lpsolver 0.1.0 → 0.2.1

data/ext/lpsolver-highs/highs/mip/HighsCliqueTable.cpp

@@ -0,0 +1,2236 @@
+/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+/*                                                                       */
+/*    This file is part of the HiGHS linear optimization suite           */
+/*                                                                       */
+/*    Available as open-source under the MIT License                     */
+/*                                                                       */
+/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+#include "mip/HighsCliqueTable.h"
+
+#include <algorithm>
+#include <cassert>
+#include <cstdio>
+#include <numeric>
+
+#include "../extern/pdqsort/pdqsort.h"
+#include "mip/HighsCutPool.h"
+#include "mip/HighsDomain.h"
+#include "mip/HighsMipSolver.h"
+#include "mip/HighsMipSolverData.h"
+#include "parallel/HighsCombinable.h"
+#include "parallel/HighsParallel.h"
+#include "presolve/HighsPostsolveStack.h"
+#include "util/HighsSplay.h"
+
+#define ADD_ZERO_WEIGHT_VARS
+
+static std::pair<HighsCliqueTable::CliqueVar, HighsCliqueTable::CliqueVar>
+sortedEdge(HighsCliqueTable::CliqueVar v1, HighsCliqueTable::CliqueVar v2) {
+  if (v1.col > v2.col) return std::make_pair(v2, v1);
+
+  return std::make_pair(v1, v2);
+}
+
+void HighsCliqueTable::unlink(HighsInt pos, HighsInt cliqueid) {
+  assert(pos >= 0);
+  --numcliquesvar[cliqueentries[pos].index()];
+
+  HighsInt cliquelen = cliques[cliqueid].end - cliques[cliqueid].start;
+  if (cliquelen == 2)
+    invertedHashListSizeTwo[cliqueentries[pos].index()].erase(cliqueid);
+  else
+    invertedHashList[cliqueentries[pos].index()].erase(cliqueid);
+}
+
+void HighsCliqueTable::link(HighsInt pos, HighsInt cliqueid) {
+  assert(pos >= 0);
+  assert(!colDeleted[cliqueentries[pos].col]);
+  ++numcliquesvar[cliqueentries[pos].index()];
+
+  HighsInt cliquelen = cliques[cliqueid].end - cliques[cliqueid].start;
+  if (cliquelen == 2)
+    invertedHashListSizeTwo[cliqueentries[pos].index()].insert(cliqueid);
+  else
+    invertedHashList[cliqueentries[pos].index()].insert(cliqueid, pos);
+}
+
+HighsInt HighsCliqueTable::findCommonCliqueId(int64_t& numQueries, CliqueVar v1,
+                                              CliqueVar v2) const {
+  ++numQueries;
+  if (!invertedHashListSizeTwo[v1.index()].empty() &&
+      !invertedHashListSizeTwo[v2.index()].empty()) {
+    const HighsInt* sizeTwoCliqueId = sizeTwoCliques.find(sortedEdge(v1, v2));
+    if (sizeTwoCliqueId != nullptr) return *sizeTwoCliqueId;
+  }
+
+  const HighsHashTree<HighsInt, HighsInt>& h1 = invertedHashList[v1.index()];
+  const HighsHashTree<HighsInt, HighsInt>& h2 = invertedHashList[v2.index()];
+
+  const HighsHashTableEntry<HighsInt, HighsInt>* commonClique =
+      h1.find_common(h2);
+
+  if (commonClique) return commonClique->key();
+  return -1;
+}
+
+void HighsCliqueTable::resolveSubstitution(CliqueVar& v) const {
+  while (colsubstituted[v.col]) {
+    Substitution subst = substitutions[colsubstituted[v.col] - 1];
+    v = v.val == 1 ? subst.replace : subst.replace.complement();
+  }
+}
+
+void HighsCliqueTable::resolveSubstitution(HighsInt& col, double& val,
+                                           double& offset) const {
+  while (colsubstituted[col]) {
+    Substitution subst = substitutions[colsubstituted[col] - 1];
+    if (subst.replace.val == 0) {
+      offset += val;
+      val = -val;
+    }
+    col = subst.replace.col;
+  }
+}
+
+HighsInt HighsCliqueTable::runCliqueSubsumption(
+    const HighsDomain& globaldom, std::vector<CliqueVar>& clique) {
+  // remove deleted cols
+  clique.erase(
+      std::remove_if(clique.begin(), clique.end(),
+                     [&](CliqueVar clqvar) { return colDeleted[clqvar.col]; }),
+      clique.end());
+
+  // return if clique does not have enough elements
+  if (clique.size() <= 2) return 0;
+
+  // callback for removing cliques
+  HighsInt nremoved = 0;
+  auto removeCliques = [&](HighsInt cliqueid) {
+    ++nremoved;
+    cliques[cliqueid].origin = kHighsIInf;
+    removeClique(cliqueid);
+  };
+
+  // check clique
+  bool redundant;
+  HighsInt dominatingOrigin;
+  cliqueSubsumption(clique, redundant, dominatingOrigin, removeCliques);
+
+  if (redundant) clique.clear();
+
+  if (!infeasvertexstack.empty()) {
+    clique.erase(
+        std::remove_if(clique.begin(), clique.end(),
+                       [&](CliqueVar v) { return globaldom.isFixed(v.col); }),
+        clique.end());
+  }
+
+  return nremoved;
+}
+
+void HighsCliqueTable::cliqueSubsumption(
+    const std::vector<CliqueVar>& clique, bool& redundant,
+    HighsInt& dominatingOrigin,
+    std::function<void(HighsInt)> removeCliqueCallback) {
+  // collect indices of cliques that contain variables from the
+  // provided vector
+  collectCliques(clique);
+
+  // initialise
+  redundant = false;
+  dominatingOrigin = kHighsIInf;
+
+  for (HighsInt cliqueid : cliquehitinds) {
+    // remember hits and zero out vector
+    HighsInt hits = cliquehits[cliqueid];
+    cliquehits[cliqueid] = 0;
+
+    if (hits == static_cast<HighsInt>(clique.size())) {
+      // clique is redundant
+      redundant = true;
+      if (cliques[cliqueid].origin != kHighsIInf &&
+          cliques[cliqueid].origin != -1)
+        dominatingOrigin = cliques[cliqueid].origin;
+    } else if (cliques[cliqueid].numActive() == hits) {
+      // clique is subset of another clique
+      if (cliques[cliqueid].equality) {
+        // subset of clique is an equality clique (stored in the clique table),
+        // thus the remaining variables can be fixed
+        bool sizeTwo = cliques[cliqueid].end - cliques[cliqueid].start == 2;
+        for (CliqueVar v : clique) {
+          bool vHasClq =
+              sizeTwo ? invertedHashListSizeTwo[v.index()].contains(cliqueid)
+                      : invertedHashList[v.index()].contains(cliqueid);
+          if (!vHasClq) infeasvertexstack.push_back(v);
+        }
+      } else {
+        // clique from clique table contains a subset of the variables, thus it
+        // can be removed
+        removeCliqueCallback(cliqueid);
+      }
+    }
+  }
+  // clear vector of cliques indices
+  cliquehitinds.clear();
+}
+
+void HighsCliqueTable::collectCliques(const std::vector<CliqueVar>& clique) {
+  // resize vector
+  if (cliquehits.size() < cliques.size()) cliquehits.resize(cliques.size());
+
+  // collect indices of cliques that contain variables from the
+  // provided vector
+  for (CliqueVar v : clique) {
+    invertedHashList[v.index()].for_each([&](HighsInt cliqueid) {
+      if (cliquehits[cliqueid] == 0) cliquehitinds.push_back(cliqueid);
+      ++cliquehits[cliqueid];
+    });
+
+    invertedHashListSizeTwo[v.index()].for_each([&](HighsInt cliqueid) {
+      if (cliquehits[cliqueid] == 0) cliquehitinds.push_back(cliqueid);
+      ++cliquehits[cliqueid];
+    });
+  }
+}
+
+void HighsCliqueTable::bronKerboschRecurse(BronKerboschData& data,
+                                           HighsInt Plen, const CliqueVar* X,
+                                           HighsInt Xlen) const {
+  double w = data.wR;
+
+  for (HighsInt i = 0; i != Plen; ++i) w += data.P[i].weight(data.sol);
+
+  if (w < data.minW - data.feastol) return;
+
+  if (Plen == 0 && Xlen == 0) {
+    std::vector<CliqueVar> clique = data.R;
+
+    if (data.minW < w - data.feastol) {
+      data.maxcliques -= data.cliques.size();
+      data.cliques.clear();
+      data.minW = w;
+    }
+    data.cliques.emplace_back(std::move(clique));
+    // do not further search for cliques that are violated less than this
+    // current clique
+    return;
+  }
+
+  ++data.ncalls;
+
+  if (data.stop()) return;
+
+  double pivweight = -1.0;
+  CliqueVar pivot{0, 0};
+
+  for (HighsInt i = 0; i != Xlen; ++i) {
+    if (X[i].weight(data.sol) > pivweight) {
+      pivweight = X[i].weight(data.sol);
+      pivot = X[i];
+      if (pivweight >= 1.0 - data.feastol) break;
+    }
+  }
+
+  if (pivweight < 1.0 - data.feastol) {
+    for (HighsInt i = 0; i != Plen; ++i) {
+      if (data.P[i].weight(data.sol) > pivweight) {
+        pivweight = data.P[i].weight(data.sol);
+        pivot = data.P[i];
+        if (pivweight >= 1.0 - data.feastol) break;
+      }
+    }
+  }
+
+  std::vector<CliqueVar> PminusNu;
+  PminusNu.reserve(Plen);
+  queryNeighbourhood(data.neighbourhoodInds, data.numNeighbourhoodQueries,
+                     pivot, data.P.data(), Plen);
+  data.neighbourhoodInds.push_back(Plen);
+  HighsInt k = 0;
+  for (HighsInt i : data.neighbourhoodInds) {
+    while (k < i) PminusNu.push_back(data.P[k++]);
+    ++k;
+  }
+
+  pdqsort(PminusNu.begin(), PminusNu.end(), [&](CliqueVar a, CliqueVar b) {
+    return std::make_pair(a.weight(data.sol), a.index()) >
+           std::make_pair(b.weight(data.sol), b.index());
+  });
+
+  std::vector<CliqueVar> localX;
+  localX.insert(localX.end(), X, X + Xlen);
+
+  for (CliqueVar v : PminusNu) {
+    HighsInt newPlen = partitionNeighbourhood(data.neighbourhoodInds,
+                                              data.numNeighbourhoodQueries, v,
+                                              data.P.data(), Plen);
+    HighsInt newXlen = partitionNeighbourhood(data.neighbourhoodInds,
+                                              data.numNeighbourhoodQueries, v,
+                                              localX.data(), localX.size());
+
+    // add v to R, update the weight, and do the recursive call
+    data.R.push_back(v);
+    double wv = v.weight(data.sol);
+    data.wR += wv;
+    bronKerboschRecurse(data, newPlen, localX.data(), newXlen);
+    if (data.stop()) return;
+
+    // remove v from R restore the weight and continue the loop in this call
+    data.R.pop_back();
+    data.wR -= wv;
+
+    w -= wv;
+    if (w < data.minW) return;
+    // find the position of v in the vertices removed from P for the recursive
+    // call
+    // and also remove it from the set P for this call
+    HighsInt vpos = -1;
+    for (HighsInt i = newPlen; i != Plen; ++i) {
+      if (data.P[i] == v) {
+        vpos = i;
+        break;
+      }
+    }
+
+    // do the removal by first swapping it to the end of P and reduce the size
+    // of P accordingly
+    assert(vpos != -1);
+
+    --Plen;
+    std::swap(data.P[vpos], data.P[Plen]);
+
+    localX.push_back(v);
+  }
+}
+
+#if 0
+static void printRow(const HighsDomain& domain, const HighsInt* inds,
+                     const double* vals, HighsInt len, double lhs, double rhs) {
+  printf("%g <= ", lhs);
+
+  for (HighsInt i = 0; i != len; ++i) {
+    char sign = vals[i] > 0 ? '+' : '-';
+    char var = domain.isBinary(inds[i]) ? 'x' : 'y';
+    printf("%c%g %c%" HIGHSINT_FORMAT " ", sign, std::abs(vals[i]), var, inds[i]);
+  }
+
+  printf("<= %g\n", rhs);
+}
+
+static void printClique(
+    const std::vector<HighsCliqueTable::CliqueVar>& clique) {
+  bool first = true;
+  for (HighsCliqueTable::CliqueVar v : clique) {
+    if (!first) printf("+ ");
+    char complemented = v.val == 0 ? '~' : ' ';
+    printf("%cx%" HIGHSINT_FORMAT " ", complemented, v.col);
+    first = false;
+  }
+
+  printf("<= 1\n");
+}
+#endif
+
+void HighsCliqueTable::doAddClique(const CliqueVar* cliquevars,
+                                   HighsInt numcliquevars, bool equality,
+                                   HighsInt origin) {
+  HighsInt cliqueid;
+
+  if (freeslots.empty()) {
+    cliqueid = cliques.size();
+    cliques.emplace_back();
+  } else {
+    cliqueid = freeslots.back();
+    freeslots.pop_back();
+  }
+
+  cliques[cliqueid].equality = equality;
+  cliques[cliqueid].origin = origin;
+
+  decltype(freespaces)::iterator it;
+  HighsInt maxEnd;
+  if (freespaces.empty() ||
+      (it = freespaces.lower_bound(
+           std::make_pair(numcliquevars, HighsInt{-1}))) == freespaces.end()) {
+    cliques[cliqueid].start = cliqueentries.size();
+    cliques[cliqueid].end = cliques[cliqueid].start + numcliquevars;
+    maxEnd = cliques[cliqueid].end;
+    cliqueentries.resize(cliques[cliqueid].end);
+  } else {
+    auto freespace = *it;
+    freespaces.erase(it);
+
+    cliques[cliqueid].start = freespace.second;
+    cliques[cliqueid].end = cliques[cliqueid].start + numcliquevars;
+    maxEnd = cliques[cliqueid].start + freespace.first;
+  }
+
+  cliques[cliqueid].numZeroFixed = 0;
+
+  bool fixtozero = false;
+  HighsInt k = cliques[cliqueid].start;
+  for (HighsInt i = 0; i != numcliquevars; ++i) {
+    CliqueVar v = cliquevars[i];
+
+    resolveSubstitution(v);
+
+    if (fixtozero) {
+      infeasvertexstack.push_back(v);
+      continue;
+    }
+
+    // due to substitutions the variable may occur together with its complement
+    // in this clique and we can fix all other variables in the clique to zero:
+    //          x + ~x + ... <= 1
+    //   <=> x + 1 - x + ... <= 1
+    //   <=>             ... <= 0
+    bool clqHasVCompl =
+        numcliquevars == 2
+            ? invertedHashListSizeTwo[v.complement().index()].contains(cliqueid)
+            : invertedHashList[v.complement().index()].contains(cliqueid);
+
+    if (clqHasVCompl) {
+      fixtozero = true;
+      for (HighsInt j = cliques[cliqueid].start; j != k; ++j) {
+        if (cliqueentries[j].col != v.col)
+          infeasvertexstack.push_back(cliqueentries[j]);
+        unlink(j, cliqueid);
+      }
+      k = cliques[cliqueid].start;
+      continue;
+    }
+
+    // due to substitutions the variable may occur twice in this clique and
+    // we can fix it to zero:  x + x + ... <= 1  <=>  2x <= 1 <=> x <= 0.5 <=>
+    // x = 0
+    bool inserted;
+    if (numcliquevars == 2)
+      inserted = invertedHashListSizeTwo[v.index()].insert(cliqueid);
+    else
+      inserted = invertedHashList[v.index()].insert(cliqueid, k);
+
+    if (!inserted) {
+      infeasvertexstack.push_back(v);
+      continue;
+    }
+
+    cliqueentries[k] = v;
+    ++numcliquesvar[v.index()];
+    ++k;
+  }
+
+  if (maxEnd > k) {
+    if (int(cliqueentries.size()) == maxEnd)
+      cliqueentries.resize(k);
+    else
+      freespaces.emplace(maxEnd - k, k);
+
+    if (cliques[cliqueid].end > k) {
+      switch (k - cliques[cliqueid].start) {
+        case 0:
+          // clique empty, so just mark it as deleted
+          cliques[cliqueid].start = -1;
+          cliques[cliqueid].end = -1;
+          freeslots.push_back(cliqueid);
+          return;
+        case 1:
+          // size 1 clique is redundant, so unlink the single linked entry
+          // and mark it as deleted
+          unlink(cliques[cliqueid].start, cliqueid);
+          cliques[cliqueid].start = -1;
+          cliques[cliqueid].end = -1;
+          freeslots.push_back(cliqueid);
+          return;
+        case 2:
+          // due to substitutions the clique became smaller and is now of size
+          // two as a result we need to link it to the size two cliqueset
+          // instead of the normal cliqueset
+          assert(cliqueid >= 0 &&
+                 cliqueid < static_cast<HighsInt>(cliques.size()));
+          assert(cliques[cliqueid].start >= 0 &&
+                 cliques[cliqueid].start <
+                     static_cast<HighsInt>(cliqueentries.size()));
+          unlink(cliques[cliqueid].start, cliqueid);
+          unlink(cliques[cliqueid].start + 1, cliqueid);
+
+          cliques[cliqueid].end = k;
+
+          link(cliques[cliqueid].start, cliqueid);
+          link(cliques[cliqueid].start + 1, cliqueid);
+          break;
+        default:
+          cliques[cliqueid].end = k;
+      }
+    }
+  }
+
+  HighsInt cliqueLen = cliques[cliqueid].end - cliques[cliqueid].start;
+  numEntries += cliqueLen;
+  if (cliqueLen == 2)
+    sizeTwoCliques.insert(
+        sortedEdge(cliqueentries[cliques[cliqueid].start],
+                   cliqueentries[cliques[cliqueid].start + 1]),
+        cliqueid);
+}
+struct ThreadNeighbourhoodQueryData {
+  int64_t numQueries;
+  std::vector<HighsInt> neighbourhoodInds;
+};
+
+void HighsCliqueTable::queryNeighbourhood(
+    std::vector<HighsInt>& neighbourhoodInds, int64_t& numQueries, CliqueVar v,
+    CliqueVar* q, HighsInt N) const {
+  neighbourhoodInds.clear();
+
+  if (numCliques(v) == 0) return;
+
+  if (numEntries - sizeTwoCliques.size() * 2 < minEntriesForParallelism) {
+    for (HighsInt i = 0; i < N; ++i) {
+      if (haveCommonClique(numQueries, v, q[i])) neighbourhoodInds.push_back(i);
+    }
+  } else {
+    auto neighbourhoodData =
+        makeHighsCombinable<ThreadNeighbourhoodQueryData>([N]() {
+          ThreadNeighbourhoodQueryData d;
+          d.neighbourhoodInds.reserve(N);
+          d.numQueries = 0;
+          return d;
+        });
+    highs::parallel::for_each(
+        0, N,
+        [this, &neighbourhoodData, v, q](HighsInt start, HighsInt end) {
+          ThreadNeighbourhoodQueryData& d = neighbourhoodData.local();
+          for (HighsInt i = start; i < end; ++i) {
+            if (haveCommonClique(d.numQueries, v, q[i]))
+              d.neighbourhoodInds.push_back(i);
+          }
+        },
+        10);
+
+    neighbourhoodData.combine_each([&](ThreadNeighbourhoodQueryData& d) {
+      neighbourhoodInds.insert(neighbourhoodInds.end(),
+                               d.neighbourhoodInds.begin(),
+                               d.neighbourhoodInds.end());
+      numQueries += d.numQueries;
+    });
+    pdqsort(neighbourhoodInds.begin(), neighbourhoodInds.end());
+  }
+}
+
+HighsInt HighsCliqueTable::partitionNeighbourhood(
+    std::vector<HighsInt>& neighbourhoodInds, int64_t& numQueries, CliqueVar v,
+    CliqueVar* q, HighsInt N) const {
+  queryNeighbourhood(neighbourhoodInds, numQueries, v, q, N);
+
+  for (size_t i = 0; i < neighbourhoodInds.size(); ++i)
+    std::swap(q[i], q[neighbourhoodInds[i]]);
+
+  return static_cast<HighsInt>(neighbourhoodInds.size());
+}
+
+HighsInt HighsCliqueTable::shrinkToNeighbourhood(
+    std::vector<HighsInt>& neighbourhoodInds, int64_t& numQueries, CliqueVar v,
+    CliqueVar* q, HighsInt N) {
+  queryNeighbourhood(neighbourhoodInds, numQueries, v, q, N);
+
+  for (size_t i = 0; i < neighbourhoodInds.size(); ++i)
+    q[i] = q[neighbourhoodInds[i]];
+
+  return static_cast<HighsInt>(neighbourhoodInds.size());
+}
+
+bool HighsCliqueTable::fixCol(HighsDomain& globaldom, CliqueVar v,
+                              bool doProcessInfeasibleVertices) {
+  bool wasfixed = globaldom.isFixed(v.col);
+  globaldom.fixCol(v.col, static_cast<double>(1 - v.val));
+  if (globaldom.infeasible()) return false;
+  if (!wasfixed) {
+    ++nfixings;
+    infeasvertexstack.push_back(v);
+    if (doProcessInfeasibleVertices) processInfeasibleVertices(globaldom);
+  }
+  return true;
+}
+
+bool HighsCliqueTable::processNewEdge(HighsDomain& globaldom, CliqueVar v1,
+                                      CliqueVar v2) {
+  if (v1.col == v2.col) {
+    if (v1.val == v2.val) {
+      fixCol(globaldom, v1, true);
+      return false;
+    }
+
+    return true;
+  }
+
+  // invertedEdgeCache.erase(sortedEdge(v1, v2));
+
+  if (haveCommonClique(v1.complement(), v2)) {
+    fixCol(globaldom, v2, true);
+    return false;
+  } else if (haveCommonClique(v2.complement(), v1)) {
+    fixCol(globaldom, v1, true);
+    return false;
+  } else {
+    // return if complements are not in a clique
+    if (!foundCover(globaldom, v1.complement(), v2.complement())) return false;
+    if (globaldom.infeasible()) return true;
+
+    foundCover(globaldom, v1, v2);
+    if (globaldom.isFixed(v1.col) || globaldom.isFixed(v2.col) ||
+        globaldom.infeasible())
+      return true;
+
+    Substitution substitution;
+    if (v2.col < v1.col) {
+      if (v1.val == 1) v2 = v2.complement();
+
+      substitution.substcol = v1.col;
+      substitution.replace = v2;
+    } else {
+      if (v2.val == 1) v1 = v1.complement();
+
+      substitution.substcol = v2.col;
+      substitution.replace = v1;
+    }
+
+    substitutions.push_back(substitution);
+    colsubstituted[substitution.substcol] = substitutions.size();
+
+    auto replace = [&](CliqueVar substitutedVar, CliqueVar replacementVar) {
+      HighsHashTree<HighsInt, HighsInt>& substList =
+          invertedHashList[substitutedVar.index()];
+      HighsHashTree<HighsInt, HighsInt>& replaceList =
+          invertedHashList[replacementVar.index()];
+      numcliquesvar[replacementVar.index()] +=
+          numcliquesvar[substitutedVar.index()];
+      numcliquesvar[substitutedVar.index()] = 0;
+
+      substList.for_each([&](HighsInt cliqueid, HighsInt location) {
+        replaceList.insert(cliqueid, location);
+        cliqueentries[location] = replacementVar;
+      });
+
+      substList.clear();
+
+      HighsHashTree<HighsInt>& substListSizeTwo =
+          invertedHashListSizeTwo[substitutedVar.index()];
+      HighsHashTree<HighsInt>& replaceListSizeTwo =
+          invertedHashListSizeTwo[replacementVar.index()];
+
+      substListSizeTwo.for_each([&](HighsInt cliqueid) {
+        HighsInt pos = cliques[cliqueid].start;
+        HighsInt otherPos = pos + 1;
+
+        if (cliqueentries[otherPos] == substitutedVar) std::swap(pos, otherPos);
+
+        replaceListSizeTwo.insert(cliqueid);
+        cliqueentries[pos] = replacementVar;
+
+        sizeTwoCliques.erase(
+            sortedEdge(substitutedVar, cliqueentries[otherPos]));
+        sizeTwoCliques.insert(
+            sortedEdge(replacementVar, cliqueentries[otherPos]), cliqueid);
+      });
+
+      substListSizeTwo.clear();
+    };
+
+    replace(CliqueVar(substitution.substcol, 1), substitution.replace);
+    replace(CliqueVar(substitution.substcol, 0),
+            substitution.replace.complement());
+
+    return true;
+  }
+}
+
+void HighsCliqueTable::addClique(const HighsMipSolver& mipsolver,
+                                 CliqueVar* cliquevars, HighsInt numcliquevars,
+                                 bool equality, HighsInt origin) {
+  HighsDomain& globaldom = mipsolver.mipdata_->domain;
+  mipsolver.mipdata_->debugSolution.checkClique(cliquevars, numcliquevars);
+  const HighsInt maxNumCliqueVars = 100;
+
+  // lambda for complementing clique
+  auto complementClique = [&]() {
+    for (HighsInt i = 0; i != numcliquevars; ++i) {
+      cliquevars[i] = cliquevars[i].complement();
+    }
+  };
+
+  // lambda for analysing the clique to see if all variables can be fixed
+  auto fixAllVarsInClique = [&](bool& hasNewEdge) {
+    for (HighsInt i = 0; i != numcliquevars; ++i) {
+      if (!globaldom.isFixed(cliquevars[i].col) ||
+          cliquevars[i].val != globaldom.col_lower_[cliquevars[i].col])
+        continue;
+      // column is fixed to 1, every other entry can be fixed to zero
+      for (HighsInt k = 0; k != numcliquevars; ++k) {
+        if (k == i) continue;
+        if (!fixCol(globaldom, cliquevars[k])) return false;
+      }
+      processInfeasibleVertices(globaldom);
+      return true;
+    }
+
+    if (numcliquevars > maxNumCliqueVars) return false;
+
+    // todo, sort new clique to allow log n lookup of membership in size by
+    // binary search
+
+    for (HighsInt i = 0; i < numcliquevars - 1; ++i) {
+      if (globaldom.isFixed(cliquevars[i].col)) continue;
+      if (numCliques(cliquevars[i]) == 0 &&
+          numCliques(cliquevars[i].complement()) == 0) {
+        hasNewEdge = true;
+        continue;
+      }
+
+      for (HighsInt j = i + 1; j < numcliquevars; ++j) {
+        if (globaldom.isFixed(cliquevars[j].col)) continue;
+
+        if (haveCommonClique(cliquevars[i], cliquevars[j])) continue;
+        // todo: Instead of haveCommonClique use findCommonClique. If the
+        // common clique is smaller than this clique check if it is a subset
+        // of this clique. If it is a subset remove the clique and iterate the
+        // process until either a common clique that is not a subset of this
+        // one is found, or no common clique exists anymore in which case we
+        // proceed with the code below and set hasNewEdge to true
+
+        hasNewEdge = true;
+
+        bool iscover = processNewEdge(globaldom, cliquevars[i], cliquevars[j]);
+        if (globaldom.infeasible()) return false;
+
+        if (!mipsolver.mipdata_->nodequeue.empty()) {
+          const auto& v1Nodes =
+              cliquevars[i].val == 1
+                  ? mipsolver.mipdata_->nodequeue.getUpNodes(cliquevars[i].col)
+                  : mipsolver.mipdata_->nodequeue.getDownNodes(
+                        cliquevars[i].col);
+          const auto& v2Nodes =
+              cliquevars[j].val == 1
+                  ? mipsolver.mipdata_->nodequeue.getUpNodes(cliquevars[j].col)
+                  : mipsolver.mipdata_->nodequeue.getDownNodes(
+                        cliquevars[j].col);
+
+          if (!v1Nodes.empty() && !v2Nodes.empty()) {
+            // general integer variables can become binary during the search
+            // and the cliques might be discovered. That means we need to take
+            // care here, since the set of nodes branched upwards or downwards
+            // are not necessarily containing domain changes setting the
+            // variables to the corresponding clique value but could be
+            // redundant bound changes setting the upper bound to u >= 1 or
+            // the lower bound to l <= 0.
+
+            // itV1 will point to the first node where v1 is fixed to val and
+            // endV1 to the end of the range of such nodes. Same for
+            // itV2/endV2 with v2.
+            auto itV1 = v1Nodes.lower_bound(std::make_pair(
+                static_cast<double>(cliquevars[i].val), kHighsIInf));
+            auto endV1 = v1Nodes.upper_bound(std::make_pair(
+                static_cast<double>(cliquevars[i].val), kHighsIInf));
+            auto itV2 = v2Nodes.lower_bound(std::make_pair(
+                static_cast<double>(cliquevars[j].val), kHighsIInf));
+            auto endV2 = v2Nodes.upper_bound(std::make_pair(
+                static_cast<double>(cliquevars[j].val), kHighsIInf));
+
+            if (itV1 != endV1 && itV2 != endV2 &&
+                (itV1->second <= std::prev(endV2)->second ||
+                 itV2->second <= std::prev(endV1)->second)) {
+              // node ranges overlap, check for nodes that can be pruned
+              while (itV1 != endV1 && itV2 != endV2) {
+                if (itV1->second < itV2->second) {
+                  ++itV1;
+                } else if (itV2->second < itV1->second) {
+                  ++itV2;
+                } else {
+                  // if (!mipsolver.submip)
+                  //   printf("node %d can be pruned\n", itV2->second);
+                  HighsInt prunedNode = itV2->second;
+                  ++itV1;
+                  ++itV2;
+                  mipsolver.mipdata_->pruned_treeweight +=
+                      mipsolver.mipdata_->nodequeue.pruneNode(prunedNode);
+                }
+              }
+            }
+          }
+        }
+
+        if (iscover) {
+          for (HighsInt k = 0; k != numcliquevars; ++k) {
+            if (k == i || k == j) continue;
+            if (!fixCol(globaldom, cliquevars[k])) return false;
+          }
+          processInfeasibleVertices(globaldom);
+          return true;
+        }
+      }
+    }
+    return false;
+  };
+
+  // lambda for checking the (complemented) clique
+  auto checkClique = [&](bool& hasNewEdge, bool complement) {
+    if (complement) complementClique();
+    bool done = fixAllVarsInClique(hasNewEdge);
+    if (complement) complementClique();
+    if (done) return true;
+    return false;
+  };
+
+  // resolve substitutions
+  for (HighsInt i = 0; i != numcliquevars; ++i) {
+    resolveSubstitution(cliquevars[i]);
+  }
+
+  // initialise flag
+  bool hasNewEdge = false;
+
+  // check if all variables can be fixed or infeasibility is detected
+  if (checkClique(hasNewEdge, false)) return;
+  if (globaldom.infeasible()) return;
+
+  if (numcliquevars == 2 && equality) {
+    // try complemented clique
+    if (checkClique(hasNewEdge, true)) return;
+    if (globaldom.infeasible()) return;
+  }
+
+  if (!hasNewEdge && origin == kHighsIInf) return;
+
+  CliqueVar* unfixedend =
+      std::remove_if(cliquevars, cliquevars + numcliquevars,
+                     [&](CliqueVar v) { return globaldom.isFixed(v.col); });
+  numcliquevars = unfixedend - cliquevars;
+  if (numcliquevars < 2) return;
+
+  doAddClique(cliquevars, numcliquevars, equality, origin);
+  processInfeasibleVertices(globaldom);
+}
+
+void HighsCliqueTable::removeClique(HighsInt cliqueid) {
+  if (cliques[cliqueid].origin != kHighsIInf && cliques[cliqueid].origin != -1)
+    deletedrows.push_back(cliques[cliqueid].origin);
+
+  HighsInt start = cliques[cliqueid].start;
+  assert(start != -1);
+  HighsInt end = cliques[cliqueid].end;
+  HighsInt len = end - start;
+  if (len == 2) {
+    sizeTwoCliques.erase(
+        sortedEdge(cliqueentries[start], cliqueentries[start + 1]));
+  }
+
+  for (HighsInt i = start; i != end; ++i) {
+    unlink(i, cliqueid);
+  }
+
+  freeslots.push_back(cliqueid);
+  freespaces.emplace(len, start);
+
+  cliques[cliqueid].start = -1;
+  cliques[cliqueid].end = -1;
+  numEntries -= len;
+}
+
+void HighsCliqueTable::extractCliques(
+    const HighsMipSolver& mipsolver, std::vector<HighsInt>& inds,
+    std::vector<double>& vals, std::vector<int8_t>& complementation, double rhs,
+    HighsInt nbin, std::vector<HighsInt>& perm, std::vector<CliqueVar>& clique,
+    double feastol) {
+  HighsImplications& implics = mipsolver.mipdata_->implications;
+  HighsDomain& globaldom = mipsolver.mipdata_->domain;
+
+  perm.resize(inds.size());
+  std::iota(perm.begin(), perm.end(), 0);
+
+  auto binaryend = std::partition(perm.begin(), perm.end(), [&](HighsInt pos) {
+    return globaldom.isBinary(inds[pos]);
+  });
+  nbin = binaryend - perm.begin();
+  HighsInt ntotal = static_cast<HighsInt>(perm.size());
+
+  // if not all variables are binary, we extract variable upper and lower bounds
+  // constraints on the non-binary variable for each binary variable in the
+  // constraint
+  if (nbin < ntotal) {
+    for (HighsInt i = 0; i != nbin; ++i) {
+      HighsInt bincol = inds[perm[i]];
+      HighsCDouble impliedub = static_cast<HighsCDouble>(rhs) - vals[perm[i]];
+      if (implics.tooManyVarBounds()) break;
+      for (HighsInt j = nbin; j != ntotal; ++j) {
+        HighsInt col = inds[perm[j]];
+        if (globaldom.isFixed(col)) continue;
+
+        HighsCDouble colub =
+            static_cast<HighsCDouble>(globaldom.col_upper_[col]) -
+            globaldom.col_lower_[col];
+        HighsCDouble implcolub = impliedub / vals[perm[j]];
+        if (mipsolver.isColIntegral(col))
+          implcolub = std::floor(static_cast<double>(implcolub) +
+                                 mipsolver.mipdata_->feastol);
+
+        if (implcolub < colub - feastol) {
+          HighsCDouble coef;
+          HighsCDouble constant;
+
+          if (complementation[perm[i]] == -1) {
+            coef = colub - implcolub;
+            constant = implcolub;
+          } else {
+            coef = implcolub - colub;
+            constant = colub;
+          }
+
+          if (complementation[perm[j]] == -1) {
+            constant -= globaldom.col_upper_[col];
+            implics.addVLB(col, bincol, -static_cast<double>(coef),
+                           -static_cast<double>(constant));
+          } else {
+            constant += globaldom.col_lower_[col];
+            implics.addVUB(col, bincol, static_cast<double>(coef),
+                           static_cast<double>(constant));
+          }
+        }
+      }
+    }
+  }
+
+  // only one binary means we do have no cliques
+  if (nbin <= 1) return;
+
+  pdqsort(perm.begin(), binaryend, [&](HighsInt p1, HighsInt p2) {
+    return std::make_pair(vals[p1], p1) > std::make_pair(vals[p2], p2);
+  });
+  // check if any cliques exists
+  if (vals[perm[0]] + vals[perm[1]] <= rhs + feastol) return;
+
+  // check if this is a set packing constraint (or easily transformable
+  // into one)
+  if (std::abs(vals[0] - vals[perm[nbin - 1]]) <= feastol &&
+      rhs < 2 * vals[perm[nbin - 1]] - feastol) {
+    // the coefficients on the binary variables are all equal and the
+    // right hand side is strictly below two times the coefficient value.
+    // Therefore the constraint can be transformed into a set packing
+    // constraint by relaxing out all non-binary variables (if any),
+    // dividing by the coefficient value of the binary variables, and then
+    // possibly rounding down the right hand side
+    clique.clear();
+
+    for (auto j = 0; j != nbin; ++j) {
+      HighsInt pos = perm[j];
+      if (complementation[pos] == -1)
+        clique.emplace_back(inds[pos], 0);
+      else
+        clique.emplace_back(inds[pos], 1);
+    }
+
+    addClique(mipsolver, clique.data(), nbin);
+    if (globaldom.infeasible()) return;
+    // printf("extracted this clique:\n");
+    // printClique(clique);
+    return;
+  }
+
+  for (HighsInt k = nbin - 1; k != 0; --k) {
+    double mincliqueval = rhs - vals[perm[k]] + feastol;
+    auto cliqueend = std::partition_point(
+        perm.begin(), perm.begin() + k,
+        [&](HighsInt p) { return vals[p] > mincliqueval; });
+
+    // no clique for this variable
+    if (cliqueend == perm.begin()) continue;
+
+    clique.clear();
+
+    for (auto j = perm.begin(); j != cliqueend; ++j) {
+      HighsInt pos = *j;
+      if (complementation[pos] == -1)
+        clique.emplace_back(inds[pos], 0);
+      else
+        clique.emplace_back(inds[pos], 1);
+    }
+
+    if (complementation[perm[k]] == -1)
+      clique.emplace_back(inds[perm[k]], 0);
+    else
+      clique.emplace_back(inds[perm[k]], 1);
+
+    // printf("extracted this clique:\n");
+    // printClique(clique);
+
+    if (clique.size() >= 2) {
+      // if (clique.size() > 2) runCliqueSubsumption(globaldom, clique);
+      // runCliqueMerging(globaldom, clique);
+      // if (clique.size() >= 2) {
+      addClique(mipsolver, clique.data(), static_cast<HighsInt>(clique.size()));
+      if (globaldom.infeasible()) return;
+      //}
+    }
+
+    // further cliques are just subsets of this clique
+    if (cliqueend == perm.begin() + k) return;
+  }
+}
+
+void HighsCliqueTable::cliquePartition(std::vector<CliqueVar>& clqVars,
+                                       std::vector<HighsInt>& partitionStart) {
+  randgen.shuffle(clqVars.data(), clqVars.size());
+
+  std::vector<HighsInt> neighbourhoodInds;
+  neighbourhoodInds.reserve(clqVars.size());
+
+  HighsInt numClqVars = clqVars.size();
+  partitionStart.clear();
+  partitionStart.reserve(clqVars.size());
+  HighsInt extensionEnd = numClqVars;
+  partitionStart.push_back(0);
+  for (HighsInt i = 0; i < numClqVars; ++i) {
+    if (i == extensionEnd) {
+      partitionStart.push_back(i);
+      extensionEnd = numClqVars;
+    }
+    CliqueVar v = clqVars[i];
+    HighsInt extensionStart = i + 1;
+    extensionEnd =
+        partitionNeighbourhood(neighbourhoodInds, numNeighbourhoodQueries, v,
+                               clqVars.data() + extensionStart,
+                               extensionEnd - extensionStart) +
+        extensionStart;
+  }
+
+  partitionStart.push_back(numClqVars);
+}
+
+void HighsCliqueTable::cliquePartition(const std::vector<double>& objective,
+                                       std::vector<CliqueVar>& clqVars,
+                                       std::vector<HighsInt>& partitionStart) {
+  randgen.shuffle(clqVars.data(), clqVars.size());
+
+  pdqsort_branchless(clqVars.begin(), clqVars.end(),
+                     [&](CliqueVar v1, CliqueVar v2) {
+                       return (2 * v1.val - 1) * objective[v1.col] >
+                              (2 * v2.val - 1) * objective[v2.col];
+                     });
+
+  std::vector<HighsInt> neighbourhoodInds;
+  neighbourhoodInds.reserve(clqVars.size());
+
+  HighsInt numClqVars = clqVars.size();
+  partitionStart.clear();
+  partitionStart.reserve(clqVars.size());
+  HighsInt extensionEnd = numClqVars;
+  partitionStart.push_back(0);
+  HighsInt lastSwappedIndex = 0;
+  for (HighsInt i = 0; i < numClqVars; ++i) {
+    if (i == extensionEnd) {
+      partitionStart.push_back(i);
+      extensionEnd = numClqVars;
+      if (lastSwappedIndex >= i)
+        pdqsort_branchless(clqVars.begin() + i,
+                           clqVars.begin() + lastSwappedIndex + 1,
+                           [&](CliqueVar v1, CliqueVar v2) {
+                             return (2 * v1.val - 1) * objective[v1.col] >
+                                    (2 * v2.val - 1) * objective[v2.col];
+                           });
+      lastSwappedIndex = 0;
+    }
+    CliqueVar v = clqVars[i];
+    HighsInt extensionStart = i + 1;
+    extensionEnd =
+        partitionNeighbourhood(neighbourhoodInds, numNeighbourhoodQueries, v,
+                               clqVars.data() + extensionStart,
+                               extensionEnd - extensionStart) +
+        extensionStart;
+    if (!neighbourhoodInds.empty())
+      lastSwappedIndex =
+          std::max(neighbourhoodInds.back() + extensionStart, lastSwappedIndex);
+  }
+
+  partitionStart.push_back(numClqVars);
+}
+
+bool HighsCliqueTable::foundCover(HighsDomain& globaldom, CliqueVar v1,
+                                  CliqueVar v2) {
+  HighsInt commonclique = findCommonCliqueId(v1, v2);
+  if (commonclique == -1) return false;
+
+  while (commonclique != -1) {
+    HighsInt start = cliques[commonclique].start;
+    HighsInt end = cliques[commonclique].end;
+
+    for (HighsInt i = start; i != end; ++i) {
+      if (cliqueentries[i] == v1 || cliqueentries[i] == v2) continue;
+      if (!fixCol(globaldom, cliqueentries[i])) return true;
+    }
+
+    removeClique(commonclique);
+    commonclique = findCommonCliqueId(v1, v2);
+  }
+
+  processInfeasibleVertices(globaldom);
+  return true;
+}
+
+void HighsCliqueTable::extractCliquesFromCut(const HighsMipSolver& mipsolver,
+                                             const HighsInt* inds,
+                                             const double* vals, HighsInt len,
+                                             double rhs) {
+  if (isFull()) return;
+
+  HighsImplications& implics = mipsolver.mipdata_->implications;
+  HighsDomain& globaldom = mipsolver.mipdata_->domain;
+
+  const double feastol = mipsolver.mipdata_->feastol;
+
+  HighsCDouble minact = 0.0;
+  HighsInt nbin = 0;
+  for (HighsInt i = 0; i != len; ++i) {
+    if (globaldom.isBinary(inds[i])) ++nbin;
+
+    if (vals[i] > 0) {
+      if (globaldom.col_lower_[inds[i]] == -kHighsInf) return;
+      minact += vals[i] * globaldom.col_lower_[inds[i]];
+    } else {
+      if (globaldom.col_upper_[inds[i]] == kHighsInf) return;
+      minact += vals[i] * globaldom.col_upper_[inds[i]];
+    }
+  }
+
+  if (rhs - minact < 0.0) {
+    minact = rhs;
+  }
+
+  for (HighsInt i = 0; i != len; ++i) {
+    if (mipsolver.isColContinuous(inds[i])) continue;
+
+    double boundVal = static_cast<double>((rhs - minact) / vals[i]);
+    if (vals[i] > 0) {
+      boundVal = std::floor(boundVal + globaldom.col_lower_[inds[i]] +
+                            globaldom.feastol());
+      globaldom.changeBound(HighsBoundType::kUpper, inds[i], boundVal,
+                            HighsDomain::Reason::unspecified());
+      if (globaldom.infeasible()) return;
+    } else {
+      boundVal = std::ceil(boundVal + globaldom.col_upper_[inds[i]] -
+                           globaldom.feastol());
+      globaldom.changeBound(HighsBoundType::kLower, inds[i], boundVal,
+                            HighsDomain::Reason::unspecified());
+      if (globaldom.infeasible()) return;
+    }
+  }
+
+  if (nbin <= 1) return;
+
+  std::vector<HighsInt> perm;
+  perm.resize(len);
+  std::iota(perm.begin(), perm.end(), 0);
+
+  auto binaryend = std::partition(perm.begin(), perm.end(), [&](HighsInt pos) {
+    return globaldom.isBinary(inds[pos]);
+  });
+
+  nbin = binaryend - perm.begin();
+
+  // if not all variables are binary, we extract variable upper and lower bounds
+  // constraints on the non-binary variable for each binary variable in the
+  // constraint:
+  if (nbin < len) {
+    for (HighsInt i = 0; i != nbin; ++i) {
+      HighsInt bincol = inds[perm[i]];
+      HighsCDouble impliedActivity = rhs - minact - std::abs(vals[perm[i]]);
+      for (HighsInt j = nbin; j != len; ++j) {
+        HighsInt col = inds[perm[j]];
+        if (globaldom.isFixed(col)) continue;
+
+        if (vals[perm[j]] > 0) {
+          double implcolub =
+              static_cast<double>(impliedActivity +
+                                  vals[perm[j]] * globaldom.col_lower_[col]) /
+              vals[perm[j]];
+          if (mipsolver.isColIntegral(col))
+            implcolub = std::floor(implcolub + mipsolver.mipdata_->feastol);
+
+          if (implcolub < globaldom.col_upper_[col] - feastol) {
+            double coef;
+            double constant;
+            if (vals[perm[i]] < 0) {
+              coef = globaldom.col_upper_[col] - implcolub;
+              constant = implcolub;
+            } else {
+              // make sure that upper bound is not infinite to avoid adding VUB
+              // with coefficient '-kHighsInf' and constant 'kHighsInf'
+              if (globaldom.col_upper_[col] == kHighsInf) continue;
+              coef = implcolub - globaldom.col_upper_[col];
+              constant = globaldom.col_upper_[col];
+            }
+            // printf("extracted VUB from cut: x%" HIGHSINT_FORMAT " <= %g*y%"
+            // HIGHSINT_FORMAT " + %g\n", col, coef,
+            //        bincol, constant);
+            implics.addVUB(col, bincol, coef, constant);
+          }
+        } else {
+          double implcollb =
+              static_cast<double>(impliedActivity +
+                                  vals[perm[j]] * globaldom.col_upper_[col]) /
+              vals[perm[j]];
+          if (mipsolver.isColIntegral(col))
+            implcollb = std::ceil(implcollb - mipsolver.mipdata_->feastol);
+
+          if (implcollb > globaldom.col_lower_[col] + feastol) {
+            double coef;
+            double constant;
+            if (vals[perm[i]] < 0) {
+              coef = globaldom.col_lower_[col] - implcollb;
+              constant = implcollb;
+            } else {
+              // make sure that lower bound is not infinite to avoid adding VLB
+              // with coefficient 'kHighsInf' and constant '-kHighsInf'
+              if (globaldom.col_lower_[col] == -kHighsInf) continue;
+              coef = implcollb - globaldom.col_lower_[col];
+              constant = globaldom.col_lower_[col];
+            }
+
+            // printf("extracted VLB from cut: x%" HIGHSINT_FORMAT " >= %g*y%"
+            // HIGHSINT_FORMAT " + %g\n", col, coef,
+            //        bincol, constant);
+            implics.addVLB(col, bincol, coef, constant);
+            // printf("extracted VLB from cut\n");
+          }
+        }
+      }
+    }
+  }
+
+  // only one binary means we do have no cliques
+  if (nbin <= 1) return;
+
+  std::vector<CliqueVar> clique;
+  clique.reserve(nbin);
+
+  pdqsort(perm.begin(), binaryend, [&](HighsInt p1, HighsInt p2) {
+    return std::make_pair(std::abs(vals[p1]), p1) >
+           std::make_pair(std::abs(vals[p2]), p2);
+  });
+  // check if any cliques exists
+  if (std::abs(vals[perm[0]]) + std::abs(vals[perm[1]]) <=
+      static_cast<double>(rhs - minact + feastol))
+    return;
+
+  HighsInt maxNewEntries =
+      std::min(mipsolver.mipdata_->numCliqueEntriesAfterPresolve + 100000 +
+                   4 * globaldom.numModelNonzeros(),
+               numEntries + 10 * nbin);
+
+  for (HighsInt k = nbin - 1; k != 0 && numEntries < maxNewEntries; --k) {
+    double mincliqueval =
+        static_cast<double>(rhs - minact - std::abs(vals[perm[k]]) + feastol);
+    auto cliqueend = std::partition_point(
+        perm.begin(), perm.begin() + k,
+        [&](HighsInt p) { return std::abs(vals[p]) > mincliqueval; });
+
+    // no clique for this variable
+    if (cliqueend == perm.begin()) continue;
+
+    clique.clear();
+
+    for (auto j = perm.begin(); j != cliqueend; ++j) {
+      HighsInt pos = *j;
+      if (vals[pos] < 0)
+        clique.emplace_back(inds[pos], 0);
+      else
+        clique.emplace_back(inds[pos], 1);
+    }
+
+    if (vals[perm[k]] < 0)
+      clique.emplace_back(inds[perm[k]], 0);
+    else
+      clique.emplace_back(inds[perm[k]], 1);
+
+    // printf("extracted this clique:\n");
+    // printClique(clique);
+    if (clique.size() >= 2) {
+      // printf("extracted clique from cut\n");
+      // if (clique.size() > 2) runCliqueSubsumption(globaldom, clique);
+
+      addClique(mipsolver, clique.data(), static_cast<HighsInt>(clique.size()));
+      if (globaldom.infeasible() || numEntries >= maxNewEntries) return;
+    }
+
+    // further cliques are just subsets of this clique
+    if (cliqueend == perm.begin() + k) return;
+  }
+}
+
+void HighsCliqueTable::extractCliques(HighsMipSolver& mipsolver,
+                                      bool transformRows) {
+  std::vector<HighsInt> inds;
+  std::vector<double> vals;
+  std::vector<HighsInt> perm;
+  std::vector<int8_t> complementation;
+  std::vector<CliqueVar> clique;
+  HighsHashTable<HighsInt, double> entries;
+  double offset;
+
+  double rhs;
+
+  HighsDomain& globaldom = mipsolver.mipdata_->domain;
+
+  for (HighsInt i = 0; i != mipsolver.numRow(); ++i) {
+    HighsInt start = mipsolver.mipdata_->ARstart_[i];
+    HighsInt end = mipsolver.mipdata_->ARstart_[i + 1];
+
+    if (mipsolver.mipdata_->postSolveStack.getOrigRowIndex(i) >=
+        mipsolver.orig_model_->num_row_)
+      break;
+
+    // catch set packing and partitioning constraints that already have the form
+    // of a clique without transformations and add those cliques with the rows
+    // being recorded
+    if (mipsolver.rowUpper(i) == 1.0) {
+      bool issetppc = true;
+
+      clique.clear();
+
+      for (HighsInt j = start; j != end; ++j) {
+        HighsInt col = mipsolver.mipdata_->ARindex_[j];
+        if (globaldom.col_upper_[col] == 0.0 &&
+            globaldom.col_lower_[col] == 0.0)
+          continue;
+
+        issetppc =
+            globaldom.isBinary(col) && mipsolver.mipdata_->ARvalue_[j] == 1.0;
+        if (!issetppc) break;
+
+        clique.emplace_back(col, 1);
+      }
+
+      if (issetppc) {
+        addClique(mipsolver, clique.data(),
+                  static_cast<HighsInt>(clique.size()),
+                  mipsolver.rowLower(i) == 1.0, i);
+        if (globaldom.infeasible()) return;
+        continue;
+      }
+    }
+    if (!transformRows || isFull()) continue;
+
+    offset = 0;
+    for (HighsInt j = start; j != end; ++j) {
+      HighsInt col = mipsolver.mipdata_->ARindex_[j];
+      double val = mipsolver.mipdata_->ARvalue_[j];
+
+      resolveSubstitution(col, val, offset);
+      entries[col] += val;
+    }
+
+    auto checkRow = [&](double rhs, HighsInt direction) {
+      if (direction * rhs == kHighsInf) return;
+      rhs = direction * (rhs - offset);
+      inds.clear();
+      vals.clear();
+      complementation.clear();
+      bool freevar = false;
+      HighsInt nbin = 0;
+
+      for (const auto& entry : entries) {
+        HighsInt col = entry.key();
+        double val = direction * entry.value();
+
+        if (std::abs(val) < mipsolver.mipdata_->epsilon) continue;
+
+        if (globaldom.isBinary(col)) ++nbin;
+
+        if (val < 0) {
+          freevar = globaldom.col_upper_[col] == kHighsInf;
+          if (freevar) break;
+
+          vals.push_back(-val);
+          inds.push_back(col);
+          complementation.push_back(-1);
+          rhs -= val * globaldom.col_upper_[col];
+        } else {
+          freevar = globaldom.col_lower_[col] == -kHighsInf;
+          if (freevar) break;
+
+          vals.push_back(val);
+          inds.push_back(col);
+          complementation.push_back(1);
+          rhs -= val * globaldom.col_lower_[col];
+        }
+      }
+
+      if (!freevar && nbin != 0) {
+        extractCliques(mipsolver, inds, vals, complementation, rhs, nbin, perm,
+                       clique, mipsolver.mipdata_->feastol);
+        if (globaldom.infeasible()) return;
+      }
+    };
+
+    checkRow(mipsolver.rowUpper(i), HighsInt{1});
+    checkRow(mipsolver.rowLower(i), HighsInt{-1});
+
+    entries.clear();
+  }
+}
+
+void HighsCliqueTable::extractObjCliques(HighsMipSolver& mipsolver) {
+  HighsInt nbin =
+      mipsolver.mipdata_->objectiveFunction.getNumBinariesInObjective();
+  if (nbin <= 1) return;
+  HighsDomain& globaldom = mipsolver.mipdata_->domain;
+  if (globaldom.getObjectiveLowerBound() == -kHighsInf) return;
+
+  const double* vals;
+  const HighsInt* inds;
+  HighsInt len;
+  double rhs;
+  globaldom.getCutoffConstraint(vals, inds, len, rhs);
+
+  std::vector<HighsInt> perm;
+  perm.resize(nbin);
+  std::iota(perm.begin(), perm.end(), 0);
+
+  auto binaryend = std::partition(perm.begin(), perm.end(), [&](HighsInt pos) {
+    return vals[pos] != 0.0 && !globaldom.isFixed(inds[pos]);
+  });
+
+  nbin = binaryend - perm.begin();
+
+  // only one binary means we do have no cliques
+  if (nbin <= 1) return;
+
+  std::vector<CliqueVar> clique;
+  clique.reserve(nbin);
+
+  pdqsort(perm.begin(), binaryend, [&](HighsInt p1, HighsInt p2) {
+    return std::make_pair(std::fabs(vals[p1]), p1) >
+           std::make_pair(std::fabs(vals[p2]), p2);
+  });
+
+  // check if any cliques exists
+  HighsCDouble minact;
+  HighsInt ninf;
+  globaldom.computeMinActivity(0, len, inds, vals, ninf, minact);
+  const double feastol = mipsolver.mipdata_->feastol;
+  if (std::fabs(vals[perm[0]]) + std::fabs(vals[perm[1]]) <=
+      static_cast<double>(rhs - minact + feastol))
+    return;
+
+  for (HighsInt k = nbin - 1; k != 0; --k) {
+    double mincliqueval =
+        static_cast<double>(rhs - minact - std::fabs(vals[perm[k]]) + feastol);
+    auto cliqueend = std::partition_point(
+        perm.begin(), perm.begin() + k,
+        [&](HighsInt p) { return std::abs(vals[p]) > mincliqueval; });
+
+    // no clique for this variable
+    if (cliqueend == perm.begin()) continue;
+
+    clique.clear();
+
+    for (auto j = perm.begin(); j != cliqueend; ++j) {
+      HighsInt pos = *j;
+      if (vals[pos] < 0)
+        clique.emplace_back(inds[pos], 0);
+      else
+        clique.emplace_back(inds[pos], 1);
+    }
+
+    if (vals[perm[k]] < 0)
+      clique.emplace_back(inds[perm[k]], 0);
+    else
+      clique.emplace_back(inds[perm[k]], 1);
+
+    // printf("extracted this clique from obj:\n");
+    // printClique(clique);
+    if (clique.size() >= 2) {
+      // printf("extracted clique from obj\n");
+      // if (clique.size() > 2) runCliqueSubsumption(globaldom, clique);
+
+      addClique(mipsolver, clique.data(), static_cast<HighsInt>(clique.size()));
+      if (globaldom.infeasible()) return;
+    }
+
+    // further cliques are just subsets of this clique
+    if (cliqueend == perm.begin() + k) return;
+  }
+}
+
+void HighsCliqueTable::processInfeasibleVertices(HighsDomain& globaldom) {
+  while (!infeasvertexstack.empty() && !globaldom.infeasible()) {
+    CliqueVar v = infeasvertexstack.back().complement();
+    infeasvertexstack.pop_back();
+
+    resolveSubstitution(v);
+    bool wasfixed = globaldom.isFixed(v.col);
+    globaldom.fixCol(v.col, static_cast<double>(v.val));
+    if (globaldom.infeasible()) return;
+    if (!wasfixed) ++nfixings;
+    if (colDeleted[v.col]) continue;
+    colDeleted[v.col] = true;
+
+    HighsHashTree<HighsInt, HighsInt> vHashLists =
+        std::move(invertedHashList[v.index()]);
+    HighsHashTree<HighsInt> vHashListsSizeTwo =
+        std::move(invertedHashListSizeTwo[v.index()]);
+
+    bool infeas = vHashLists.for_each([&](HighsInt cliqueid) {
+      HighsInt start = cliques[cliqueid].start;
+      HighsInt end = cliques[cliqueid].end;
+
+      for (HighsInt i = start; i != end; ++i) {
+        if (cliqueentries[i].col == v.col) continue;
+        if (!fixCol(globaldom, cliqueentries[i])) return true;
+      }
+
+      removeClique(cliqueid);
+      return false;
+    });
+
+    if (infeas) return;
+
+    infeas = vHashListsSizeTwo.for_each([&](HighsInt cliqueid) {
+      HighsInt start = cliques[cliqueid].start;
+      HighsInt end = cliques[cliqueid].end;
+
+      for (HighsInt i = start; i != end; ++i) {
+        if (cliqueentries[i].col == v.col) continue;
+        if (!fixCol(globaldom, cliqueentries[i])) return true;
+      }
+
+      removeClique(cliqueid);
+      return false;
+    });
+
+    if (infeas) return;
+
+    vHashLists = std::move(invertedHashList[v.complement().index()]);
+    vHashListsSizeTwo =
+        std::move(invertedHashListSizeTwo[v.complement().index()]);
+
+    if (inPresolve) {
+      // during presolve we only count the number of zeros within each clique
+      // and only remove fully redundant cliques that are larger than two
+      // in the process since during presolve a lot of cliques of size two
+      // may be found by probing and will be deleted upon rebuild anyways
+      vHashLists.for_each([&](HighsInt cliqueid) {
+        cliques[cliqueid].numZeroFixed += 1;
+        if (cliques[cliqueid].numActive() <= 1) removeClique(cliqueid);
+      });
+      continue;
+    }
+
+    vHashListsSizeTwo.for_each(
+        [&](HighsInt cliqueid) { removeClique(cliqueid); });
+
+    assert(cliquehitinds.empty());
+    std::vector<CliqueVar> clq;
+    vHashLists.for_each([&](HighsInt cliqueid) {
+      // assert(cliqueentries[entry.value()].val == 1 - v.val);
+
+      cliques[cliqueid].numZeroFixed += 1;
+      if (cliques[cliqueid].numActive() <= 1) {
+        removeClique(cliqueid);
+      } else if (cliques[cliqueid].numZeroFixed >=
+                 std::max(
+                     HighsInt{10},
+                     (cliques[cliqueid].end - cliques[cliqueid].start) >> 1)) {
+        clq.assign(cliqueentries.begin() + cliques[cliqueid].start,
+                   cliqueentries.begin() + cliques[cliqueid].end);
+
+        auto computeNumDeleted = [&](const std::vector<CliqueVar>& clq) {
+          HighsInt numDel = 0;
+          for (CliqueVar x : clq) numDel += colDeleted[x.col];
+          return numDel;
+        };
+
+        assert(computeNumDeleted(clq) == cliques[cliqueid].numZeroFixed);
+
+        removeClique(cliqueid);
+        clq.erase(std::remove_if(clq.begin(), clq.end(),
+                                 [&](CliqueVar x) {
+                                   return globaldom.isFixed(x.col) &&
+                                          globaldom.col_lower_[x.col] ==
+                                              1 - x.val;
+                                 }),
+                  clq.end());
+        if (clq.size() > 1) doAddClique(clq.data(), clq.size());
+      }
+    });
+  }
+
+  propagateAndCleanup(globaldom);
+}
+
+void HighsCliqueTable::propagateAndCleanup(HighsDomain& globaldom) {
+  const auto& domchgstack = globaldom.getDomainChangeStack();
+  HighsInt start = domchgstack.size();
+  globaldom.propagate();
+  HighsInt end = domchgstack.size();
+
+  while (!globaldom.infeasible() && start != end) {
+    for (HighsInt k = start; k != end; ++k) {
+      HighsInt col = domchgstack[k].column;
+      if (!globaldom.isFixed(col)) continue;
+      if (globaldom.col_lower_[col] != 1.0 && globaldom.col_lower_[col] != 0.0)
+        continue;
+
+      HighsInt fixval = static_cast<HighsInt>(globaldom.col_lower_[col]);
+      CliqueVar v(col, 1 - fixval);
+      if (numCliques(v) != 0) {
+        vertexInfeasible(globaldom, col, 1 - fixval);
+        if (globaldom.infeasible()) return;
+      }
+    }
+    start = domchgstack.size();
+    globaldom.propagate();
+    end = domchgstack.size();
+  }
+}
+
+void HighsCliqueTable::vertexInfeasible(HighsDomain& globaldom, HighsInt col,
+                                        HighsInt val) {
+  bool wasfixed = globaldom.isFixed(col);
+  globaldom.fixCol(col, static_cast<double>(1 - val));
+  if (globaldom.infeasible()) return;
+  if (!wasfixed) ++nfixings;
+  infeasvertexstack.emplace_back(col, val);
+  processInfeasibleVertices(globaldom);
+}
+
+void HighsCliqueTable::separateCliques(const HighsMipSolver& mipsolver,
+                                       const std::vector<double>& sol,
+                                       HighsCutPool& cutpool, double feastol) {
+  BronKerboschData data(sol);
+  data.feastol = feastol;
+  data.maxNeighbourhoodQueries = 1000000 +
+                                 int64_t{100} * mipsolver.numNonzero() +
+                                 mipsolver.mipdata_->total_lp_iterations * 1000;
+  if (numNeighbourhoodQueries > data.maxNeighbourhoodQueries) return;
+  data.maxNeighbourhoodQueries -= numNeighbourhoodQueries;
+  const HighsDomain& globaldom = mipsolver.mipdata_->domain;
+
+  for (HighsInt i : mipsolver.mipdata_->integral_cols) {
+    if (colsubstituted[i] || colDeleted[i]) continue;
+#ifdef ADD_ZERO_WEIGHT_VARS
+    if (numCliques(i, 0) != 0) {
+      if (CliqueVar(i, 0).weight(sol) > feastol)
+        data.P.emplace_back(i, 0);
+      else
+        data.Z.emplace_back(i, 0);
+    }
+    if (numCliques(i, 1) != 0) {
+      if (CliqueVar(i, 1).weight(sol) > feastol)
+        data.P.emplace_back(i, 1);
+      else
+        data.Z.emplace_back(i, 1);
+    }
+#else
+    if (numcliquesvar[CliqueVar(i, 0).index()] != 0 &&
+        CliqueVar(i, 0).weight(sol) > feastol)
+      data.P.emplace_back(i, 0);
+    if (numcliquesvar[CliqueVar(i, 1).index()] != 0 &&
+        CliqueVar(i, 1).weight(sol) > feastol)
+      data.P.emplace_back(i, 1);
+#endif
+  }
+
+  // auto t1 = std::chrono::high_resolution_clock::now();
+  bronKerboschRecurse(data, data.P.size(), nullptr, 0);
+
+  // auto t2 = std::chrono::high_resolution_clock::now();
+
+  // printf(
+  //     "bron kerbosch: %" HIGHSINT_FORMAT " calls, %" HIGHSINT_FORMAT "
+  //     cliques, %ldms\n", data.ncalls, int(data.cliques.size()),
+  //     std::chrono::duration_cast<std::chrono::milliseconds>(t2 -
+  //     t1).count());
+
+  bool runcliquesubsumption = false;
+  std::vector<HighsInt> inds;
+  std::vector<double> vals;
+  for (std::vector<CliqueVar>& clique : data.cliques) {
+#ifdef ADD_ZERO_WEIGHT_VARS
+    HighsInt extensionend = static_cast<HighsInt>(data.Z.size());
+    for (CliqueVar v : clique) {
+      extensionend = partitionNeighbourhood(data.neighbourhoodInds,
+                                            data.numNeighbourhoodQueries, v,
+                                            data.Z.data(), extensionend);
+      if (extensionend == 0) break;
+    }
+
+    if (extensionend != 0) {
+      randgen.shuffle(data.Z.data(), extensionend);
+
+      for (HighsInt i = 0; i < extensionend; ++i) {
+        HighsInt k = i + 1;
+        extensionend =
+            k + partitionNeighbourhood(data.neighbourhoodInds,
+                                       data.numNeighbourhoodQueries, data.Z[i],
+                                       data.Z.data() + k, extensionend - k);
+      }
+
+      clique.insert(clique.end(), data.Z.begin(),
+                    data.Z.begin() + extensionend);
+    }
+#endif
+
+    double rhs = 1;
+    runcliquesubsumption = cliques.size() > 2;
+    inds.clear();
+    vals.clear();
+
+    for (CliqueVar v : clique) {
+      inds.push_back(v.col);
+      if (v.val == 0) {
+        vals.push_back(-1);
+        rhs -= 1;
+      } else
+        vals.push_back(1);
+    }
+
+    rhs = std::floor(rhs + 0.5);
+
+    cutpool.addCut(mipsolver, inds.data(), vals.data(), inds.size(), rhs, true,
+                   false, false);
+  }
+
+  numNeighbourhoodQueries += data.numNeighbourhoodQueries;
+
+  if (runcliquesubsumption) {
+    for (std::vector<CliqueVar>& clique : data.cliques) {
+      HighsInt nremoved = runCliqueSubsumption(globaldom, clique);
+
+      if (clique.empty()) continue;
+      if (nremoved != 0) doAddClique(clique.data(), clique.size(), false, -1);
+    }
+  }
+}
+
+std::vector<std::vector<HighsCliqueTable::CliqueVar>>
+HighsCliqueTable::separateCliques(const std::vector<double>& sol,
+                                  const HighsDomain& globaldom,
+                                  double feastol) {
+  exit(0);
+#if 0
+  BronKerboschData data(sol);
+  data.feastol = feastol;
+
+  HighsInt numcols = globaldom.col_lower_.size();
+  assert(int(numcliquesvar.size()) == 2 * numcols);
+  for (HighsInt i = 0; i != numcols; ++i) {
+    if (colsubstituted[i]) continue;
+
+    if (numcliquesvar[CliqueVar(i, 0).index()] != 0 &&
+        CliqueVar(i, 0).weight(sol) > feastol)
+      data.P.emplace_back(i, 0);
+    if (numcliquesvar[CliqueVar(i, 1).index()] != 0 &&
+        CliqueVar(i, 1).weight(sol) > feastol)
+      data.P.emplace_back(i, 1);
+  }
+
+  bronKerboschRecurse(data, data.P.size(), nullptr, 0);
+
+  return std::move(data.cliques);
+#endif
+}
+
+std::vector<std::vector<HighsCliqueTable::CliqueVar>>
+HighsCliqueTable::computeMaximalCliques(const std::vector<CliqueVar>& vars,
+                                        double feastol) {
+  // return if there are no variables
+  if (vars.empty())
+    return std::vector<std::vector<HighsCliqueTable::CliqueVar>>{};
+
+  // find max column index in clique variables
+  size_t maxcolindex = 0;
+  for (const auto& var : vars)
+    maxcolindex = std::max(static_cast<size_t>(var.col), maxcolindex);
+
+  // set up data
+  std::vector<double> sol;
+  sol.resize(maxcolindex + 1);
+  for (const auto& var : vars) sol[var.col] = var.val;
+  BronKerboschData data(sol);
+  data.feastol = feastol;
+
+  for (const auto& var : vars) {
+    if (colsubstituted[var.col] || colDeleted[var.col]) continue;
+    if (numCliques(var) != 0) data.P.emplace_back(var);
+  }
+
+  bronKerboschRecurse(data, data.P.size(), nullptr, 0);
+
+  return std::move(data.cliques);
+}
+
+void HighsCliqueTable::addImplications(HighsDomain& domain, HighsInt col,
+                                       HighsInt val) {
+  CliqueVar v(col, val);
+
+  while (colsubstituted[v.col]) {
+    assert(static_cast<HighsInt>(substitutions.size()) >
+           colsubstituted[v.col] - 1);
+    Substitution subst = substitutions[colsubstituted[v.col] - 1];
+    v = v.val == 1 ? subst.replace : subst.replace.complement();
+    if (v.val == 1) {
+      if (domain.col_lower_[v.col] == 1.0) continue;
+
+      domain.changeBound(HighsBoundType::kLower, v.col, 1.0,
+                         HighsDomain::Reason::cliqueTable(col, val));
+      if (domain.infeasible()) return;
+    } else {
+      if (domain.col_upper_[v.col] == 0.0) continue;
+
+      domain.changeBound(HighsBoundType::kUpper, v.col, 0.0,
+                         HighsDomain::Reason::cliqueTable(col, val));
+      if (domain.infeasible()) return;
+    }
+  }
+
+  auto doFixings = [&](HighsInt cliqueid) {
+    HighsInt start = cliques[cliqueid].start;
+    HighsInt end = cliques[cliqueid].end;
+
+    for (HighsInt i = start; i != end; ++i) {
+      if (cliqueentries[i].col == v.col) continue;
+
+      if (cliqueentries[i].val == 1) {
+        if (domain.col_upper_[cliqueentries[i].col] == 0.0) continue;
+
+        domain.changeBound(HighsBoundType::kUpper, cliqueentries[i].col, 0.0,
+                           HighsDomain::Reason::cliqueTable(col, val));
+        if (domain.infeasible()) return true;
+      } else {
+        if (domain.col_lower_[cliqueentries[i].col] == 1.0) continue;
+
+        domain.changeBound(HighsBoundType::kLower, cliqueentries[i].col, 1.0,
+                           HighsDomain::Reason::cliqueTable(col, val));
+        if (domain.infeasible()) return true;
+      }
+    }
+
+    return false;
+  };
+
+  bool infeas = invertedHashList[v.index()].for_each(doFixings);
+
+  if (infeas) return;
+
+  invertedHashListSizeTwo[v.index()].for_each(doFixings);
+}
+
+void HighsCliqueTable::cleanupFixed(HighsDomain& globaldom) {
+  HighsInt numcol = globaldom.col_upper_.size();
+  HighsInt oldnfixings = nfixings;
+  for (HighsInt i = 0; i != numcol; ++i) {
+    if (colDeleted[i] || !globaldom.isFixed(i)) continue;
+    if (globaldom.col_lower_[i] != 1.0 && globaldom.col_lower_[i] != 0.0)
+      continue;
+
+    HighsInt fixval = static_cast<HighsInt>(globaldom.col_lower_[i]);
+    CliqueVar v(i, 1 - fixval);
+
+    vertexInfeasible(globaldom, v.col, v.val);
+    if (globaldom.infeasible()) return;
+  }
+
+  if (nfixings != oldnfixings) propagateAndCleanup(globaldom);
+}
+
+HighsInt HighsCliqueTable::getNumImplications(HighsInt col) {
+  // first count all cliques as one implication, so that cliques of size two
+  // are accounted for already
+  HighsInt i0 = CliqueVar(col, 0).index();
+  HighsInt i1 = CliqueVar(col, 1).index();
+  HighsInt numimplics = numcliquesvar[i0] + numcliquesvar[i1];
+
+  // now loop over cliques larger than size two and add the cliquelength - 1 as
+  // additional implications
+  auto countImplics = [&](HighsInt cliqueid) {
+    HighsInt nimplics = cliques[cliqueid].end - cliques[cliqueid].start - 1;
+    nimplics *= (1 + cliques[cliqueid].equality);
+    numimplics += nimplics - 1;
+  };
+  invertedHashList[i0].for_each(countImplics);
+  invertedHashList[i1].for_each(countImplics);
+  return numimplics;
+}
+
+HighsInt HighsCliqueTable::getNumImplications(HighsInt col, bool val) {
+  HighsInt iVal = CliqueVar(col, val).index();
+
+  // each size two clique is one implication
+  HighsInt numimplics = numcliquesvar[iVal];
+
+  // now loop over cliques larger than size two and add the cliquelength - 1 as
+  // additional implications
+  invertedHashList[iVal].for_each([&](HighsInt cliqueid) {
+    HighsInt nimplics = cliques[cliqueid].end - cliques[cliqueid].start - 1;
+    nimplics *= (1 + cliques[cliqueid].equality);
+    numimplics += nimplics - 1;
+  });
+
+  return numimplics;
+}
+
+void HighsCliqueTable::runCliqueMerging(HighsDomain& globaldomain,
+                                        std::vector<CliqueVar>& clique,
+                                        bool equation) {
+  CliqueVar extensionstart;
+  HighsInt numcliques = kHighsIInf;
+  iscandidate.resize(invertedHashList.size());
+  std::vector<HighsInt> neighbourhoodInds;
+  neighbourhoodInds.reserve(invertedHashList.size());
+
+  HighsInt initialCliqueSize = clique.size();
+  for (HighsInt i = 0; i != initialCliqueSize; ++i) {
+    if (globaldomain.isFixed(clique[i].col)) continue;
+
+    HighsInt thisNumClqs = numCliques(clique[i]);
+    if (thisNumClqs < numcliques) {
+      numcliques = thisNumClqs;
+      extensionstart = clique[i];
+    }
+  }
+
+  if (numcliques == kHighsIInf) {
+    clique.clear();
+    return;
+  }
+
+  for (HighsInt i = 0; i != initialCliqueSize; ++i)
+    iscandidate[clique[i].index()] = true;
+
+  auto addCands = [&](HighsInt cliqueid) {
+    HighsInt start = cliques[cliqueid].start;
+    HighsInt end = cliques[cliqueid].end;
+
+    for (HighsInt i = start; i != end; ++i) {
+      if (iscandidate[cliqueentries[i].index()] ||
+          globaldomain.isFixed(cliqueentries[i].col))
+        continue;
+
+      iscandidate[cliqueentries[i].index()] = true;
+      clique.push_back(cliqueentries[i]);
+    }
+  };
+
+  invertedHashList[extensionstart.index()].for_each(
+      [&](HighsInt cliqueid) { addCands(cliqueid); });
+
+  invertedHashListSizeTwo[extensionstart.index()].for_each(
+      [&](HighsInt cliqueid) { addCands(cliqueid); });
+
+  HighsInt sizeWithCandidates = clique.size();
+  for (HighsInt i = 0; i != sizeWithCandidates; ++i)
+    iscandidate[clique[i].index()] = false;
+
+  for (HighsInt i = 0; i != initialCliqueSize &&
+                       initialCliqueSize < static_cast<HighsInt>(clique.size());
+       ++i) {
+    if (clique[i] == extensionstart) continue;
+
+    HighsInt newSize =
+        initialCliqueSize +
+        shrinkToNeighbourhood(neighbourhoodInds, numNeighbourhoodQueries,
+                              clique[i], clique.data() + initialCliqueSize,
+                              clique.size() - initialCliqueSize);
+    clique.erase(clique.begin() + newSize, clique.end());
+  }
+
+  if (static_cast<size_t>(initialCliqueSize) < clique.size()) {
+    // todo, shuffle extension vars?
+    randgen.shuffle(clique.data() + initialCliqueSize,
+                    clique.size() - initialCliqueSize);
+    HighsInt i = initialCliqueSize;
+    while (i < static_cast<HighsInt>(clique.size())) {
+      CliqueVar extvar = clique[i];
+      i += 1;
+
+      HighsInt newSize = i + shrinkToNeighbourhood(
+                                 neighbourhoodInds, numNeighbourhoodQueries,
+                                 extvar, clique.data() + i, clique.size() - i);
+      clique.erase(clique.begin() + newSize, clique.end());
+    }
+  }
+
+  if (equation) {
+    for (HighsInt i = initialCliqueSize;
+         i < static_cast<HighsInt>(clique.size()); ++i)
+      vertexInfeasible(globaldomain, clique[i].col, clique[i].val);
+  } else {
+    runCliqueSubsumption(globaldomain, clique);
+
+    if (!clique.empty()) {
+      clique.erase(
+          std::remove_if(clique.begin(), clique.end(),
+                         [&](CliqueVar v) {
+                           return globaldomain.isFixed(v.col) &&
+                                  static_cast<int>(
+                                      globaldomain.col_lower_[v.col]) ==
+                                      static_cast<int>(1 - v.val);
+                         }),
+          clique.end());
+    }
+  }
+
+  processInfeasibleVertices(globaldomain);
+}
+
+void HighsCliqueTable::runCliqueMerging(HighsDomain& globaldomain) {
+  std::vector<CliqueVar> extensionvars;
+  iscandidate.resize(invertedHashList.size());
+  std::vector<HighsInt> neighbourhoodInds;
+  neighbourhoodInds.reserve(invertedHashList.size());
+
+  HighsInt numcliqueslots = static_cast<HighsInt>(cliques.size());
+  const HighsInt maxNewEntries = numEntries + globaldomain.numModelNonzeros();
+  bool haveNonModelCliquesToMerge = false;
+  for (HighsInt k = 0; k != numcliqueslots; ++k) {
+    if (cliques[k].start == -1) continue;
+    if (!cliques[k].equality && cliques[k].origin == kHighsIInf) continue;
+    if (cliques[k].origin == -1) {
+      haveNonModelCliquesToMerge = true;
+      continue;
+    }
+    HighsInt numclqvars = cliques[k].end - cliques[k].start;
+    assert(numclqvars != 0);
+    if (numclqvars == 0) continue;
+
+    CliqueVar* clqvars = &cliqueentries[cliques[k].start];
+
+    CliqueVar extensionstart = clqvars[0];
+    HighsInt numcliques = numCliques(clqvars[0]);
+    for (HighsInt i = 1; i != numclqvars; ++i) {
+      HighsInt thisNumClqs = numCliques(clqvars[i]);
+      if (thisNumClqs < numcliques) {
+        numcliques = thisNumClqs;
+        extensionstart = clqvars[i];
+      }
+    }
+
+    for (HighsInt i = 0; i != numclqvars; ++i)
+      iscandidate[clqvars[i].index()] = true;
+
+    auto addCands = [&](HighsInt cliqueid) {
+      HighsInt start = cliques[cliqueid].start;
+      HighsInt end = cliques[cliqueid].end;
+
+      for (HighsInt i = start; i != end; ++i) {
+        if (iscandidate[cliqueentries[i].index()] ||
+            globaldomain.isFixed(cliqueentries[i].col))
+          continue;
+
+        iscandidate[cliqueentries[i].index()] = true;
+        extensionvars.push_back(cliqueentries[i]);
+      }
+    };
+
+    invertedHashList[extensionstart.index()].for_each(
+        [&](HighsInt cliqueid) { addCands(cliqueid); });
+
+    invertedHashListSizeTwo[extensionstart.index()].for_each(
+        [&](HighsInt cliqueid) { addCands(cliqueid); });
+
+    for (HighsInt i = 0; i != numclqvars; ++i)
+      iscandidate[clqvars[i].index()] = false;
+    for (CliqueVar v : extensionvars) iscandidate[v.index()] = false;
+
+    for (HighsInt i = 0; i != numclqvars && !extensionvars.empty(); ++i) {
+      if (clqvars[i] == extensionstart) continue;
+
+      HighsInt newSize = shrinkToNeighbourhood(
+          neighbourhoodInds, numNeighbourhoodQueries, clqvars[i],
+          extensionvars.data(), static_cast<HighsInt>(extensionvars.size()));
+      extensionvars.erase(extensionvars.begin() + newSize, extensionvars.end());
+    }
+
+    if (!extensionvars.empty()) {
+      // todo, shuffle extension vars?
+      randgen.shuffle(extensionvars.data(),
+                      static_cast<HighsInt>(extensionvars.size()));
+      HighsInt i = 0;
+      while (i < static_cast<HighsInt>(extensionvars.size())) {
+        CliqueVar extvar = extensionvars[i];
+        i += 1;
+
+        HighsInt newSize =
+            i + shrinkToNeighbourhood(
+                    neighbourhoodInds, numNeighbourhoodQueries, extvar,
+                    extensionvars.data() + i,
+                    static_cast<HighsInt>(extensionvars.size()) - i);
+        extensionvars.erase(extensionvars.begin() + newSize,
+                            extensionvars.end());
+      }
+    }
+
+    if (cliques[k].equality) {
+      for (CliqueVar v : extensionvars)
+        vertexInfeasible(globaldomain, v.col, v.val);
+    } else {
+      HighsInt originrow = cliques[k].origin;
+      cliques[k].origin = kHighsIInf;
+
+      size_t numExtensions = extensionvars.size();
+      extensionvars.insert(extensionvars.end(),
+                           cliqueentries.begin() + cliques[k].start,
+                           cliqueentries.begin() + cliques[k].end);
+      extensionvars.erase(
+          std::remove_if(
+              extensionvars.begin() + numExtensions, extensionvars.end(),
+              [&](CliqueVar clqvar) { return colDeleted[clqvar.col]; }),
+          extensionvars.end());
+      removeClique(k);
+
+      // callback for removing cliques
+      auto removeCliques = [&](HighsInt cliqueid) { removeClique(cliqueid); };
+
+      // check extension
+      bool redundant;
+      HighsInt dominatingOrigin;
+      cliqueSubsumption(extensionvars, redundant, dominatingOrigin,
+                        removeCliques);
+
+      if (!redundant) {
+        for (size_t i = 0; i < numExtensions; ++i)
+          cliqueextensions.emplace_back(originrow, extensionvars[i]);
+
+        extensionvars.erase(
+            std::remove_if(extensionvars.begin(), extensionvars.end(),
+                           [&](CliqueVar v) {
+                             return globaldomain.isFixed(v.col) &&
+                                    static_cast<int>(
+                                        globaldomain.col_lower_[v.col]) ==
+                                        static_cast<int>(1 - v.val);
+                           }),
+            extensionvars.end());
+
+        if (extensionvars.size() > 1)
+          doAddClique(extensionvars.data(),
+                      static_cast<HighsInt>(extensionvars.size()), false,
+                      originrow);
+      } else {
+        // the extended clique is redundant, check if the row can be removed
+        if (dominatingOrigin != kHighsIInf)
+          deletedrows.push_back(originrow);
+        else {
+          // this clique is redundant in the cliquetable but its row is not
+          // necessarily. Also there might be rows that have been deleted due to
+          // being dominated by this row after adding the lifted entries so they
+          // must be added to the cliqueextension vector
+          for (size_t i = 0; i < numExtensions; ++i)
+            cliqueextensions.emplace_back(originrow, extensionvars[i]);
+        }
+      }
+    }
+
+    extensionvars.clear();
+    processInfeasibleVertices(globaldomain);
+
+    if (numEntries >= maxNewEntries) break;
+    // printf("nonzeroDelta: %d, maxNonzeroDelta: %d\n", nonzeroDelta,
+    // maxNonzeroDelta);
+  }
+
+  if (haveNonModelCliquesToMerge) {
+    for (HighsInt k = 0; k != numcliqueslots; ++k) {
+      if (cliques[k].start == -1) continue;
+      if (cliques[k].origin != -1) continue;
+      // if (cliques[k].end - cliques[k].start <= 1000) continue;
+
+      // printf("numEntries before: %d\n", numEntries);
+      extensionvars.clear();
+      extensionvars.insert(extensionvars.end(),
+                           cliqueentries.begin() + cliques[k].start,
+                           cliqueentries.begin() + cliques[k].end);
+      removeClique(k);
+      runCliqueMerging(globaldomain, extensionvars);
+
+      if (extensionvars.size() > 1)
+        doAddClique(extensionvars.data(),
+                    static_cast<HighsInt>(extensionvars.size()));
+    }
+  }
+}
+
+void HighsCliqueTable::rebuild(
+    HighsInt ncols, const presolve::HighsPostsolveStack& postSolveStack,
+    const HighsDomain& globaldomain,
+    const std::vector<HighsInt>& orig2reducedcol,
+    const std::vector<HighsInt>& orig2reducedrow) {
+  HighsCliqueTable newCliqueTable(ncols);
+  newCliqueTable.setPresolveFlag(inPresolve);
+  newCliqueTable.setMinEntriesForParallelism(minEntriesForParallelism);
+  for (size_t i = 0; i != cliques.size(); ++i) {
+    if (cliques[i].start == -1) continue;
+    HighsInt oldnumvars = cliques[i].end - cliques[i].start;
+
+    for (HighsInt k = cliques[i].start; k != cliques[i].end; ++k) {
+      HighsInt col = orig2reducedcol[cliqueentries[k].col];
+
+      if (col == -1 || !globaldomain.isBinary(col) ||
+          !postSolveStack.isColLinearlyTransformable(col))
+        cliqueentries[k].col = kHighsIInf;
+      else
+        cliqueentries[k].col = col;
+    }
+
+    auto newend =
+        std::remove_if(cliqueentries.begin() + cliques[i].start,
+                       cliqueentries.begin() + cliques[i].end,
+                       [](CliqueVar v) { return v.col == kHighsIInf; });
+    HighsInt numvars = static_cast<HighsInt>(
+        newend - (cliqueentries.begin() + cliques[i].start));
+    // since we do not know how variables in the clique that have been deleted
+    // are replaced (i.e. are they fixed to 0 or 1, or substituted) we relax
+    // them out which means the equality status needs to be set to false
+    if (numvars <= 1) continue;
+
+    HighsInt origin = cliques[i].origin != kHighsIInf ? -1 : kHighsIInf;
+    newCliqueTable.doAddClique(
+        &cliqueentries[cliques[i].start], numvars,
+        numvars != oldnumvars ? false : cliques[i].equality, origin);
+  }
+
+  *this = std::move(newCliqueTable);
+}
+
+void HighsCliqueTable::buildFrom(const HighsLp* origModel,
+                                 const HighsCliqueTable& init) {
+  assert(init.colsubstituted.size() == colsubstituted.size());
+  HighsInt ncols = init.colsubstituted.size();
+  HighsCliqueTable newCliqueTable(ncols);
+  newCliqueTable.setPresolveFlag(inPresolve);
+  newCliqueTable.setPresolveFlag(minEntriesForParallelism);
+  HighsInt ncliques = init.cliques.size();
+  std::vector<CliqueVar> clqBuffer;
+  clqBuffer.reserve(2 * static_cast<size_t>(origModel->num_col_));
+  for (HighsInt i = 0; i != ncliques; ++i) {
+    if (init.cliques[i].start == -1) continue;
+    if (init.cliques[i].numActive() <= 1) continue;
+
+    clqBuffer.assign(init.cliqueentries.begin() + init.cliques[i].start,
+                     init.cliqueentries.begin() + init.cliques[i].end);
+    clqBuffer.erase(std::remove_if(clqBuffer.begin(), clqBuffer.end(),
+                                   [origModel](CliqueVar v) {
+                                     return origModel->col_lower_[v.col] !=
+                                                0.0 ||
+                                            origModel->col_upper_[v.col] != 1.0;
+                                   }),
+                    clqBuffer.end());
+    if (clqBuffer.size() <= 1) continue;
+
+    HighsInt origin = init.cliques[i].origin != kHighsIInf ? -1 : kHighsIInf;
+    newCliqueTable.doAddClique(clqBuffer.data(),
+                               static_cast<HighsInt>(clqBuffer.size()), false,
+                               origin);
+  }
+
+  newCliqueTable.colsubstituted = init.colsubstituted;
+  newCliqueTable.substitutions = init.substitutions;
+  *this = std::move(newCliqueTable);
+}