17 papers · ranked by Valyu relevance
Gary B. Smith, Vaishak Belle, Ronald P. A. Petrick
In many scenarios where robots or autonomous systems may be deployed, the capacity to infer and reason about the intentions of other agents can improve the performance or utility of the system. For example, a smart home or assisted living facility is better able to select assistive services to deploy if it understands…
Daan Fierens, Guy Van den Broeck, Joris Renkens, Dimitar Shterionov + 4 more
'Bernd Gutmann' 'Ingo Thon' 'Gerda Janssens' 'Luc De Raedt'] Probabilistic logic programs are logic programs in which some of the facts are annotated with probabilities. This paper investigates how classical inference and learning tasks known from the graphical model community can be tackled for probabilistic logic…
Robin Manhaeve, Sebastijan Dumančić, Angelika Kimmig, Thomas Demeester + 1 more
'Thomas Demeester' 'Luc De Raedt'] We introduce DeepProbLog, a neural probabilistic logic programming language that incorporates deep learning by means of neural predicates. We show how existing inference and learning techniques of the underlying probabilistic logic programming language ProbLog can be adapted for the…
Francesca Toni, Nico Potyka, Markus Ulbricht, Pietro Totis
ProbLog is a popular probabilistic logic programming language/tool, widely used for applications requiring to deal with inherent uncertainties in structured domains. In this paper we study connections between ProbLog and a variant of another well-known formalism combining symbolic reasoning and reasoning under…
Vaishak Belle
Probabilistic planning attempts to incorporate stochastic models directly into the planning process, which is the problem of synthesizing a sequence of actions that achieves some objective for a putative agent. Probabilistic programming has rapidly emerged as a key paradigm to integrate probabilistic concepts with…
Daan Fierens, Guy Van den Broeck, Ingo Thon, Bernd Gutmann + 1 more
'Luc De Raedt'] Probabilistic logic programs are logic programs in which some of the facts are annotated with probabilities. Several classical probabilistic inference tasks (such as MAP and computing marginals) have not yet received a lot of attention for this formalism. The contribution of this paper is that we…
Wang-Zhou Dai, Zhihua Zhou
Recent years have seen a surge of interest in Probabilistic Logic Programming (PLP) and Statistical Relational Learning (SRL) models that combine logic with probabilities. Structure learning of these systems is an intersection area of Inductive Logic Programming (ILP) and statistical learning (SL). However, ILP cannot…
Francisco Henrique Otte Vieira de Faria, Arthur Colombini Gusmão, Fábio Gagliardi Cozman, Denis Deratani Mauá
'Fábio Gagliardi Cozman' 'Denis Deratani Mauá'] ProbLog is a state-of-art combination of logic programming and probabilities; in particular ProbLog offers parameter learning through a variant of the EM algorithm. However, the resulting learning algorithm is rather slow, even when the data are complete. In this short…
Ali Madani, Bryan McCann, Nikhil Naik, Nitish Shirish Keskar + 4 more
Generative modeling for protein engineering is key to solving fundamental problems in synthetic biology, medicine, and material science. We pose protein engineering as an unsupervised sequence generation problem in order to leverage the exponentially growing set of proteins that lack costly, structural annotations. We…
Soumya Nayak, Ramanathan Sowdhamini
Proteases are enzymes that break down proteins, and serine proteases are an important subset of these enzymes. Prolyl oligopeptidase (POP) is a family of serine proteases (S9 family) that has the ability to cleave peptide bonds involving proline residues and it is unique for its ability to cleave various small…
Nadav Rappoport, Michal Linial
ProtoBug ([http://www.protobug.cs.huji.ac.il]()) is a database and resource of protein families in Arthropod genomes. ProtoBug platform presents the relatedness of complete proteomes from 17 insects as well as a proteome of the crustacean, Daphnia pulex. The represented proteomes from insects include louse, bee…
Jaime Moreno, Henrik Nielsen, Ole Winther, Felix Teufel
Protein subcellular location prediction is a widely explored task in bioinformatics because of its importance in proteomics research. We propose DeepLocPro, an extension to the popular method DeepLoc, tailored specifically to archaeal and bacterial organisms. DeepLocPro is a multiclass subcellular location prediction…
Christian J A Sigrist, Béatrice A Cuche, Edouard de Castro, Elisabeth Coudert + 2 more
PROSITE ([https://prosite.expasy.org/]()) is a database of entries documenting protein domains, families, and functional sites, along with the associated patterns and profiles used to identify them. It is complemented by ProRule, a rule collection that enhances the discriminatory power of these profiles and patterns by…
Ronen Gabizon, Amit Shraga, Paul Gehrtz, Ella Livnah + 6 more
PROteolysis Targeting Chimeras (PROTACs) represent an exciting inhibitory modality with many advantages, including sub-stoichiometric degradation of targets. Their scope, though, is still limited to-date by the requirement for a sufficiently potent target binder. A solution that proved useful in tackling challenging…
Jin Su, Xibin Zhou, Xuting Zhang, Fajie Yuan
ProTrek, a tri-modal protein language model, enables contrastive learning of protein sequence, structure, and function (SSF). Through its natural language search interface, users can navigate the vast protein universe in seconds, accessing nine distinct search tasks that cover all possible pairwise combinations of SSF.…
SARAH K. MARTIN, TAYLOR B. VAUGHAN, TIMOTHY ATKINSON, HAINING ZHU + 1 more
'NATASHA KYPRIANOU'] Prostate cancer progression involves activation of signaling pathways controlling cell proliferation, apoptosis, anoikis, angiogenesis and metastasis. The current PSA-based test for the diagnosis of prostate cancer lacks sensitivity and specificity, resulting in missed diagnoses and unnecessary…
Karina Chan, Preethi Soundarya Sathyamurthi, Markus Queisser, Michael Mullin + 3 more
Proteolysis targeting chimeras (PROTACs) are a family of heterobifunctional molecules that are now realising their promise as a therapeutic strategy for targeted protein degradation. However, one limitation of existing designs is the lack of cell-selective targeting of the protein degrading payload. This manuscript…