determining optimal risk retention and transfer.
method Economic foundation for incident-specific cyber insurance with Pareto optimality.
result Illustrates feasibility of designing incident-specific indemnities for both parties.
CosML combines domain-specific meta-learners for cross-domain few-shot classification.
problem Generalizing to unseen domains while meta-learning on multiple seen domains.
method CosML trains domain-specific meta-learners and combines their meta-parameters in the parameter space.
result CosML outperforms state-of-the-art methods and achieves strong cross-domain generalization.
Interventional domain adaptation improves feature transferability by removing spurious correlations.
problem Improper feature transferability due to spurious correlations in domain adaptation.
method Intervention strategy using unlabeled target data to generate counterfactual features and train discriminability invariance.
result Consistent performance improvements over state-of-the-art approaches in various domain adaptation tasks.
Computer algorithms are written with the intent that when run they perform a useful function. Typically any information obtained is unknown until the algorithm is run. However, if the behavior of an algorithm can be fully described by precomputing just once how this algorithm will respond when executed on any input, th…
New definition of patient-specific root causes of disease using counterfactuals.
problem Lack of rigorous mathematical formulation for automatic detection of root causes.
method Proposes a counterfactual definition matching clinical intuition and uses Shapley values for causal contribution scores.
result Adapts to disease prevalence, accounts for noisy labels, and admits fast computation.
Study shows specific states produce Khovanov homology torsion.
problem Understanding torsion in Khovanov homology.
method Proved specific sum of enhanced states produce torsion.
result Proved specific states produce Khovanov homology torsion of order two.
In this paper, we propose a deep multimodal fusion network to fuse multiple modalities (face, iris, and fingerprint) for person identification. The proposed deep multimodal fusion algorithm consists of multiple streams of modality-specific Convolutional Neural Networks (CNNs), which are jointly optimized at multiple fe…
We introduce the notion of a stochastic probabilistic program and present a reference implementation of a probabilistic programming facility supporting specification of stochastic probabilistic programs and inference in them. Stochastic probabilistic programs allow straightforward specification and efficient inference …